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Peng J, Ding X, Shih PY, Meng Q, Ding X, Zhang M, Aliper A, Ren F, Lu H, Zhavoronkov A. Discovery of 1(2H)-phthalazinone and 1(2H)-isoquinolinone derivatives as potent hematopoietic progenitor kinase 1 (HPK1) inhibitors. Eur J Med Chem 2024; 279:116877. [PMID: 39303515 DOI: 10.1016/j.ejmech.2024.116877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Revised: 09/11/2024] [Accepted: 09/11/2024] [Indexed: 09/22/2024]
Abstract
Although immune checkpoint inhibitors (ICIs) have been a revelation for treating several cancers, an unmet need remains to broaden ICI therapeutic scope and increase their response rates in clinical trials. Hematopoietic progenitor kinase 1 (HPK1) is a negative regulator of T cell activation and has previously been identified as a promising target for immunotherapy. Herein, we report the discovery of a series of HPK1 inhibitors with novel 1(2H)-phthalazinone and 1(2H)-isoquinolinone scaffolds. Among them, compound 24 demonstrated potent in vitro activity (HPK1 IC50 value of 10.4 nM) and cellular activity (pSLP76 EC50 = 41 nM & IL-2 EC50 = 108 nM). Compound 24 exhibited favorable mouse and rat pharmacokinetic profiles with reasonable oral exposure. Compound 24 showed potent in vivo anti-tumor activity in a CT26 syngeneic tumor model with 95 % tumor growth inhibition in combination with anti-PD-1.
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Affiliation(s)
- Jingjing Peng
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai, 201203, China
| | - Xiaoyu Ding
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai, 201203, China
| | - Pei-Yu Shih
- Insilico Medicine Taiwan Ltd, Suite 1303, No. 333, Sec. 1, Keelung Rd, Xinyi District, Taipei, 110, Taiwan
| | - Qingyuan Meng
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai, 201203, China
| | - Xiao Ding
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai, 201203, China
| | - Man Zhang
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai, 201203, China
| | - Alex Aliper
- Insilico Medicine AI Limited, Masdar City, Abu Dhabi 145748, United Arab Emirates
| | - Feng Ren
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai, 201203, China
| | - Hongfu Lu
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai, 201203, China.
| | - Alex Zhavoronkov
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai, 201203, China; Insilico Medicine AI Limited, Masdar City, Abu Dhabi 145748, United Arab Emirates.
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Zhang Y, Mastouri M, Zhang Y. Accelerating drug discovery, development, and clinical trials by artificial intelligence. MED 2024; 5:1050-1070. [PMID: 39173629 DOI: 10.1016/j.medj.2024.07.026] [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] [Received: 04/01/2024] [Revised: 05/21/2024] [Accepted: 07/25/2024] [Indexed: 08/24/2024]
Abstract
Artificial intelligence (AI) has profoundly advanced the field of biomedical research, which also demonstrates transformative capacity for innovation in drug development. This paper aims to deliver a comprehensive analysis of the progress in AI-assisted drug development, particularly focusing on small molecules, RNA, and antibodies. Moreover, this paper elucidates the current integration of AI methodologies within the industrial drug development framework. This encompasses a detailed examination of the industry-standard drug development process, supplemented by a review of medications presently undergoing clinical trials. Conclusively, the paper tackles a predominant obstacle within the AI pharmaceutical sector: the absence of AI-conceived drugs receiving approval. This paper also advocates for the adoption of large language models and diffusion models as a viable strategy to surmount this challenge. This review not only underscores the significant potential of AI in drug discovery but also deliberates on the challenges and prospects within this dynamically progressing field.
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Affiliation(s)
- Yilun Zhang
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China; School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong, China
| | - Mohamed Mastouri
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China
| | - Yang Zhang
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China.
