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Hajim WI, Zainudin S, Mohd Daud K, Alheeti K. Optimized models and deep learning methods for drug response prediction in cancer treatments: a review. PeerJ Comput Sci 2024; 10:e1903. [PMID: 38660174 PMCID: PMC11042005 DOI: 10.7717/peerj-cs.1903] [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: 09/05/2023] [Accepted: 01/31/2024] [Indexed: 04/26/2024]
Abstract
Recent advancements in deep learning (DL) have played a crucial role in aiding experts to develop personalized healthcare services, particularly in drug response prediction (DRP) for cancer patients. The DL's techniques contribution to this field is significant, and they have proven indispensable in the medical field. This review aims to analyze the diverse effectiveness of various DL models in making these predictions, drawing on research published from 2017 to 2023. We utilized the VOS-Viewer 1.6.18 software to create a word cloud from the titles and abstracts of the selected studies. This study offers insights into the focus areas within DL models used for drug response. The word cloud revealed a strong link between certain keywords and grouped themes, highlighting terms such as deep learning, machine learning, precision medicine, precision oncology, drug response prediction, and personalized medicine. In order to achieve an advance in DRP using DL, the researchers need to work on enhancing the models' generalizability and interoperability. It is also crucial to develop models that not only accurately represent various architectures but also simplify these architectures, balancing the complexity with the predictive capabilities. In the future, researchers should try to combine methods that make DL models easier to understand; this will make DRP reviews more open and help doctors trust the decisions made by DL models in cancer DRP.
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Affiliation(s)
- Wesam Ibrahim Hajim
- Department of Applied Geology, College of Sciences, Tirkit University, Tikrit, Salah ad Din, Iraq
- Center for Artificial Intelligence Technology, Faculty of Information Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Suhaila Zainudin
- Center for Artificial Intelligence Technology, Faculty of Information Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Kauthar Mohd Daud
- Center for Artificial Intelligence Technology, Faculty of Information Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Khattab Alheeti
- Department of Computer Networking Systems, College of Computer Sciences and Information Technology, University of Anbar, Al Anbar, Ramadi, Iraq
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2
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Wong EY, Chu TN, Ladi-Seyedian SS. Genomics and Artificial Intelligence: Prostate Cancer. Urol Clin North Am 2024; 51:27-33. [PMID: 37945100 DOI: 10.1016/j.ucl.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Artificial intelligence (AI) is revolutionizing prostate cancer genomics research. By leveraging machine learning and deep learning algorithms, researchers can rapidly analyze vast genomic datasets to identify patterns and correlations that may be missed by traditional methods. These AI-driven insights can lead to the discovery of novel biomarkers, enhance the accuracy of diagnosis, and predict disease progression and treatment response. As such, AI is becoming an indispensable tool in the pursuit of personalized medicine for prostate cancer.
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Affiliation(s)
- Elyssa Y Wong
- Catherine & Joseph Aresty Department of Urology, Center for Robotic Simulation & Education, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Timothy N Chu
- Catherine & Joseph Aresty Department of Urology, Center for Robotic Simulation & Education, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Seyedeh-Sanam Ladi-Seyedian
- Catherine & Joseph Aresty Department of Urology, Center for Robotic Simulation & Education, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA.
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3
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Bazarkin A, Morozov A, Androsov A, Fajkovic H, Rivas JG, Singla N, Koroleva S, Teoh JYC, Zvyagin AV, Shariat SF, Somani B, Enikeev D. Assessment of Prostate and Bladder Cancer Genomic Biomarkers Using Artificial Intelligence: a Systematic Review. Curr Urol Rep 2024; 25:19-35. [PMID: 38099997 DOI: 10.1007/s11934-023-01193-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 01/14/2024]
Abstract
PURPOSE OF REVIEW The aim of the systematic review is to assess AI's capabilities in the genetics of prostate cancer (PCa) and bladder cancer (BCa) to evaluate target groups for such analysis as well as to assess its prospects in daily practice. RECENT FINDINGS In total, our analysis included 27 articles: 10 articles have reported on PCa and 17 on BCa, respectively. The AI algorithms added clinical value and demonstrated promising results in several fields, including cancer detection, assessment of cancer development risk, risk stratification in terms of survival and relapse, and prediction of response to a specific therapy. Besides clinical applications, genetic analysis aided by the AI shed light on the basic urologic cancer biology. We believe, our results of the AI application to the analysis of PCa, BCa data sets will help to identify new targets for urological cancer therapy. The integration of AI in genomic research for screening and clinical applications will evolve with time to help personalizing chemotherapy, prediction of survival and relapse, aid treatment strategies such as reducing frequency of diagnostic cystoscopies, and clinical decision support, e.g., by predicting immunotherapy response. These factors will ultimately lead to personalized and precision medicine thereby improving patient outcomes.
