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Mukhtar RM, Abdelmoniem N, Elrufaie HA, Edris A, Ghaboosh H, Mahgoub MA, Garelnabi EAE, Osman W, Sherif AE, Ashour A, Ghazawi KF, Samman WA, Alhaddad AA, Bafail R, Ibrahim SRM, Mohamed GA, Alzain AA. Unlocking the potential of approved drugs for the allosteric inhibition of tropomyosin-receptor kinase A using molecular docking and molecular dynamics studies. Front Chem 2023; 11:1205724. [PMID: 37351516 PMCID: PMC10282146 DOI: 10.3389/fchem.2023.1205724] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/22/2023] [Indexed: 06/24/2023] Open
Abstract
Tropomyosin-receptor kinase A (TrkA) is the primary isoform among the tropomyosin-receptor kinases that have been associated with human cancer development, contributing to approximately 7.4% of all cancer cases. TrkA represents an attractive target for cancer treatment; however, currently available TrkA inhibitors face limitations in terms of resistance development and potential toxicity. Hence, the objective of this study was to identify new allosteric-approved inhibitors of TrkA that can overcome these challenges and be employed in cancer therapy. To achieve this goal, a screening of 9,923 drugs from the ChEMBL database was conducted to assess their repurposing potential using molecular docking. The top 49 drug candidates, exhibiting the highest docking scores (-11.569 to -7.962 kcal/mol), underwent MM-GBSA calculations to evaluate their binding energies. Delanzomib and tibalosin, the top two drugs with docking scores of -10.643 and -10.184 kcal/mol, respectively, along with MM-GBSA dG bind values of -67.96 and -50.54 kcal/mol, were subjected to 200 ns molecular dynamic simulations, confirming their stable interactions with TrkA. Based on these findings, we recommend further experimental evaluation of delanzomib and tibalosin to determine their potential as allosteric inhibitors of TrkA. These drugs have the potential to provide more effective and less toxic therapeutic alternatives. The approach employed in this study, which involves repurposing drugs through molecular docking and molecular dynamics, serves as a valuable tool for identifying novel drug candidates with distinct therapeutic uses. This methodology can contribute to reducing the attrition rate and expediting the process of drug discovery.
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Affiliation(s)
- Rua M. Mukhtar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Nihal Abdelmoniem
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Hisham A. Elrufaie
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Alaa Edris
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Hiba Ghaboosh
- Department of Pharmaceutics, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Mohanad A. Mahgoub
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Elrashied A. E. Garelnabi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Khartoum, Khartoum, Sudan
| | - Wadah Osman
- Department of Pharmacognosy, Faculty of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-kharj, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, University of Khartoum, Khartoum, Sudan
| | - Asmaa E. Sherif
- Department of Pharmacognosy, Faculty of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-kharj, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Ahmed Ashour
- Department of Pharmacognosy, Faculty of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-kharj, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Kholoud F. Ghazawi
- Clinical Pharmacy Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Waad A. Samman
- Department of Pharmacology and Toxicology, College of Pharmacy, Taibah University, Al-Madinah Al-Munawwarah, Saudi Arabia
| | - Aisha A. Alhaddad
- Department of Pharmacology and Toxicology, College of Pharmacy, Taibah University, Al-Madinah Al-Munawwarah, Saudi Arabia
| | - Rawan Bafail
- Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, Taibah University, Medina, Saudi Arabia
| | - Sabrin R. M. Ibrahim
- Preparatory Year Program, Department of Chemistry, Batterjee Medical College, Jeddah, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Gamal A. Mohamed
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulrahim A. Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
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Elrufaie HA, Mohamed LM, Hamd AY, Bala NA, Elbadawi FA, Ghaboosh H, Alzain AA. Discovery of novel natural products as rhodesain inhibitors for human African trypanosomiasis using in silico techniques. J Biomol Struct Dyn 2022:1-13. [PMID: 35751127 DOI: 10.1080/07391102.2022.2092550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Human African Trypanosomiasis (HAT) or sleeping sickness is caused by the Trypanosoma brucei rhodesiense, a subspecies of the Trypanosomatide family. The parasite is associated with high morbidity and mortality rate in both animals and humans, claimed to be more fatal than other vector-transmitted diseases such as malaria. The majority of existing medications are highly toxic, not effective in the late chronic phase of the disease, and require maximum dosages to fully eradicate the parasite. In this study, we used computational methods to find out natural products that inhibit the Rhodesain, a parasitic enzyme that plays an important role in the parasite's pathogenicity, multiplication, and ability to pass through the host's blood-brain barrier. A library of 270540 natural products from ZINC databases was processed by using e-pharmacophore hypnosis and screening procedures, molecular docking, ADMET processes, and MM-GBSA calculations. This led to the identification of 3 compounds (ZINC000096269390, ZINC000035485292, and ZINC000035485242) which were then subjected to molecular dynamics. The findings of this study showed excellent binding affinity and stability toward the Rhodesain and suggest they may be a hopeful treatment for HAT in the future if further clinical trials were performed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hisham A Elrufaie
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Linda M Mohamed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Aya Y Hamd
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Noor A Bala
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | | | - Hiba Ghaboosh
- Department of Pharmaceutics, University of Gezira, Wad Madani, Sudan
| | - Abdulrahim A Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
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