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Balasundaram A, Doss GPC. A computational examination of the therapeutic advantages of fourth-generation ALK inhibitors TPX-0131 and repotrectinib over third-generation lorlatinib for NSCLC with ALK F1174C/L/V mutations. Front Mol Biosci 2024; 10:1306046. [PMID: 38274094 PMCID: PMC10808363 DOI: 10.3389/fmolb.2023.1306046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Background: In non-small-cell lung cancer (NSCLC), a pivotal factor in promoting cancer development is the rearrangement in the anaplastic lymphoma kinase ALK gene, resulting in elevated ALK protein expression. F1174C/L/V is the acquired secondary resistant mutation in ALK. Significant survival improvements have been seen while tyrosine kinase inhibitors specifically target ALK. Nevertheless, the emergence of drug resistance hinders the clinical effectiveness of these drugs. Objective: This research sought to find the binding affinity/inhibitory effects of the existing drug lorlatinib (LOR) and upcoming TPX-0131 (zotizalkib/TPX) and repotrectinib (TPX-0005/REP) inhibitors against ALK F1174C/L/V mutations using computational approaches to identify potential strategies over resistance. Methods: We conducted molecular docking, molecular dynamics simulation, and MMPBSA calculations to investigate how compact macrocyclic inhibitors, such as TPX-0131 and repotrectinib, fit within the ATP-binding boundary and differ from LOR. Results: Our results demonstrated that TPX-0131 and repotrectinib contributed to higher binding energy in F1174C and F1174L mutations than LOR. Repotrectinib showed greater binding energy in the F1174V mutation, whereas LOR and TPX-0131 exhibited similar binding energy. However, all three inhibitors showed significant binding energy toward F1174C/L/V mutations found in NSCLC. Conclusion: This comparative study of the potential binding effects of fourth-generation inhibitors TPX-0131 and repotrectinib and third-generation inhibitor LOR for ALK F1174C/L/V mutations revealed the atomistic insights of the binding mechanism. These computational findings enable us to carry out further research for the clinical implementation of fourth-generation ALK inhibitors on ALK-positive NSCLC.
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Zhao J, Li X, Fan R, Qin Y, Wang Z, Wang B, Li S, Fan J, Wu X, Liu H, Guan Y, Liang Y, Zhang X, Guo Y. Primary resistance to first- and second-generation ALK inhibitors in a non-small cell lung cancer patient with coexisting ALK rearrangement and an ALK F1174L-cis-S1189C de novo mutation: A case report. Front Pharmacol 2022; 13:1060460. [PMID: 36506539 PMCID: PMC9727108 DOI: 10.3389/fphar.2022.1060460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/11/2022] [Indexed: 11/24/2022] Open
Abstract
The effectiveness of the tyrosine kinase inhibitor ALK (TKI) for non-small cell lung cancer has been confirmed. However, resistance to ALK-TKIs seems inevitable. Mutations in the ALK kinase domain have been reported as an important mechanism of acquired resistance to ALK therapy. However, patients with de novo ALK kinase domain mutations and ALK rearrangements who were not treated with ALK inhibitors have rarely been reported. Here, we report a case of primary drug resistance to first- and second-generation ALK inhibitors in a NSCLC patient with ALK-rearrangement. The next-generation sequencing test of the pathological biopsy showed that the de novo ALK kinase domain mutation F1174L-cis-S1189C may be the cause of primary drug resistance.
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Affiliation(s)
- Jiuzhou Zhao
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China
| | - Xiang Li
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Ruizhe Fan
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Yaping Qin
- School of Basic Medical Sciences, Academy of Medical Sciences, Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Zhizhong Wang
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China
| | - Bo Wang
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China
| | - Shaomei Li
- Department of Medical Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Jianfeng Fan
- Department of Medical Imaging, Zhenping People’s Hospital, Nanyang, China
| | - Xinxin Wu
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China
| | - Hongxia Liu
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China
| | - Yuping Guan
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Yinfeng Liang
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Xiao Zhang
- Department of Medical Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Yongjun Guo
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China,*Correspondence: Yongjun Guo,
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Adnan M, Koli S, Mohammad T, Siddiqui AJ, Patel M, Alshammari N, Bardakci F, Elasbali AM, Hassan MI. Searching for Novel Anaplastic Lymphoma Kinase Inhibitors: Structure-Guided Screening of Natural Compounds for a Tyrosine Kinase Therapeutic Target in Cancers. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:461-470. [PMID: 35925819 DOI: 10.1089/omi.2022.0067] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase molecular target with broad importance for drug discovery, especially in the field of cancer therapeutics. ALK belongs to the insulin receptor superfamily that is involved in various malignancies, including non-small cell lung cancer, anaplastic large cell lymphoma, and neuroblastoma. ALK has been shown to play a role in cancer progression and metastasis, making it one of the prime targets to develop novel anticancer therapeutics. In this context, natural compounds can be an important resource to unravel novel ALK inhibitors. In this study, we report a structure-based virtual screening of natural compounds from the ZINC database, with an eye to potential inhibitors of ALK. Molecular docking was performed on a natural compound library, and top hits holding good binding affinity, docking score, and specificity toward ALK were selected. The hits were further evaluated based on the PAINS (pan-assay interference compounds) filter, ADMET (absorption, distribution, metabolism, excretion, toxicity) properties, PASS (prediction of activity spectra for substances) analysis, and two-dimensional interaction of protein-ligand complexes. Importantly, two natural compounds (ZINC03845566 and ZINC03999625) were identified as potential candidates for ALK, having appreciable affinity and specificity toward the ALK binding pocket and depicting drug-like properties as predicted from ADMET analysis and their physicochemical parameters. An all-atom molecular dynamics simulation for 100 ns on ALK promised stable ALK-ligand complexes. Hence, we conclude that ZINC03845566 and ZINC03999625 can act as potential ALK inhibitors against cancers where ALK plays a role, for example, in lung cancer, among others. All in all, these findings inform future discovery and translational research for ALK inhibitors as anticancer drugs.