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Aribindi K, Liu GY, Albertson TE. Emerging pharmacological options in the treatment of idiopathic pulmonary fibrosis (IPF). Expert Rev Clin Pharmacol 2024; 17:817-835. [PMID: 39192604 PMCID: PMC11441789 DOI: 10.1080/17512433.2024.2396121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/20/2024] [Indexed: 08/29/2024]
Abstract
INTRODUCTION Idiopathic pulmonary fibrosis (IPF) is a progressive-fibrosing lung disease with a median survival of less than 5 years. Currently, two agents, pirfenidone and nintedanib are approved for this disease, and both have been shown to reduce the rate of decline in lung function in patients with IPF. However, both have significant adverse effects and neither completely arrest the decline in lung function. AREAS COVERED Thirty experimental agents with unique mechanisms of action that are being evaluated for the treatment of IPF are discussed. These agents work through various mechanisms of action, these include inhibition of transcription nuclear factor k-B on fibroblasts, reduced expression of metalloproteinase 7, the generation of more lysophosphatidic acids, blocking the effects of transforming growth factor ß, and reducing reactive oxygen species as examples of some unique mechanisms of action of these agents. EXPERT OPINION New drug development has the potential to expand the treatment options available in the treatment of IPF patients. It is expected that the adverse drug effect profiles will be more favorable than current agents. It is further anticipated that these new agents or combinations of agents will arrest the fibrosis, not just slow the fibrotic process.
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Affiliation(s)
- Katyayini Aribindi
- Department of Internal Medicine, Division of Pulmonary, Critical Care & Sleep Medicine, University of California Davis, School of Medicine, Sacramento, CA, USA
- Department of Medicine, Department of Veterans Affairs Northern California Health Care System, Mather, CA, USA
| | - Gabrielle Y Liu
- Department of Internal Medicine, Division of Pulmonary, Critical Care & Sleep Medicine, University of California Davis, School of Medicine, Sacramento, CA, USA
| | - Timothy E Albertson
- Department of Internal Medicine, Division of Pulmonary, Critical Care & Sleep Medicine, University of California Davis, School of Medicine, Sacramento, CA, USA
- Department of Medicine, Department of Veterans Affairs Northern California Health Care System, Mather, CA, USA
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Li X, Liu S, Liu D, Yu M, Wu X, Wang H. Application of Virtual Drug Study to New Drug Research and Development: Challenges and Opportunity. Clin Pharmacokinet 2024; 63:1239-1249. [PMID: 39225885 DOI: 10.1007/s40262-024-01416-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
In recent years, virtual drug study, as an emerging research strategy, has become increasingly important in guiding and promoting new drug research and development. Researchers can integrate a variety of technical methods to improve the efficiency of all phases of new drug research and development, including the use of artificial intelligence, modeling and simulation for target identification, compound screening and pharmacokinetic characteristics evaluation, and the application of clinical trial simulation to carry out clinical research. This paper aims to elaborate on the application of virtual drug study in the key stages of new drug research and development and discuss the opportunities and challenges it faces in supporting new drug research and development.
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Affiliation(s)
- Xiuqi Li
- Clinical Pharmacology Research Center, Peking Union Medical College Hospital, State Key Laboratory of Complex Severe and Rare Diseases, NMPA Key Laboratory for Clinical Research and Evaluation of Drug, Beijing Key Laboratory of Clinical PK & PD Investigation for Innovative Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Shupeng Liu
- Clinical Pharmacology Research Center, Peking Union Medical College Hospital, State Key Laboratory of Complex Severe and Rare Diseases, NMPA Key Laboratory for Clinical Research and Evaluation of Drug, Beijing Key Laboratory of Clinical PK & PD Investigation for Innovative Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Dan Liu
- College of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, China
| | - Mengyang Yu
- Clinical Pharmacology Research Center, Peking Union Medical College Hospital, State Key Laboratory of Complex Severe and Rare Diseases, NMPA Key Laboratory for Clinical Research and Evaluation of Drug, Beijing Key Laboratory of Clinical PK & PD Investigation for Innovative Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xiaofei Wu
- Clinical Pharmacology Research Center, Peking Union Medical College Hospital, State Key Laboratory of Complex Severe and Rare Diseases, NMPA Key Laboratory for Clinical Research and Evaluation of Drug, Beijing Key Laboratory of Clinical PK & PD Investigation for Innovative Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Hongyun Wang
- Clinical Pharmacology Research Center, Peking Union Medical College Hospital, State Key Laboratory of Complex Severe and Rare Diseases, NMPA Key Laboratory for Clinical Research and Evaluation of Drug, Beijing Key Laboratory of Clinical PK & PD Investigation for Innovative Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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Zhou B, Zheng Y, Suo Z, Zhang M, Xu W, Wang L, Ge D, Qu Y, Wang Q, Zheng H, Ni C. The role of lncRNAs related ceRNA regulatory network in multiple hippocampal pathological processes during the development of perioperative neurocognitive disorders. PeerJ 2024; 12:e17775. [PMID: 39135955 PMCID: PMC11318589 DOI: 10.7717/peerj.17775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/28/2024] [Indexed: 08/15/2024] Open
