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Alam MS, Sultana A, Kibria MK, Khanam A, Wang G, Mollah MNH. Identification of Hub of the Hub-Genes From Different Individual Studies for Early Diagnosis, Prognosis, and Therapies of Breast Cancer. Bioinform Biol Insights 2024; 18:11779322241272386. [PMID: 39239087 PMCID: PMC11375675 DOI: 10.1177/11779322241272386] [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: 01/01/2024] [Accepted: 07/09/2024] [Indexed: 09/07/2024] Open
Abstract
Breast cancer (BC) is a complex disease, which causes of high mortality rate in women. Early diagnosis and therapeutic improvements may reduce the mortality rate. There were more than 74 individual studies that have suggested BC-causing hub-genes (HubGs) in the literature. However, we observed that their HubG sets are not so consistent with each other. It may be happened due to the regional and environmental variations with the sample units. Therefore, it was required to explore hub of the HubG (hHubG) sets that might be more representative for early diagnosis and therapies of BC in different country regions and their environments. In this study, we selected top-ranked 10 HubGs (CCNB1, CDK1, TOP2A, CCNA2, ESR1, EGFR, JUN, ACTB, TP53, and CCND1) as the hHubG set by the protein-protein interaction network analysis based on all of 74 individual HubG sets. The hHubG set enrichment analysis detected some crucial biological processes, molecular functions, and pathways that are significantly associated with BC progressions. The expression analysis of hHubGs by box plots in different stages of BC progression and BC prediction models indicated that the proposed hHubGs can be considered as the early diagnostic and prognostic biomarkers. Finally, we suggested hHubGs-guided top-ranked 10 candidate drug molecules (SORAFENIB, AMG-900, CHEMBL1765740, ENTRECTINIB, MK-6592, YM201636, masitinib, GSK2126458, TG-02, and PAZOPANIB) by molecular docking analysis for the treatment against BC. We investigated the stability of top-ranked 3 drug-target complexes (SORAFENIB vs ESR1, AMG-900 vs TOP2A, and CHEMBL1765740 vs EGFR) by computing their binding free energies based on 100-ns molecular dynamic (MD) simulation based Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) approach and found their stable performance. The literature review also supported our findings much more for BC compared with the results of individual studies. Therefore, the findings of this study may be useful resources for early diagnosis, prognosis, and therapies of BC.
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Affiliation(s)
- Md Shahin Alam
- Center of Translational Medicine, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Suzhou, China
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China
- Bioinformatics Laboratory (Dry), Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
| | - Adiba Sultana
- Bioinformatics Laboratory (Dry), Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
- Medical Big Data Center, Guangdong Provincial People's Hospital/Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Md Kaderi Kibria
- Bioinformatics Laboratory (Dry), Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
| | - Alima Khanam
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Guanghui Wang
- Center of Translational Medicine, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Suzhou, China
| | - Md Nurul Haque Mollah
- Bioinformatics Laboratory (Dry), Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
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Geuns-Meyer S, Cee VJ, Deak HL, Du B, Hodous BL, Nguyen HN, Olivieri PR, Schenkel LB, Vaida KR, Andrews P, Bak A, Be X, Beltran PJ, Bush TL, Chaves MK, Chung G, Dai Y, Eden P, Hanestad K, Huang L, Lin MHJ, Tang J, Ziegler B, Radinsky R, Kendall R, Patel VF, Payton M. Discovery of N-(4-(3-(2-aminopyrimidin-4-yl)pyridin-2-yloxy)phenyl)-4-(4-methylthiophen-2-yl)phthalazin-1-amine (AMG 900), a highly selective, orally bioavailable inhibitor of aurora kinases with activity against multidrug-resistant cancer cell lines. J Med Chem 2015; 58:5189-207. [PMID: 25970324 DOI: 10.1021/acs.jmedchem.5b00183] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Efforts to improve upon the physical properties and metabolic stability of Aurora kinase inhibitor 14a revealed that potency against multidrug-resistant cell lines was compromised by increased polarity. Despite its high in vitro metabolic intrinsic clearance, 23r (AMG 900) showed acceptable pharmacokinetic properties and robust pharmacodynamic activity. Projecting from in vitro data to in vivo target coverage was not practical due to disjunctions between enzyme and cell data, complex and apparently contradictory indicators of binding kinetics, and unmeasurable free fraction in plasma. In contrast, it was straightforward to relate pharmacokinetics to pharmacodynamics and efficacy by following the time above a threshold concentration. On the basis of its oral route of administration, a selectivity profile that favors Aurora-driven pharmacology and its activity against multidrug-resistant cell lines, 23r was identified as a potential best-in-class Aurora kinase inhibitor. In phase 1 dose expansion studies with G-CSF support, 23r has shown promising single agent activity.
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Affiliation(s)
- Stephanie Geuns-Meyer
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Victor J Cee
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Holly L Deak
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Bingfan Du
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Brian L Hodous
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Hanh Nho Nguyen
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Philip R Olivieri
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Laurie B Schenkel
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Karina R Vaida
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Paul Andrews
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Annette Bak
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Xuhai Be
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Pedro J Beltran
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Tammy L Bush
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Mary K Chaves
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Grace Chung
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Yang Dai
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Patrick Eden
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Kelly Hanestad
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Liyue Huang
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Min-Hwa Jasmine Lin
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Jin Tang
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Beth Ziegler
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Robert Radinsky
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Richard Kendall
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Vinod F Patel
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Marc Payton
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
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