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Affiliation(s)
- Mohd Adnan
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha'il, Ha'il, Saudi Arabia
| | - Saadgee Koli
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Arif Jamal Siddiqui
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Mitesh Patel
- Department of Biotechnology, Parul Institute of Applied Sciences and Centre of Research for Development, Parul University, Vadodara, India
| | - Nawaf Alshammari
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Fevzi Bardakci
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | | | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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Perrella F, Coppola F, Petrone A, Platella C, Montesarchio D, Stringaro A, Ravagnan G, Fuggetta MP, Rega N, Musumeci D. Interference of Polydatin/Resveratrol in the ACE2:Spike Recognition during COVID-19 Infection. A Focus on Their Potential Mechanism of Action through Computational and Biochemical Assays. Biomolecules 2021; 11:1048. [PMID: 34356672 PMCID: PMC8301781 DOI: 10.3390/biom11071048] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022] Open
Abstract
In the search for new therapeutic strategies to contrast SARS-CoV-2, we here studied the interaction of polydatin (PD) and resveratrol (RESV)-two natural stilbene polyphenols with manifold, well known biological activities-with Spike, the viral protein essential for virus entry into host cells, and ACE2, the angiotensin-converting enzyme present on the surface of multiple cell types (including respiratory epithelial cells) which is the main host receptor for Spike binding. Molecular Docking simulations evidenced that both compounds can bind Spike, ACE2 and the ACE2:Spike complex with good affinity, although the interaction of PD appears stronger than that of RESV on all the investigated targets. Preliminary biochemical assays revealed a significant inhibitory activity of the ACE2:Spike recognition with a dose-response effect only in the case of PD.
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Affiliation(s)
- Fulvio Perrella
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (F.P.); (F.C.); (A.P.); (C.P.); (D.M.)
| | - Federico Coppola
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (F.P.); (F.C.); (A.P.); (C.P.); (D.M.)
| | - Alessio Petrone
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (F.P.); (F.C.); (A.P.); (C.P.); (D.M.)
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (F.P.); (F.C.); (A.P.); (C.P.); (D.M.)
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (F.P.); (F.C.); (A.P.); (C.P.); (D.M.)
| | - Annarita Stringaro
- National Center for Drug Research and Evaluation, Italian National Institute of Health, 00161 Rome, Italy;
| | - Giampietro Ravagnan
- Institute of Translational Pharmacology, Consiglio Nazionale delle Ricerche, 00133 Rome, Italy;
| | - Maria Pia Fuggetta
- Institute of Translational Pharmacology, Consiglio Nazionale delle Ricerche, 00133 Rome, Italy;
| | - Nadia Rega
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (F.P.); (F.C.); (A.P.); (C.P.); (D.M.)
- Centro di Ricerca Interdipartimentale sui Biomateriali, University of Naples Federico II, Piazzale Tecchio, 80125 Naples, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (F.P.); (F.C.); (A.P.); (C.P.); (D.M.)
- Institute of Biostructures and Bioimages, Consiglio Nazionale delle Ricerche, 80134 Naples, Italy
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Making NSCLC Crystal Clear: How Kinase Structures Revolutionized Lung Cancer Treatment. CRYSTALS 2020. [DOI: 10.3390/cryst10090725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The parallel advances of different scientific fields provide a contemporary scenario where collaboration is not a differential, but actually a requirement. In this context, crystallography has had a major contribution on the medical sciences, providing a “face” for targets of diseases that previously were known solely by name or sequence. Worldwide, cancer still leads the number of annual deaths, with 9.6 million associated deaths, with a major contribution from lung cancer and its 1.7 million deaths. Since the relationship between cancer and kinases was unraveled, these proteins have been extensively explored and became associated with drugs that later attained blockbuster status. Crystallographic structures of kinases related to lung cancer and their developed and marketed drugs provided insight on their conformation in the absence or presence of small molecules. Notwithstanding, these structures were also of service once the initially highly successful drugs started to lose their effectiveness in the emergence of mutations. This review focuses on a subclassification of lung cancer, non-small cell lung cancer (NSCLC), and major oncogenic driver mutations in kinases, and how crystallographic structures can be used, not only to provide awareness of the function and inhibition of these mutations, but also how these structures can be used in further computational studies aiming at addressing these novel mutations in the field of personalized medicine.
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