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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] [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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Flori L, Brogi S, Sirous H, Calderone V. Disruption of Irisin Dimerization by FDA-Approved Drugs: A Computational Repurposing Approach for the Potential Treatment of Lipodystrophy Syndromes. Int J Mol Sci 2023; 24:ijms24087578. [PMID: 37108741 PMCID: PMC10145865 DOI: 10.3390/ijms24087578] [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: 03/22/2023] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
In this paper, we present the development of a computer-based repurposing approach to identify FDA-approved drugs that are potentially able to interfere with irisin dimerization. It has been established that altered levels of irisin dimers are a pure hallmark of lipodystrophy (LD) syndromes. Accordingly, the identification of compounds capable of slowing down or precluding the irisin dimers' formation could represent a valuable therapeutic strategy in LD. Combining several computational techniques, we identified five FDA-approved drugs with satisfactory computational scores (iohexol, XP score = -7.70 kcal/mol, SP score = -5.5 kcal/mol, ΔGbind = -61.47 kcal/mol, ΔGbind (average) = -60.71 kcal/mol; paromomycin, XP score = -7.23 kcal/mol, SP score = -6.18 kcal/mol, ΔGbind = -50.14 kcal/mol, ΔGbind (average) = -49.13 kcal/mol; zoledronate, XP score = -6.33 kcal/mol, SP score = -5.53 kcal/mol, ΔGbind = -32.38 kcal/mol, ΔGbind (average) = -29.42 kcal/mol; setmelanotide, XP score = -6.10 kcal/mol, SP score = -7.24 kcal/mol, ΔGbind = -56.87 kcal/mol, ΔGbind (average) = -62.41 kcal/mol; and theophylline, XP score = -5.17 kcal/mol, SP score = -5.55 kcal/mol, ΔGbind = -33.25 kcal/mol, ΔGbind (average) = -35.29 kcal/mol) that are potentially able to disrupt the dimerization of irisin. For this reason, they deserve further investigation to characterize them as irisin disruptors. Remarkably, the identification of drugs targeting this process can offer novel therapeutic opportunities for the treatment of LD. Furthermore, the identified drugs could provide a starting point for a repositioning approach, synthesizing novel analogs with improved efficacy and selectivity against the irisin dimerization process.
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Affiliation(s)
- Lorenzo Flori
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran
| | - Hajar Sirous
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran
| | - Vincenzo Calderone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
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Lang X, Liu J, Zhang G, Feng X, Dan W. Knowledge Mapping of Drug Repositioning's Theme and Development. Drug Des Devel Ther 2023; 17:1157-1174. [PMID: 37096060 PMCID: PMC10122475 DOI: 10.2147/dddt.s405906] [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: 01/25/2023] [Accepted: 04/11/2023] [Indexed: 04/26/2023] Open
Abstract
Background In recent years, the emergence of new diseases and resistance to known diseases have led to increasing demand for new drugs. By means of bibliometric analysis, this paper studied the relevant articles on drug repositioning in recent years and analyzed the current research foci and trends. Methodology The Web of Science database was searched to collect all relevant literature on drug repositioning from 2001 to 2022. These data were imported into CiteSpace and bibliometric online analysis platforms for bibliometric analysis. The processed data and visualized images predict the development trends in the research field. Results The quality and quantity of articles published after 2011 have improved significantly, with 45 of them cited more than 100 times. Articles posted by journals from different countries have high citation values. Authors from other institutions have also collaborated to analyze drug rediscovery. Keywords found in the literature include molecular docking (N=223), virtual screening (N=170), drug discovery (N=126), machine learning (N=125), and drug-target interaction (N=68); these words represent the core content of drug repositioning. Conclusion The key focus of drug research and development is related to the discovery of new indications for drugs. Researchers are starting to retarget drugs after analyzing online databases and clinical trials. More and more drugs are being targeted at other diseases to treat more patients, based on saving money and time. It is worth noting that researchers need more financial and technical support to complete drug development.
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Affiliation(s)
- Xiaona Lang
- Pharmacy Department, Tianjin Hospital, Tianjin, People’s Republic of China
| | - Jinlei Liu
- Cardiology Department, Guang ‘anmen Hospital, Chinese Academy of Traditional Chinese Medicine, Beijing, People’s Republic of China
| | - Guangzhong Zhang
- Dermatological Department, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, People’s Republic of China
| | - Xin Feng
- Pharmacy Department, Tianjin Hospital, Tianjin, People’s Republic of China
| | - Wenchao Dan
- Dermatological Department, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, People’s Republic of China
- Correspondence: Wenchao Dan, Dermatological Department, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, People’s Republic of China, Tel +86 13652001152, Email
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López-Urrutia E, Padilla-Benavides T, Pérez-Plasencia C, Campos-Parra AD. Editorial: Repurposed Drugs Targeting Cancer Signaling Pathways: Dissecting New Mechanism of Action Through In Vitro and In Vivo Analyses. Front Oncol 2021; 11:773429. [PMID: 34671566 PMCID: PMC8521020 DOI: 10.3389/fonc.2021.773429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Eduardo López-Urrutia
- Laboratorio de Genómica Funcional, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México (UNAM), Tlalnepantla, Mexico
| | | | - Carlos Pérez-Plasencia
- Laboratorio de Genómica Funcional, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México (UNAM), Tlalnepantla, Mexico.,Laboratorio de Genómica, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Alma D Campos-Parra
- Laboratorio de Genómica, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
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Dubey KK, Indu, Sharma M. Reprogramming of antibiotics to combat antimicrobial resistance. Arch Pharm (Weinheim) 2020; 353:e2000168. [DOI: 10.1002/ardp.202000168] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/04/2020] [Accepted: 07/11/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Kashyap K. Dubey
- Bioprocess Engineering Laboratory, Department of Biotechnology Central University of Haryana Mahendergarh Haryana India
- School of Biotechnology Jawaharlal Nehru University New Delhi India
| | - Indu
- Bioprocess Engineering Laboratory, Department of Biotechnology Central University of Haryana Mahendergarh Haryana India
| | - Manisha Sharma
- Bioprocess Engineering Laboratory, Department of Biotechnology Central University of Haryana Mahendergarh Haryana India
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Satish Kumar K, Velayutham R, Roy KK. A systematic computational analysis of human matrix metalloproteinase 13 (MMP-13) crystal structures and structure-based identification of prospective drug candidates as MMP-13 inhibitors repurposable for osteoarthritis. J Biomol Struct Dyn 2019; 38:3074-3086. [PMID: 31378153 DOI: 10.1080/07391102.2019.1651221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Ravichandiran Velayutham
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
| | - Kuldeep K. Roy
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
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