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Roney M, Issahaku AR, Huq AKMM, Sapari S, Abdul Razak FI, Wilhelm A, Zamri NB, Sharmin S, Islam MR, Mohd Aluwi MFF. In Silico Exploration of Isoxazole Derivatives of Usnic Acid: Novel Therapeutic Prospects Against α-Amylase for Diabetes Treatment. Cell Biochem Biophys 2024:10.1007/s12013-024-01419-1. [PMID: 39020086 DOI: 10.1007/s12013-024-01419-1] [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: 06/21/2024] [Accepted: 07/10/2024] [Indexed: 07/19/2024]
Abstract
Diabetes mellitus (DM) a metabolic disorder characterized by high blood sugar levels causing damage to various organs over time. Current anti-diabetic drugs have limitations and side effects, prompting a search for new inhibitors targeting the α-amylase enzyme. This study aims to discover such inhibitors from thirty isoxazole derivatives of usnic acid using in silico approaches. The potential inhibitory effects of compounds were investigated using ADMET, molecular docking, molecular dynamic simulation, principal component analysis and density functional theory studies. ADMET analysis exhibited a wide range of physicochemical, pharmacokinetic, and drug-like qualities with no significant side effects which were then investigated using molecular docking experiment to determine the lead compound with the best binding affinity for the α-amylase enzyme. All compounds showed good binding affinity against α-amylase enzyme (-7.9 to -9.2 kcal/mol) where compound-13 showed the best binding affinity of -9.2 kcal/mol forming hydrogen bonds with Leu162, Tyr62, Glu233 and Asp300 amino acids. Furthermore, the binding posture and the stability of the compound-13-α-amylase enzyme complex was confirmed by molecular dynamic simulation experiment. Moreover, compound-13 showed binding energy value of -27.92 ± 5.61 kcal/mol, which indicated it could be an α-amylase inhibitor. Additionally, the reactivity of compound-13 was further confirmed by density functional theory analysis. The above findings suggest compound-13 to be a potential α-amylase inhibitor in DM. And setting the stage for further in vitro and in vivo experimental validation.
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Affiliation(s)
- Miah Roney
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Persiaran Tun Khalil Yaakob, Kuantan, Pahang, Malaysia
- Centre for Bio-aromatic Research, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Persiaran Tun Khalil Yaakob, Kuantan, Pahang, Malaysia
| | - Abdul Rashid Issahaku
- Department of Chemistry, University of the Free State, 205 Nelson Mandela Avenue, Bloemfontein, 9301, South Africa
| | - A K M Moyeenul Huq
- Centre for Drug and Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz-50300, Kuala Lumpur, Malaysia
| | - Suhaila Sapari
- Department of Chemistry, Faculty of Science, University Technology of Malaysia, Skudai, 81310, Johor Bahru, Johor, Malaysia
| | - Fazira Ilyana Abdul Razak
- Department of Chemistry, Faculty of Science, University Technology of Malaysia, Skudai, 81310, Johor Bahru, Johor, Malaysia
| | - Anke Wilhelm
- Centre for Drug and Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz-50300, Kuala Lumpur, Malaysia
| | - Normaiza Binti Zamri
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Persiaran Tun Khalil Yaakob, Kuantan, Pahang, Malaysia
| | - Sabrina Sharmin
- School of Pharmacy, BRAC University, 66 Mohakhali, Dhaka, 1212, Bangladesh
| | - Md Robiul Islam
- School of Pharmacy, BRAC University, 66 Mohakhali, Dhaka, 1212, Bangladesh
| | - Mohd Fadhlizil Fasihi Mohd Aluwi
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Persiaran Tun Khalil Yaakob, Kuantan, Pahang, Malaysia.
- Centre for Bio-aromatic Research, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Persiaran Tun Khalil Yaakob, Kuantan, Pahang, Malaysia.