Abstract
Background Perioperative neurocognitive disorders (PND) refer to neurocognitive abnormalities during perioperative period, which are a great challenge for elderly patients and associated with increased morbidity and mortality. Our studies showed that long non-coding RNAs (lncRNAs) regulate mitochondrial function and aging-related pathologies in the aged hippocampus after anesthesia, and lncRNAs are associated with multiple neurodegenerations. However, the regulatory role of lncRNAs in PND-related pathological processes remains unclear. Methods A total of 18-month mice were assigned to control and surgery (PND) groups, mice in PND group received sevoflurane anesthesia and laparotomy. Cognitive function was assessed with fear conditioning test. Hippocampal RNAs were isolated for sequencing, lncRNA and microRNA libraries were constructed, mRNAs were identified, Gene Ontology (GO) analysis were performed, and lncRNA-microRNA-mRNA networks were established. qPCR was performed for gene expression verification. Results A total of 312 differentially expressed (DE) lncRNAs, 340 DE-Transcripts of Uncertain Coding Potential (TUCPs), and 2,003 DEmRNAs were identified in the hippocampus between groups. The lncRNA-microRNA-mRNA competing endogenous RNA (ceRNA) network was constructed with 29 DElncRNAs, 90 microRNAs, 493 DEmRNAs, 148 lncRNA-microRNA interaction pairs, 794 microRNA-mRNA interaction pairs, and 110 lncRNA-mRNA co-expression pairs. 795 GO terms were obtained. Based on the frequencies of involved pathological processes, BP terms were divided into eight categories: neurological system alternation, neuronal development, metabolism alternation, immunity and neuroinflammation, apoptosis and autophagy, cellular communication, molecular modification, and behavior changes. LncRNA-microRNA-mRNA ceRNA networks in these pathological categories were constructed, and involved pathways and targeted genes were revealed. The top relevant lncRNAs in these ceRNA networks included RP23-65G6.4, RP24-396L14.1, RP23-251I16.2, XLOC_113622, RP24-496E14.1, etc., and the top relevant mRNAs in these ceRNA networks included Dlg4 (synaptic function), Avp (lipophagy), Islr2 (synaptic function), Hcrt (regulation of awake behavior), Tnc (neurotransmitter uptake). Conclusion In summary, we have constructed the lncRNA-associated ceRNA network during PND development in mice, explored the role of lncRNAs in multiple pathological processes in the mouse hippocampus, and provided insights into the potential mechanisms and therapeutic gene targets for PND.
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Affiliation(s)
- Bowen Zhou
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuxiang Zheng
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zizheng Suo
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mingzhu Zhang
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenjie Xu
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lijuan Wang
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dazhuang Ge
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yinyin Qu
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
| | - Qiang Wang
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hui Zheng
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Cheng Ni
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Sidorenko D, Pushkov S, Sakip A, Leung GHD, Lok SWY, Urban A, Zagirova D, Veviorskiy A, Tihonova N, Kalashnikov A, Kozlova E, Naumov V, Pun FW, Aliper A, Ren F, Zhavoronkov A. Precious2GPT: the combination of multiomics pretrained transformer and conditional diffusion for artificial multi-omics multi-species multi-tissue sample generation. NPJ AGING 2024; 10:37. [PMID: 39117678 PMCID: PMC11310469 DOI: 10.1038/s41514-024-00163-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024]
Abstract
Synthetic data generation in omics mimics real-world biological data, providing alternatives for training and evaluation of genomic analysis tools, controlling differential expression, and exploring data architecture. We previously developed Precious1GPT, a multimodal transformer trained on transcriptomic and methylation data, along with metadata, for predicting biological age and identifying dual-purpose therapeutic targets potentially implicated in aging and age-associated diseases. In this study, we introduce Precious2GPT, a multimodal architecture that integrates Conditional Diffusion (CDiffusion) and decoder-only Multi-omics Pretrained Transformer (MoPT) models trained on gene expression and DNA methylation data. Precious2GPT excels in synthetic data generation, outperforming Conditional Generative Adversarial Networks (CGANs), CDiffusion, and MoPT. We demonstrate that Precious2GPT is capable of generating representative synthetic data that captures tissue- and age-specific information from real transcriptomics and methylomics data. Notably, Precious2GPT surpasses other models in age prediction accuracy using the generated data, and it can generate data beyond 120 years of age. Furthermore, we showcase the potential of using this model in identifying gene signatures and potential therapeutic targets in a colorectal cancer case study.
