Dataset Information

Evaluation of Artificial Intelligence in Participating Structure-Based Virtual Screening for Identifying Novel Interleukin-1 Receptor Associated Kinase-1 Inhibitors.

ABSTRACT: Interleukin-1 receptor associated kinase-1 (IRAK1) exhibits important roles in inflammation, infection, and autoimmune diseases; however, only a few inhibitors have been discovered. In this study, at first, a discriminatory structure-based virtual screening (SBVS) was employed, but only one active compound (compound 1, IC50 = 2.25 ?M) was identified. The low hit rate (2.63%) which derives from the weak discriminatory power of docking among high-scored molecules was observed in our virtual screening (VS) process for IRAK1 inhibitor. Furthermore, an artificial intelligence (AI) method, which employed a support vector machine (SVM) model, integrated information of molecular docking, pharmacophore scoring and molecular descriptors was constructed to enhance the traditional IRAK1-VS protocol. Using AI, it was found that VS of IRAK1 inhibitors excluded by over 50% of the inactive compounds, which could significantly improve the prediction accuracy of the SBVS model. Moreover, four active molecules (two of which exhibited comparative IC50 with compound 1) were accurately identified from a set of highly similar candidates. Amongst, compounds with better activity exhibited good selectivity against IRAK4. The AI assisted workflow could serve as an effective tool for enhancement of SBVS.

SUBMITTER: Che J

PROVIDER: S-EPMC7494739 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Evaluation of Artificial Intelligence in Participating Structure-Based Virtual Screening for Identifying Novel Interleukin-1 Receptor Associated Kinase-1 Inhibitors.

Che Jinxin J Feng Ruiwei R Gao Jian J Yu Hongyun H Weng Qinjie Q He Qiaojun Q Dong Xiaowu X Wu Jian J Yang Bo B

Frontiers in oncology 20200903

Interleukin-1 receptor associated kinase-1 (IRAK1) exhibits important roles in inflammation, infection, and autoimmune diseases; however, only a few inhibitors have been discovered. In this study, at first, a discriminatory structure-based virtual screening (SBVS) was employed, but only one active compound (compound <b>1</b>, IC<sub>50</sub> = 2.25 μM) was identified. The low hit rate (2.63%) which derives from the weak discriminatory power of docking among high-scored molecules was observed in ...[more]

PMID: 33014870

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Project description:The drug development process is a major challenge in the pharmaceutical industry since it takes a substantial amount of time and money to move through all the phases of developing of a new drug. One extensively used method to minimize the cost and time for the drug development process is computer-aided drug design (CADD). CADD allows better focusing on experiments, which can reduce the time and cost involved in researching new drugs. In this context, structure-based virtual screening (SBVS) is robust and useful and is one of the most promising in silico techniques for drug design. SBVS attempts to predict the best interaction mode between two molecules to form a stable complex, and it uses scoring functions to estimate the force of non-covalent interactions between a ligand and molecular target. Thus, scoring functions are the main reason for the success or failure of SBVS software. Many software programs are used to perform SBVS, and since they use different algorithms, it is possible to obtain different results from different software using the same input. In the last decade, a new technique of SBVS called consensus virtual screening (CVS) has been used in some studies to increase the accuracy of SBVS and to reduce the false positives obtained in these experiments. An indispensable condition to be able to utilize SBVS is the availability of a 3D structure of the target protein. Some virtual databases, such as the Protein Data Bank, have been created to store the 3D structures of molecules. However, sometimes it is not possible to experimentally obtain the 3D structure. In this situation, the homology modeling methodology allows the prediction of the 3D structure of a protein from its amino acid sequence. This review presents an overview of the challenges involved in the use of CADD to perform SBVS, the areas where CADD tools support SBVS, a comparison between the most commonly used tools, and the techniques currently used in an attempt to reduce the time and cost in the drug development process. Finally, the final considerations demonstrate the importance of using SBVS in the drug development process.

