Emerging Promise of Computational Techniques in Anti-Cancer Research: At a Glance
Abstract
:1. Introduction
2. Anticancer Drug Target Prediction
3. Computer-Aided Drug Discovery and Design
3.1. Computer-Aided Drug Design Based on Ligands
3.2. Drug Design Using Structure-Based Computer Assistance
Compound | Function | Therapeutic Area | Approval Time | References |
---|---|---|---|---|
Captopril | ACE inhibitor | Diabetic nephropathy, hypertension, congestive heart failure, myocardial infarction | 1975 | [60,61] |
Cimetidine | H2 receptor antagonist | Heartburn and peptic ulcer therapy | 1978 | [62] |
Dorzolamide | Inhibitor of carbonic anhydrase | Antiglaucoma agent | 1989 | [63,64] |
Saquinavir | Inhibitor of HIV-1 protease | Antiretroviral medication to treat HIV or AIDS | 1995 | [65,66] |
Zanamivir | Inhibitor of neuraminidase | Antiviral (influenza A and influenza B) | 1999 | [67,68,69,70] |
Nelfinavir | Inhibitor of HIV protease | Antiretroviral medication to treat HIV or AIDS | 1999 | [71] |
Lopinavir | HIV protease inhibitor with peptidomimetic properties | Antiretroviral medication used to treat HIV/AIDS in patients who have developed resistance to other protease inhibitors. | 2000 | [72] |
Darunavir | Inhibitor of nonpeptic HIV protease | Antiretroviral for HIV/AIDS | 2006 | [73,74] |
Imatinib | Inhibitor of tyrosine kinase | Chronic myeloid leukemia | 1990 | [75,76] |
Gefitinib | Epidermal growth factor receptor (EGFR) kinase inhibitor | Non-small-cell lung cancer (NSCLC) | 2003 | [77,78] |
Erlotinib | EGFR kinase inhibitor | Pancreatic cancer, NSCLC | 2005 | [79] |
Sorafenib | Vascular endothelial growth factor receptor (VEGFR) kinase inhibitor | Thyroid cancer, renal cancer, liver cancer | 2005 | [80,81] |
Lapatinib | Erb-B2 receptor tyrosine kinase 2 (ERBB2)/EGFR inhibitor | Breast cancer | 2007 | [82,83] |
Abiraterone | Inhibitor of androgen synthesis | Hormone refractory prostate cancer or metastatic castration-resistant prostate cancer | 2011 | [84,85] |
Crizotinib | Anaplastic lymphoma kinase (ALK) inhibitor | NSCLC | 2011 | [86,87,88] |
4. Anticancer Small Organic Molecules Design via a Computational Approach
4.1. Anticancer Small Molecule Design
4.2. Computational Method for Anticancer Peptide Design
5. Structure-Based Approach
5.1. Docking of Molecules
5.2. Pharmacophore Mapping Based on Structure
6. Drug Development Based on Ligands
6.1. Searching for Similarities
6.2. Ligand-Based Pharmacophore Mapping
6.3. Modeling with QSAR
7. Artificial Intelligence Aids in the Discovery of Anticancer Drugs
8. Discovering New Drug Binding Sites through the Use of MD Simulation
9. Integration of Structure- and Ligand-Based Approaches
9.1. Pseudoreceptor Modeling
9.2. Proteochemometric Modeling
10. Current Trends in Computational Approaches for Anticancer Drug Delivery Systems
11. Successful Stories in Computational Drug Discovery
12. Conclusions and Future Perspectives
Author Contributions
Funding
Conflicts of Interest
References
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Gene Expression Omnibus (GEO) | GEO is a free, open-access repository for functional genomics data that accepts submissions of MIAME-compliant data. | Gene expression omnibus. Available online: http://www.ncbi.nlm.nih.gov/geo (accessed on 23 January 2022) |
The Cancer Genome Atlas (TCGA) | Genomic statistics from >10,000 patient tissue samples from >30 prevalent cancers, such as exome, SNP, methylation, mRNA, miRNA, and clinical. | The Cancer Genome Atlas Program. Available online: http://cancergenome.nih.gov (accessed on 23 January 2022) |
Genetic Association Database (GAD) | A database of information on genetic associations with serious illnesses and disorders. | Gender and Development Program. GAD Activities Sex Disaggregated Data. Available online: http://www.tapi.dost.gov.ph/resources/gad-databases (accessed on 23 January 2022) |
Catalogue Of Somatic Mutations In Cancer (COSMIC) | A thorough resource for learning about somatic mutations’ effects on human cancer. | Catalogue Of Somatic Mutations In Cancer. Available online: https://cancer.sanger.ac.uk/cosmic (accessed on 23 January 2022) |
