Dataset Information

Application of Computational Biology and Artificial Intelligence Technologies in Cancer Precision Drug Discovery.

ABSTRACT: Artificial intelligence (AI) proves to have enormous potential in many areas of healthcare including research and chemical discoveries. Using large amounts of aggregated data, the AI can discover and learn further transforming these data into "usable" knowledge. Being well aware of this, the world's leading pharmaceutical companies have already begun to use artificial intelligence to improve their research regarding new drugs. The goal is to exploit modern computational biology and machine learning systems to predict the molecular behaviour and the likelihood of getting a useful drug, thus saving time and money on unnecessary tests. Clinical studies, electronic medical records, high-resolution medical images, and genomic profiles can be used as resources to aid drug development. Pharmaceutical and medical researchers have extensive data sets that can be analyzed by strong AI systems. This review focused on how computational biology and artificial intelligence technologies can be implemented by integrating the knowledge of cancer drugs, drug resistance, next-generation sequencing, genetic variants, and structural biology in the cancer precision drug discovery.

SUBMITTER: Nagarajan N

PROVIDER: S-EPMC6925679 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Application of Computational Biology and Artificial Intelligence Technologies in Cancer Precision Drug Discovery.

Nagarajan Nagasundaram N Yapp Edward K Y EKY Le Nguyen Quoc Khanh NQK Kamaraj Balu B Al-Subaie Abeer Mohammed AM Yeh Hui-Yuan HY

BioMed research international 20191111

Artificial intelligence (AI) proves to have enormous potential in many areas of healthcare including research and chemical discoveries. Using large amounts of aggregated data, the AI can discover and learn further transforming these data into "usable" knowledge. Being well aware of this, the world's leading pharmaceutical companies have already begun to use artificial intelligence to improve their research regarding new drugs. The goal is to exploit modern computational biology and machine learn ...[more]

PMID: 31886259

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Project description:The application of artificial intelligence (AI) has been considered a revolutionary change in drug discovery and development. In 2020, the AlphaFold computer program predicted protein structures for the whole human genome, which has been considered a remarkable breakthrough in both AI applications and structural biology. Despite the varying confidence levels, these predicted structures could still significantly contribute to structure-based drug design of novel targets, especially the ones with no or limited structural information. In this work, we successfully applied AlphaFold to our end-to-end AI-powered drug discovery engines, including a biocomputational platform PandaOmics and a generative chemistry platform Chemistry42. A novel hit molecule against a novel target without an experimental structure was identified, starting from target selection towards hit identification, in a cost- and time-efficient manner. PandaOmics provided the protein of interest for the treatment of hepatocellular carcinoma (HCC) and Chemistry42 generated the molecules based on the structure predicted by AlphaFold, and the selected molecules were synthesized and tested in biological assays. Through this approach, we identified a small molecule hit compound for cyclin-dependent kinase 20 (CDK20) with a binding constant Kd value of 9.2 ± 0.5 μM (n = 3) within 30 days from target selection and after only synthesizing 7 compounds. Based on the available data, a second round of AI-powered compound generation was conducted and through this, a more potent hit molecule, ISM042-2-048, was discovered with an average Kd value of 566.7 ± 256.2 nM (n = 3). Compound ISM042-2-048 also showed good CDK20 inhibitory activity with an IC50 value of 33.4 ± 22.6 nM (n = 3). In addition, ISM042-2-048 demonstrated selective anti-proliferation activity in an HCC cell line with CDK20 overexpression, Huh7, with an IC50 of 208.7 ± 3.3 nM, compared to a counter screen cell line HEK293 (IC50 = 1706.7 ± 670.0 nM). This work is the first demonstration of applying AlphaFold to the hit identification process in drug discovery.

Dataset Information

Application of Computational Biology and Artificial Intelligence Technologies in Cancer Precision Drug Discovery.

Publications

Application of Computational Biology and Artificial Intelligence Technologies in Cancer Precision Drug Discovery.

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