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Affiliation(s)
- Denis Sidorenko
- Insilico Medicine Hong Kong Ltd., Unit 310, 3/F, Building 8W Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Stefan Pushkov
- Insilico Medicine Hong Kong Ltd., Unit 310, 3/F, Building 8W Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Akhmed Sakip
- Insilico Medicine Hong Kong Ltd., Unit 310, 3/F, Building 8W Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Geoffrey Ho Duen Leung
- Insilico Medicine Hong Kong Ltd., Unit 310, 3/F, Building 8W Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Sarah Wing Yan Lok
- Insilico Medicine Hong Kong Ltd., Unit 310, 3/F, Building 8W Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Anatoly Urban
- Insilico Medicine Hong Kong Ltd., Unit 310, 3/F, Building 8W Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Diana Zagirova
- Insilico Medicine Hong Kong Ltd., Unit 310, 3/F, Building 8W Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Alexander Veviorskiy
- Insilico Medicine AI Limited, Level 6, Unit 08, Block A, IRENA HQ Building, Masdar City, Abu Dhabi, UAE
| | - Nina Tihonova
- Insilico Medicine AI Limited, Level 6, Unit 08, Block A, IRENA HQ Building, Masdar City, Abu Dhabi, UAE
| | - Aleksandr Kalashnikov
- Insilico Medicine AI Limited, Level 6, Unit 08, Block A, IRENA HQ Building, Masdar City, Abu Dhabi, UAE
| | - Ekaterina Kozlova
- Insilico Medicine Hong Kong Ltd., Unit 310, 3/F, Building 8W Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Vladimir Naumov
- Insilico Medicine Hong Kong Ltd., Unit 310, 3/F, Building 8W Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Frank W Pun
- Insilico Medicine Hong Kong Ltd., Unit 310, 3/F, Building 8W Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Alex Aliper
- Insilico Medicine AI Limited, Level 6, Unit 08, Block A, IRENA HQ Building, Masdar City, Abu Dhabi, UAE
| | - Feng Ren
- Insilico Medicine Shanghai Ltd., Suite 902, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong, Shanghai, 201203, China
| | - Alex Zhavoronkov
- Insilico Medicine Hong Kong Ltd., Unit 310, 3/F, Building 8W Hong Kong Science and Technology Park, Hong Kong SAR, China.
- Insilico Medicine AI Limited, Level 6, Unit 08, Block A, IRENA HQ Building, Masdar City, Abu Dhabi, UAE.
- Buck Institute for Research on Aging, Novato, CA, 94945, USA.
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Sinha S, McLaren E, Mullick M, Singh S, Boland BS, Ghosh P. FORWARD: A Learning Framework for Logical Network Perturbations to Prioritize Targets for Drug Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.602603. [PMID: 39071297 PMCID: PMC11275938 DOI: 10.1101/2024.07.16.602603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Despite advances in artificial intelligence (AI), target-based drug development remains a costly, complex and imprecise process. We introduce F.O.R.W.A.R.D [ Framework for Outcome-based Research and Drug Development ], a network-based target prioritization approach and test its utility in the challenging therapeutic area of Inflammatory Bowel Diseases (IBD), which is a chronic condition of multifactorial origin. F.O.R.W.A.R.D leverages real-world outcomes, using a machine-learning classifier trained on transcriptomic data from seven prospective randomized clinical trials involving four drugs. It establishes a molecular signature of remission as the therapeutic goal and computes, by integrating principles of network connectivity, the likelihood that a drug's action on its target(s) will induce the remission-associated genes. Benchmarking F.O.R.W.A.R.D against 210 completed clinical trials on 52 targets showed a perfect predictive accuracy of 100%. The success of F.O.R.W.A.R.D was achieved despite differences in targets, mechanisms, and trial designs. F.O.R.W.A.R.D-driven in-silico phase '0' trials revealed its potential to inform trial design, justify re-trialing failed drugs, and guide early terminations. With its extendable applications to other therapeutic areas and its iterative refinement with emerging trials, F.O.R.W.A.R.D holds the promise to transform drug discovery by generating foresight from hindsight and impacting research and development as well as human-in-the-loop clinical decision-making.