Project description:ImportanceMammography screening currently relies on subjective human interpretation. Artificial intelligence (AI) advances could be used to increase mammography screening accuracy by reducing missed cancers and false positives.ObjectiveTo evaluate whether AI can overcome human mammography interpretation limitations with a rigorous, unbiased evaluation of machine learning algorithms.Design, setting, and participantsIn this diagnostic accuracy study conducted between September 2016 and November 2017, an international, crowdsourced challenge was hosted to foster AI algorithm development focused on interpreting screening mammography. More than 1100 participants comprising 126 teams from 44 countries participated. Analysis began November 18, 2016.Main outcomes and measurementsAlgorithms used images alone (challenge 1) or combined images, previous examinations (if available), and clinical and demographic risk factor data (challenge 2) and output a score that translated to cancer yes/no within 12 months. Algorithm accuracy for breast cancer detection was evaluated using area under the curve and algorithm specificity compared with radiologists' specificity with radiologists' sensitivity set at 85.9% (United States) and 83.9% (Sweden). An ensemble method aggregating top-performing AI algorithms and radiologists' recall assessment was developed and evaluated.ResultsOverall, 144 231 screening mammograms from 85 580 US women (952 cancer positive ≤12 months from screening) were used for algorithm training and validation. A second independent validation cohort included 166 578 examinations from 68 008 Swedish women (780 cancer positive). The top-performing algorithm achieved an area under the curve of 0.858 (United States) and 0.903 (Sweden) and 66.2% (United States) and 81.2% (Sweden) specificity at the radiologists' sensitivity, lower than community-practice radiologists' specificity of 90.5% (United States) and 98.5% (Sweden). Combining top-performing algorithms and US radiologist assessments resulted in a higher area under the curve of 0.942 and achieved a significantly improved specificity (92.0%) at the same sensitivity.Conclusions and relevanceWhile no single AI algorithm outperformed radiologists, an ensemble of AI algorithms combined with radiologist assessment in a single-reader screening environment improved overall accuracy. This study underscores the potential of using machine learning methods for enhancing mammography screening interpretation.

Project description:BackgroundCorneal topography is a clinically validated examination method for keratoconus. However, there is no clear guideline regarding patient selection for corneal topography. We developed and validated a novel artificial intelligence (AI) model to identify patients who would benefit from corneal topography based on basic ophthalmologic examinations, including a survey of visual impairment, best-corrected visual acuity (BCVA) measurement, intraocular pressure (IOP) measurement, and autokeratometry.MethodsA total of five AI models (three individual models with fully connected neural network including the XGBoost, and the TabNet models, and two ensemble models with hard and soft voting methods) were trained and validated. We used three datasets collected from the records of 2,613 patients' basic ophthalmologic examinations from two institutions to train and validate the AI models. We trained the AI models using a dataset from a third medical institution to determine whether corneal topography was needed to detect keratoconus. Finally, prospective intra-validation dataset (internal test dataset) and extra-validation dataset from a different medical institution (external test dataset) were used to assess the performance of the AI models.ResultsThe ensemble model with soft voting method outperformed all other AI models in sensitivity when predicting which patients needed corneal topography (90.5% in internal test dataset and 96.4% in external test dataset). In the error analysis, most of the predicting error occurred within the range of the subclinical keratoconus and the suspicious D-score in the Belin-Ambrósio enhanced ectasia display. In the feature importance analysis, out of 18 features, IOP was the highest ranked feature when comparing the average value of the relative attributions of three individual AI models, followed by the difference in the value of mean corneal power.ConclusionAn AI model using the results of basic ophthalmologic examination has the potential to recommend corneal topography for keratoconus. In this AI algorithm, IOP and the difference between the two eyes, which may be undervalued clinical information, were important factors in the success of the AI model, and may be worth further reviewing in research and clinical practice for keratoconus screening.

Dataset Information

Evaluation of Artificial Intelligence in Participating Structure-Based Virtual Screening for Identifying Novel Interleukin-1 Receptor Associated Kinase-1 Inhibitors.

Publications

Evaluation of Artificial Intelligence in Participating Structure-Based Virtual Screening for Identifying Novel Interleukin-1 Receptor Associated Kinase-1 Inhibitors.

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