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Affiliation(s)
- Andrey Bazarkin
- Institute for Urology and Reproductive Health, Sechenov University, Moscow, Russia
| | - Andrey Morozov
- Institute for Urology and Reproductive Health, Sechenov University, Moscow, Russia
| | - Alexander Androsov
- Department of Pediatric Surgery, Division of Pediatric Urology and Andrology, Sechenov University, Moscow, Russia
| | - Harun Fajkovic
- Department of Urology and Comprehensive Cancer Center, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Karl Landsteiner Institute of Urology and Andrology, Vienna, Austria
| | - Juan Gomez Rivas
- Department of Urology, Clinico San Carlos University Hospital, Madrid, Spain
| | - Nirmish Singla
- School of Medicine, Brady Urological Institute, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Svetlana Koroleva
- Clinical Institute for Children Health Named After N.F. Filatov, Sechenov University, Moscow, Russia
| | - Jeremy Yuen-Chun Teoh
- Department of Surgery, S.H. Ho Urology Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Andrei V Zvyagin
- Institute of Molecular Theranostics, Sechenov University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, Moscow, Russia
| | - Shahrokh François Shariat
- Department of Urology and Comprehensive Cancer Center, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Karl Landsteiner Institute of Urology and Andrology, Vienna, Austria
- Department of Urology, Weill Cornell Medical College, New York, NY, USA
- Department of Urology, University of Texas Southwestern, Dallas, TX, USA
- Department of Urology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
- Division of Urology, Department of Special Surgery, Jordan University Hospital, The University of Jordan, Amman, Jordan
| | - Bhaskar Somani
- Department of Urology, University Hospital Southampton, Southampton, United Kingdom
| | - Dmitry Enikeev
- Institute for Urology and Reproductive Health, Sechenov University, Moscow, Russia.
- Department of Urology and Comprehensive Cancer Center, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.
- Karl Landsteiner Institute of Urology and Andrology, Vienna, Austria.
- Division of Urology, Rabin Medical Center, Petah Tikva, Israel.
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Schaduangrat N, Anuwongcharoen N, Charoenkwan P, Shoombuatong W. DeepAR: a novel deep learning-based hybrid framework for the interpretable prediction of androgen receptor antagonists. J Cheminform 2023; 15:50. [PMID: 37149650 PMCID: PMC10163717 DOI: 10.1186/s13321-023-00721-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 04/08/2023] [Indexed: 05/08/2023] Open
Abstract
Drug resistance represents a major obstacle to therapeutic innovations and is a prevalent feature in prostate cancer (PCa). Androgen receptors (ARs) are the hallmark therapeutic target for prostate cancer modulation and AR antagonists have achieved great success. However, rapid emergence of resistance contributing to PCa progression is the ultimate burden of their long-term usage. Hence, the discovery and development of AR antagonists with capability to combat the resistance, remains an avenue for further exploration. Therefore, this study proposes a novel deep learning (DL)-based hybrid framework, named DeepAR, to accurately and rapidly identify AR antagonists by using only the SMILES notation. Specifically, DeepAR is capable of extracting and learning the key information embedded in AR antagonists. Firstly, we established a benchmark dataset by collecting active and inactive compounds against AR from the ChEMBL database. Based on this dataset, we developed and optimized a collection of baseline models by using a comprehensive set of well-known molecular descriptors and machine learning algorithms. Then, these baseline models were utilized for creating probabilistic features. Finally, these probabilistic features were combined and used for the construction of a meta-model based on a one-dimensional convolutional neural network. Experimental results indicated that DeepAR is a more accurate and stable approach for identifying AR antagonists in terms of the independent test dataset, by achieving an accuracy of 0.911 and MCC of 0.823. In addition, our proposed framework is able to provide feature importance information by leveraging a popular computational approach, named SHapley Additive exPlanations (SHAP). In the meanwhile, the characterization and analysis of potential AR antagonist candidates were achieved through the SHAP waterfall plot and molecular docking. The analysis inferred that N-heterocyclic moieties, halogenated substituents, and a cyano functional group were significant determinants of potential AR antagonists. Lastly, we implemented an online web server by using DeepAR (at http://pmlabstack.pythonanywhere.com/DeepAR ). We anticipate that DeepAR could be a useful computational tool for community-wide facilitation of AR candidates from a large number of uncharacterized compounds.