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Zhou X, Chen X, Pan Q, Wang S, Li J, Yang Y. Exploring the role of candidalysin in the pathogenicity of Candida albicans by gene set enrichment analysis and evolutionary dynamics. Am J Transl Res 2024; 16:3191-3210. [PMID: 39114682 PMCID: PMC11301511 DOI: 10.62347/izym9087] [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: 04/12/2024] [Accepted: 05/20/2024] [Indexed: 08/10/2024]
Abstract
AIMS To explore the pathogenic mechanisms of Candida albicans (C. albicans), focusing on its impact on human health, particularly through invasive infections in the gastrointestinal and respiratory tracts. METHODS In this study, we evaluated the demographic and clinical profiles of 7 pneumonia patients. Meanwhile, we used Gene Set Enrichment Analysis (GSEA) and Evolutionary Dynamics method to analyze the role of candidalysin in C. albicans pathogenicity. RESULTS By analyzing genomic data and conducting biomedical text mining, we identified novel mutation sites in the candidalysin coding gene ECE1-III, shedding light into the genetic diversity within C. albicans strains and their potential implications for antifungal resistance. Our results revealed significant associations between C. albicans and respiratory as well as gastrointestinal diseases, emphasizing the fungus's role in the pathogenesis of these diseases. Additionally, we identified a new mutation site in the C. albicans strain YF2-5, isolated from patients with pneumonia. This mutation may be associated with its heightened pathogenicity. CONCLUSION Our research advances the understanding of C. albicans pathogenicity and opens new avenues for developing targeted antifungal therapies. By focusing on the molecular basis of fungal virulence, we aim to contribute to the development of more effective treatment strategies, addressing the challenge of multidrug resistance in invasive fungal infections.
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Affiliation(s)
- Xingchen Zhou
- Bioinformatics Center of AMMS, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious DiseasesBeijing 100850, China
| | - Xiaolin Chen
- Sir Run Run Hospital, Nanjing Medical UniversityNanjing 210009, Jiangsu, China
| | - Qianglong Pan
- Sir Run Run Hospital, Nanjing Medical UniversityNanjing 210009, Jiangsu, China
| | - Shengqi Wang
- Bioinformatics Center of AMMS, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious DiseasesBeijing 100850, China
| | - Jing Li
- School of Life Science and Technology, China Pharmaceutical UniversityNanjing 210009, Jiangsu, China
| | - Ying Yang
- Bioinformatics Center of AMMS, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious DiseasesBeijing 100850, China
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9
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Huang X, Lee S, Chen K, Kawaguchi R, Wiskow O, Ghosh S, Frost D, Perrault L, Pandey R, Klim JR, Boivin B, Hermawan C, Livak KJ, Geschwind DH, Wainger BJ, Eggan KC, Bean BP, Woolf CJ. Downregulation of the silent potassium channel Kv8.1 increases motor neuron vulnerability in amyotrophic lateral sclerosis. Brain Commun 2024; 6:fcae202. [PMID: 38911266 PMCID: PMC11191651 DOI: 10.1093/braincomms/fcae202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 04/10/2024] [Accepted: 06/07/2024] [Indexed: 06/25/2024] Open
Abstract
While voltage-gated potassium channels have critical roles in controlling neuronal excitability, they also have non-ion-conducting functions. Kv8.1, encoded by the KCNV1 gene, is a 'silent' ion channel subunit whose biological role is complex since Kv8.1 subunits do not form functional homotetramers but assemble with Kv2 to modify its ion channel properties. We profiled changes in ion channel expression in amyotrophic lateral sclerosis patient-derived motor neurons carrying a superoxide dismutase 1(A4V) mutation to identify what drives their hyperexcitability. A major change identified was a substantial reduction of KCNV1/Kv8.1 expression, which was also observed in patient-derived neurons with C9orf72 expansion. We then studied the effect of reducing KCNV1/Kv8.1 expression in healthy motor neurons and found it did not change neuronal firing but increased vulnerability to cell death. A transcriptomic analysis revealed dysregulated metabolism and lipid/protein transport pathways in KCNV1/Kv8.1-deficient motor neurons. The increased neuronal vulnerability produced by the loss of KCNV1/Kv8.1 was rescued by knocking down Kv2.2, suggesting a potential Kv2.2-dependent downstream mechanism in cell death. Our study reveals, therefore, unsuspected and distinct roles of Kv8.1 and Kv2.2 in amyotrophic lateral sclerosis-related neurodegeneration.