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Siregar KAAK, Syaifie PH, Jauhar MM, Arda AG, Rochman NT, Kustiawan PM, Mardliyati E. Revealing curcumin therapeutic targets on SRC, PPARG, MAPK8 and HSP90 as liver cirrhosis therapy based on comprehensive bioinformatic study. J Biomol Struct Dyn 2024:1-18. [PMID: 38217310 DOI: 10.1080/07391102.2023.2301534] [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: 08/20/2023] [Accepted: 12/09/2023] [Indexed: 01/15/2024]
Abstract
Cirrhosis naturally progresses through three stages: compensated, decompensated, and late decompensated, which carry an elevated risk of death. Although curcumin's anti-cirrhosis effects have been studied, underlying mechanism in preventing cirrhosis progression and the correlation between curcumin's action with upregulated genes remains insufficiently explored. In this study, we employed network pharmacology approach to construct a drug-target-disease network through bioinformatics and validate the findings with molecular docking and dynamic simulation. The curcumin-targeted liver cirrhosis network encompassed 54 nodes with 282 edges in protein-protein interactions (PPI) network. By utilizing network centrality analysis, we identified eight crucial genes. KEGG enrichment pathway revealed that these crucial genes are involved in pathway of cancer, endocrine resistance, estrogen signaling, chemical carcinogenesis-receptor activation, lipid metabolism, and atherosclerosis. Notably, these eight genes predominantly participate in cancer-related pathways. Further investigation revealed upregulation of four genes and downregulation of four others in hepatocellular carcinoma patients. These upregulated genes-MAPK8, SRC, PPARG, and HSP90AA1-strongly correlated with reduced survival probability in liver hepatocellular carcinoma patients with survival times approximately under 4000 days (∼11 years). Molecular docking and molecular dynamic results exhibited curcumin's superior binding affinities and stability compared to native ligands of MAPK8, SRC, PPARG, and HSP90AA1 within 50 ns simulations. Moreover, MM-GBSA analysis showed stronger binding energy of curcumin to MAPK8, SRC, and HSP90AA1 than native ligand. In conclusion, this study provides valuable insights into curcumin's potential mechanisms in preventing liver cirrhosis progression, specifically in HCC. These findings offer a theoretical basis for further pharmacological research into anti-HCC effect of curcumin.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Khalish Arsy Al Khairy Siregar
- Faculty of Pharmacy, Universitas Muhammadiyah Kalimantan Timur, Samarinda, Indonesia
- Center of Excellence Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
| | - Putri Hawa Syaifie
- Center of Excellence Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
| | | | - Adzani Gaisani Arda
- Center of Excellence Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
| | - Nurul Taufiqu Rochman
- Center of Excellence Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
- Research Center for Advanced Material, National Research and Innovation Agency (BRIN), South Tangerang, Indonesia
| | | | - Etik Mardliyati
- Center of Excellence Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
- Research Center for Vaccine and Drug, National Research and Innovation Agency (BRIN), Bogor, Indonesia
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Identification of Potential RBPJ-Specific Inhibitors for Blocking Notch Signaling in Breast Cancer Using a Drug Repurposing Strategy. Pharmaceuticals (Basel) 2022; 15:ph15050556. [PMID: 35631382 PMCID: PMC9146688 DOI: 10.3390/ph15050556] [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: 03/17/2022] [Revised: 04/25/2022] [Accepted: 04/25/2022] [Indexed: 11/29/2022] Open
Abstract
Notch signaling is a key parameter in regulating cell fate during tissue homeostasis, and an aberrant Notch pathway can result in mammary gland carcinoma and has been associated with poor breast cancer diagnosis. Although inhibiting Notch signaling would be advantageous in the treatment of breast cancer, the currently available Notch inhibitors have a variety of side effects and their clinical trials have been discontinued. Thus, in search of a more effective and safer Notch inhibitor, inhibiting recombinant signal binding protein for immunoglobin kappaJ region (RBPJ) specifically makes sense, as RBPJ forms a transcriptional complex that activates Notch signaling. From our established database of more than 10,527 compounds, a drug repurposing strategy-combined docking study and molecular dynamic simulation were used to identify novel RBPJ-specific inhibitors. The compounds with the best performance were examined using an in vitro cellular assay and an in vivo anticancer investigation. Finally, an FDA-approved antibiotic, fidaxomicin, was identified as a potential RBPJ inhibitor, and its ability to block RBPJ-dependent transcription and thereby inhibit breast cancer growth was experimentally verified. Our study demonstrated that fidaxomicin suppressed Notch signaling and may be repurposed for the treatment of breast cancer.
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