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Affiliation(s)
- Nalini Schaduangrat
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Nuttapat Anuwongcharoen
- Department of Community Medical Technology, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Phasit Charoenkwan
- Modern Management and Information Technology, College of Arts, Media and Technology, Chiang Mai University, Chiang Mai, 50200, Thailand.
| | - Watshara Shoombuatong
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand.
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Zhang H, Zhang L, Xu Y, Chen S, Ma Z, Yao M, Li F, Li B, Yuan Y. Simulating androgen receptor selection in designer yeast. Synth Syst Biotechnol 2022; 7:1108-1116. [PMID: 36017332 PMCID: PMC9386396 DOI: 10.1016/j.synbio.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/08/2022] [Accepted: 07/20/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Haoran Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, PR China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Lu Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, PR China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Yipeng Xu
- Department of Urology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
| | - Shaoyong Chen
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02215, USA
| | - Zhenyi Ma
- School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, PR China
| | - Mingdong Yao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, PR China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Fangyin Li
- Department of Urology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
| | - Bo Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, PR China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, PR China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
- Corresponding author. Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, PR China.
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6
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Brito Pache MC, Sant’Ana DA, Araújo Rozales JV, de Moraes Weber VA, Silva Oliveira Junior AD, Garcia V, Pistori H, Naka MH. Prediction of fingerling biomass with deep learning. ECOL INFORM 2022. [DOI: 10.1016/j.ecoinf.2022.101785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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7
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The promising role of new molecular biomarkers in prostate cancer: from coding and non-coding genes to artificial intelligence approaches. Prostate Cancer Prostatic Dis 2022; 25:431-443. [PMID: 35422101 PMCID: PMC9385485 DOI: 10.1038/s41391-022-00537-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/24/2022] [Accepted: 03/30/2022] [Indexed: 12/15/2022]
Abstract
Background Risk stratification or progression in prostate cancer is performed with the support of clinical-pathological data such as the sum of the Gleason score and serum levels PSA. For several decades, methods aimed at the early detection of prostate cancer have included the determination of PSA serum levels. The aim of this systematic review is to provide an overview about recent advances in the discovery of new molecular biomarkers through transcriptomics, genomics and artificial intelligence that are expected to improve clinical management of the prostate cancer patient. Methods An exhaustive search was conducted by Pubmed, Google Scholar and Connected Papers using keywords relating to the genetics, genomics and artificial intelligence in prostate cancer, it includes “biomarkers”, “non-coding RNAs”, “lncRNAs”, “microRNAs”, “repetitive sequence”, “prognosis”, “prediction”, “whole-genome sequencing”, “RNA-Seq”, “transcriptome”, “machine learning”, and “deep learning”. Results New advances, including the search for changes in novel biomarkers such as mRNAs, microRNAs, lncRNAs, and repetitive sequences, are expected to contribute to an earlier and accurate diagnosis for each patient in the context of precision medicine, thus improving the prognosis and quality of life of patients. We analyze several aspects that are relevant for prostate cancer including its new molecular markers associated with diagnosis, prognosis, and prediction to therapy and how bioinformatic approaches such as machine learning and deep learning can contribute to clinic. Furthermore, we also include current techniques that will allow an earlier diagnosis, such as Spatial Transcriptomics, Exome Sequencing, and Whole-Genome Sequencing. Conclusion Transcriptomic and genomic analysis have contributed to generate knowledge in the field of prostate carcinogenesis, new information about coding and non-coding genes as biomarkers has emerged. Synergies created by the implementation of artificial intelligence to analyze and understand sequencing data have allowed the development of clinical strategies that facilitate decision-making and improve personalized management in prostate cancer.