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Affiliation(s)
- Xuan Huang
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Seungkyu Lee
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Kuchuan Chen
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Riki Kawaguchi
- Department of Psychiatry and Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ole Wiskow
- Department of Stem Cell and Regenerative Biology and Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Sulagna Ghosh
- Department of Stem Cell and Regenerative Biology and Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Devlin Frost
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Laura Perrault
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Roshan Pandey
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph R Klim
- Department of Stem Cell and Regenerative Biology and Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Bruno Boivin
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Crystal Hermawan
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Kenneth J Livak
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Daniel H Geschwind
- Department of Psychiatry and Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Brian J Wainger
- Department of Neurology, Mass General Brigham and Harvard Medical School, Boston, MA 02114, USA
| | - Kevin C Eggan
- Department of Stem Cell and Regenerative Biology and Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Bruce P Bean
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Clifford J Woolf
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
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Kamya P, Ozerov IV, Pun FW, Tretina K, Fokina T, Chen S, Naumov V, Long X, Lin S, Korzinkin M, Polykovskiy D, Aliper A, Ren F, Zhavoronkov A. PandaOmics: An AI-Driven Platform for Therapeutic Target and Biomarker Discovery. J Chem Inf Model 2024; 64:3961-3969. [PMID: 38404138 PMCID: PMC11134400 DOI: 10.1021/acs.jcim.3c01619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/27/2024]
Abstract
PandaOmics is a cloud-based software platform that applies artificial intelligence and bioinformatics techniques to multimodal omics and biomedical text data for therapeutic target and biomarker discovery. PandaOmics generates novel and repurposed therapeutic target and biomarker hypotheses with the desired properties and is available through licensing or collaboration. Targets and biomarkers generated by the platform were previously validated in both in vitro and in vivo studies. PandaOmics is a core component of Insilico Medicine's Pharma.ai drug discovery suite, which also includes Chemistry42 for the de novo generation of novel small molecules, and inClinico─a data-driven multimodal platform that forecasts a clinical trial's probability of successful transition from phase 2 to phase 3. In this paper, we demonstrate how the PandaOmics platform can efficiently identify novel molecular targets and biomarkers for various diseases.
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Affiliation(s)
- Petrina Kamya
- Insilico
Medicine Canada Inc., 3710-1250 René-Lévesque Blvd. W, Montreal, Quebec, Canada H3B 4W8
| | - Ivan V. Ozerov
- Insilico
Medicine Hong Kong Limited, Hong Kong Science and Technology Park, Hong Kong
| | - Frank W. Pun
- Insilico
Medicine Hong Kong Limited, Hong Kong Science and Technology Park, Hong Kong
| | - Kyle Tretina
- Insilico
Medicine Hong Kong Limited, Hong Kong Science and Technology Park, Hong Kong
| | - Tatyana Fokina
- Insilico
Medicine Hong Kong Limited, Hong Kong Science and Technology Park, Hong Kong
| | - Shan Chen
- Insilico
Medicine Shanghai Limited, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Vladimir Naumov
- Insilico
Medicine Hong Kong Limited, Hong Kong Science and Technology Park, Hong Kong
| | - Xi Long
- Insilico
Medicine Hong Kong Limited, Hong Kong Science and Technology Park, Hong Kong
| | - Sha Lin
- Insilico
Medicine Shanghai Limited, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Mikhail Korzinkin
- Insilico
Medicine Hong Kong Limited, Hong Kong Science and Technology Park, Hong Kong
| | - Daniil Polykovskiy
- Insilico
Medicine Canada Inc., 3710-1250 René-Lévesque Blvd. W, Montreal, Quebec, Canada H3B 4W8
| | - Alex Aliper
- Insilico
Medicine AI Limited, Level 6, Unit 08, Block A, IRENA HQ Building, P.O.