Online Mendelian Inheritance in Man (OMIM) | Relationship between genetic traits, especially diseases, and genes. | An Online Catalog of Human Genes and Genetic Disorders. Available online: http://www.omim.org (accessed on 23 January 2022) |
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Therapeutic Target (TTD) | A database that offers details on the diseases targeted, the investigated and undiscovered therapeutic protein and nucleic acid targets, the relevant methods, and the medications that are specific to each target. | Therapeutic Target Database. Available online: https://openebench.bsc.es/tool/ttd (accessed on 23 January 2022) |
Genomics of Drug Sensitivity in Cancer (GDSC) | A database of 138 identified anticancer compounds (on average 525 cell lines studied for each drug) representing more than 1000 distinct cancer cell lines. | Genomics of Drug Sensitivity in Cancer. Available online: http://www.cancerrxgene.org/download (accessed on 23 January 2022) |
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Name | Molecular Formula | ATC Code | Therapeutic Area | Target and Function | Year of Approval |
---|---|---|---|---|---|
Alpelisib | C19H22F3N5O2S | L01EM03 | Breast cancer | PI3K inhibitor | 2019 [181] |
Cladribine | C10H12ClN5O3 | L04AA40 | Hairy cell leukemia | Adenosine deaminase inhibitor | 2019 [182] |
Darolutamide | C19H19ClN6O2 | L02BB06 | Prostate cancer | Androgen receptor inhibitor | 2019 [183] |
Entrectinib | C31H34F2N6O2 | L01EX14 | Non-small-cell lung cancer and solid tumors | Tyrosine kinase inhibitor | 2019 [88] |
Erdafitinib | C25H30N6O2 | L01EN01 | Urothelial carcinoma | FGFR tyrosine inhibitor | 2019 [184] |
Fedratinib Hydrochloride | C27H36N6O3S | L01EJ02 | Myelofibrosis | Tyrosine kinase inhibitor | 2019 [185] |
Selinexor | C17H11F6N7O | L01XX66 | Multiple myeloma | Nuclear export inhibitor | 2019 [186] |
Zanubrutinib | C27H29N5O3 | L01EL03 | Mantle cell lymphoma | Bruton′s tyrosine kinase inhibitor | 2019 [187] |
Abemaciclib | C27H32F2N8 | L01EF03 | Breast cancer | Cyclin-dependent kinase inhibitor | 2018 [188] |
Apalutamide | C21H15F4N5O2S | L02BB05 | Prostate cancer | Androgen receptor inhibitor | 2018 [189] |
Binimetinib | C17H15BrF2N4O3 | L01EE03 | Melanoma | MEk1 and MEK2 inhibitor | 2018 [190] |
Dacomitinib | C24H27ClFN5O3 | L01EB07 | Non-small-cell lung cancer | Oral kinase inhibitor | 2018 [191] |
Duvelisib | C22H17ClN6O | L01EM04 | Chronic lymphocytic leukemia (CLL) and follicular lymphoma (FL) | PI3K kinase inhibitor | 2018 [192] |
Encorafenib | C22H27Cl1F1N7O4S1 | L01EC03 | Colorectal cancer and melanoma | BRAF kinase inhibitor | 2018 [190] |
Gilteritinib Fumarate | C62H92N16O10 | L01EX13 | Acute myeloid leukemia | Tyrosine kinase inhibitor | 2018 [193] |
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Rahman, M.M.; Islam, M.R.; Rahman, F.; Rahaman, M.S.; Khan, M.S.; Abrar, S.; Ray, T.K.; Uddin, M.B.; Kali, M.S.K.; Dua, K.; et al. Emerging Promise of Computational Techniques in Anti-Cancer Research: At a Glance. Bioengineering 2022, 9, 335. https://doi.org/10.3390/bioengineering9080335
Rahman MM, Islam MR, Rahman F, Rahaman MS, Khan MS, Abrar S, Ray TK, Uddin MB, Kali MSK, Dua K, et al. Emerging Promise of Computational Techniques in Anti-Cancer Research: At a Glance. Bioengineering. 2022; 9(8):335. https://doi.org/10.3390/bioengineering9080335
Chicago/Turabian StyleRahman, Md. Mominur, Md. Rezaul Islam, Firoza Rahman, Md. Saidur Rahaman, Md. Shajib Khan, Sayedul Abrar, Tanmay Kumar Ray, Mohammad Borhan Uddin, Most. Sumaiya Khatun Kali, Kamal Dua, and et al. 2022. "Emerging Promise of Computational Techniques in Anti-Cancer Research: At a Glance" Bioengineering 9, no. 8: 335. https://doi.org/10.3390/bioengineering9080335
APA StyleRahman, M. M., Islam, M. R., Rahman, F., Rahaman, M. S., Khan, M. S., Abrar, S., Ray, T. K., Uddin, M. B., Kali, M. S. K., Dua, K., Kamal, M. A., & Chellappan, D. K. (2022). Emerging Promise of Computational Techniques in Anti-Cancer Research: At a Glance. Bioengineering, 9(8), 335. https://doi.org/10.3390/bioengineering9080335