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8
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Gao Y, Lyu Q, Luo P, Li M, Zhou R, Zhang J, Lyu Q. Applications of Machine Learning to Predict Cisplatin Resistance in Lung Cancer. Int J Gen Med 2021; 14:5911-5925. [PMID: 34588799 PMCID: PMC8473573 DOI: 10.2147/ijgm.s329644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/03/2021] [Indexed: 12/25/2022] Open
Abstract
Purpose Lung cancer, mainly lung adenocarcinoma, lung squamous cell carcinoma and small cell lung cancer, has the highest incidence and cancer-related mortality worldwide. Platinum-based chemotherapy plays an important role in the treatment of various lung cancer subtypes, but not all patients benefit from this treatment regimen; thus, it is worth identifying lung cancer patients who are resistant or sensitive to platinum-based therapy. Methods The drug response and sequencing data of 170 lung cancer cell lines were downloaded from the Genomics of Drug Sensitivity in Cancer (GDSC) database, and support vector machines (SVMs) and beam search were used to select an optimal gene panel that can predict the sensitivity of cell lines to cisplatin. Then, we used available cell line data to explore the potential mechanisms. Results In this work, the drug response and sequencing data of 170 lung cancer cell lines were downloaded from the GDSC database, and SVMs and beam search were used to screen a panel of genes related to lung cancer cell line resistance to cisplatin. A final panel of nine genes (PLXNC1, KIAA0649, SPTBN4, SLC14A2, F13A1, COL5A1, SCN2A, PLEC, and ALMS1) was identified, and achieved an area under the curve (AUC) of 0.873 ± 0.004. The natural logarithm of the half maximal inhibitory concentration (lnIC50) values of the mutant-type (panel-MT) group was significantly higher than that of the wild-type (panel-WT) group, regardless of the lung cancer subtype. The differentially expressed pathways between the two groups may explain this difference. Conclusion In this study, we found that a panel of nine genes can accurately predict sensitivity to cisplatin, which may provide individualized treatment recommendations to improve the prognosis of patients with lung cancer.
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Affiliation(s)
- Yanan Gao
- Department of Radiotherapy, Affiliated Cancer Hospital, Zhengzhou University, Zhengzhou, People's Republic of China
| | - Qiong Lyu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Mujiao Li
- School of Biomedical Engineering, Southern Medical University, Guangzhou, People's Republic of China
| | - Rui Zhou
- School of Biomedical Engineering, Southern Medical University, Guangzhou, People's Republic of China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Qingwen Lyu
- Department of Information, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
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9
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DDV: A Taxonomy for Deep Learning Methods in Detecting Prostate Cancer. Neural Process Lett 2021. [DOI: 10.1007/s11063-021-10485-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Novaes MT, Ferreira de Carvalho OL, Guimarães Ferreira PH, Nunes Tiraboschi TL, Silva CS, Zambrano JC, Gomes CM, de Paula Miranda E, Abílio de Carvalho Júnior O, de Bessa Júnior J. Prediction of secondary testosterone deficiency using machine learning: A comparative analysis of ensemble and base classifiers, probability calibration, and sampling strategies in a slightly imbalanced dataset. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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11
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Karasev D, Sobolev B, Lagunin A, Filimonov D, Poroikov V. Prediction of Protein-ligand Interaction Based on Sequence Similarity and Ligand Structural Features. Int J Mol Sci 2020; 21:ijms21218152. [PMID: 33142754 PMCID: PMC7663273 DOI: 10.3390/ijms21218152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 01/09/2023] Open
Abstract
Computationally predicting the interaction of proteins and ligands presents three main directions: the search of new target proteins for ligands, the search of new ligands for targets, and predicting the interaction of new proteins and new ligands. We proposed an approach providing the fuzzy classification of protein sequences based on the ligand structural features to analyze the latter most complicated case. We tested our approach on five protein groups, which represented promised targets for drug-like ligands and differed in functional peculiarities. The training sets were built with the original procedure overcoming the data ambiguity. Our study showed the effective prediction of new targets for ligands with an average accuracy of 0.96. The prediction of new ligands for targets displayed the average accuracy 0.95; accuracy estimates were close to our previous results, comparable in accuracy to those of other methods or exceeded them. Using the fuzzy coefficients reflecting the target-to-ligand specificity, we provided predicting interactions for new proteins and new ligands; the obtained accuracy values from 0.89 to 0.99 were acceptable for such a sophisticated task. The protein kinase family case demonstrated the ability to account for subtle features of proteins and ligands required for the specificity of protein–ligand interaction.
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Affiliation(s)
- Dmitry Karasev
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow 119121, Russia; (B.S.); (A.L.); (D.F.); (V.P.)
- Correspondence:
| | - Boris Sobolev
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow 119121, Russia; (B.S.); (A.L.); (D.F.); (V.P.)
| | - Alexey Lagunin
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow 119121, Russia; (B.S.); (A.L.); (D.F.); (V.P.)
- Department of Bioinformatics, Russian National Research Medical University, Moscow 117997, Russia
| | - Dmitry Filimonov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow 119121, Russia; (B.S.); (A.L.); (D.F.); (V.P.)
| | - Vladimir Poroikov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow 119121, Russia; (B.S.); (A.L.); (D.F.); (V.P.)
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Kafka M, Mayr F, Temml V, Möller G, Adamski J, Höfer J, Schwaiger S, Heidegger I, Matuszczak B, Schuster D, Klocker H, Bektic J, Stuppner H, Eder IE. Dual Inhibitory Action of a Novel AKR1C3 Inhibitor on Both Full-Length AR and the Variant AR-V7 in Enzalutamide Resistant Metastatic Castration Resistant Prostate Cancer. Cancers (Basel) 2020; 12:E2092. [PMID: 32731472 PMCID: PMC7465893 DOI: 10.3390/cancers12082092] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/15/2020] [Accepted: 07/22/2020] [Indexed: 11/23/2022] Open
Abstract
The expanded use of second-generation antiandrogens revolutionized the treatment landscape of progressed prostate cancer. However, resistances to these novel drugs are already the next obstacle to be solved. Various previous studies depicted an involvement of the enzyme AKR1C3 in the process of castration resistance as well as in the resistance to 2nd generation antiandrogens like enzalutamide. In our study, we examined the potential of natural AKR1C3 inhibitors in various prostate cancer cell lines and a three-dimensional co-culture spheroid model consisting of cancer cells and cancer-associated fibroblasts (CAFs) mimicking enzalutamide resistant prostate cancer. One of our compounds, named MF-15, expressed strong antineoplastic effects especially in cell culture models with significant enzalutamide resistance. Furthermore, MF-15 exhibited a strong effect on androgen receptor (AR) signaling, including significant inhibition of AR activity, downregulation of androgen-regulated genes, lower prostate specific antigen (PSA) production, and decreased AR and AKR1C3 expression, indicating a bi-functional effect. Even more important, we demonstrated a persisting inhibition of AR activity in the presence of AR-V7 and further showed that MF-15 non-competitively binds within the DNA binding domain of the AR. The data suggest MF-15 as useful drug to overcome enzalutamide resistance.
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Affiliation(s)
- Mona Kafka
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (M.K.); (J.H.); (I.H.); (H.K.); (J.B.)
| | - Fabian Mayr
- Institute of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (F.M.); (V.T.); (S.S.); (H.S.)
| | - Veronika Temml
- Institute of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (F.M.); (V.T.); (S.S.); (H.S.)
| | - Gabriele Möller
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, 85764 Neuherberg, Germany; (G.M.); (J.A.)
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, 85764 Neuherberg, Germany; (G.M.); (J.A.)
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 637551, Singapore
- Lehrstuhl für Experimentelle Genetik, Technische Universität München, 85354 Freising-Weihenstephan, Germany
| | - Julia Höfer
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (M.K.); (J.H.); (I.H.); (H.K.); (J.B.)
| | - Stefan Schwaiger
- Institute of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (F.M.); (V.T.); (S.S.); (H.S.)
| | - Isabel Heidegger
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (M.K.); (J.H.); (I.H.); (H.K.); (J.B.)
| | - Barbara Matuszczak
- Institute of Pharmacy/Pharmaceutical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (B.M.); (D.S.)
| | - Daniela Schuster
- Institute of Pharmacy/Pharmaceutical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (B.M.); (D.S.)
- Institute of Pharmacy, Department of Pharmaceutical and Medicinal Chemistry, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Helmut Klocker
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (M.K.); (J.H.); (I.H.); (H.K.); (J.B.)
| | - Jasmin Bektic
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (M.K.); (J.H.); (I.H.); (H.K.); (J.B.)
| | - Hermann Stuppner
- Institute of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (F.M.); (V.T.); (S.S.); (H.S.)
| | - Iris E. Eder
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (M.K.); (J.H.); (I.H.); (H.K.); (J.B.)
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