Box 145748, Masdar City, Abu Dhabi, United Arab Emirates
| | - Feng Ren
- Insilico
Medicine Shanghai Limited, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Alex Zhavoronkov
- Insilico
Medicine Hong Kong Limited, Hong Kong Science and Technology Park, Hong Kong
- Insilico
Medicine AI Limited, Level 6, Unit 08, Block A, IRENA HQ Building, P.O.
Box 145748, Masdar City, Abu Dhabi, United Arab Emirates
- Buck
Institute for Research on Aging, Novato, California 94945, United States
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11
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Sahu M, Vashishth S, Kukreti N, Gulia A, Russell A, Ambasta RK, Kumar P. Synergizing drug repurposing and target identification for neurodegenerative diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 205:111-169. [PMID: 38789177 DOI: 10.1016/bs.pmbts.2024.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Despite dedicated research efforts, the absence of disease-curing remedies for neurodegenerative diseases (NDDs) continues to jeopardize human society and stands as a challenge. Drug repurposing is an attempt to find new functionality of existing drugs and take it as an opportunity to discourse the clinically unmet need to treat neurodegeneration. However, despite applying this approach to rediscover a drug, it can also be used to identify the target on which a drug could work. The primary objective of target identification is to unravel all the possibilities of detecting a new drug or repurposing an existing drug. Lately, scientists and researchers have been focusing on specific genes, a particular site in DNA, a protein, or a molecule that might be involved in the pathogenesis of the disease. However, the new era discusses directing the signaling mechanism involved in the disease progression, where receptors, ion channels, enzymes, and other carrier molecules play a huge role. This review aims to highlight how target identification can expedite the whole process of drug repurposing. Here, we first spot various target-identification methods and drug-repositioning studies, including drug-target and structure-based identification studies. Moreover, we emphasize various drug repurposing approaches in NDDs, namely, experimental-based, mechanism-based, and in silico approaches. Later, we draw attention to validation techniques and stress on drugs that are currently undergoing clinical trials in NDDs. Lastly, we underscore the future perspective of synergizing drug repurposing and target identification in NDDs and present an unresolved question to address the issue.
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Affiliation(s)
- Mehar Sahu
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Shrutikirti Vashishth
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Neha Kukreti
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Ashima Gulia
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Ashish Russell
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Rashmi K Ambasta
- Department of Biotechnology and Microbiology, SRM University, Sonepat, Haryana, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India.
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12
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Ren F, Aliper A, Chen J, Zhao H, Rao S, Kuppe C, Ozerov IV, Zhang M, Witte K, Kruse C, Aladinskiy V, Ivanenkov Y, Polykovskiy D, Fu Y, Babin E, Qiao J, Liang X, Mou Z, Wang H, Pun FW, Ayuso PT, Veviorskiy A, Song D, Liu S, Zhang B, Naumov V, Ding X, Kukharenko A, Izumchenko E, Zhavoronkov A. A small-molecule TNIK inhibitor targets fibrosis in preclinical and clinical models. Nat Biotechnol 2024:10.1038/s41587-024-02143-0. [PMID: 38459338 DOI: 10.1038/s41587-024-02143-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/16/2024] [Indexed: 03/10/2024]
Abstract
Idiopathic pulmonary fibrosis (IPF) is an aggressive interstitial lung disease with a high mortality rate. Putative drug targets in IPF have failed to translate into effective therapies at the clinical level. We identify TRAF2- and NCK-interacting kinase (TNIK) as an anti-fibrotic target using a predictive artificial intelligence (AI) approach. Using AI-driven methodology, we generated INS018_055, a small-molecule TNIK inhibitor, which exhibits desirable drug-like properties and anti-fibrotic activity across different organs in vivo through oral, inhaled or topical administration. INS018_055 possesses anti-inflammatory effects in addition to its anti-fibrotic profile, validated in multiple in vivo studies. Its safety and tolerability as well as pharmacokinetics were validated in a randomized, double-blinded, placebo-controlled phase I clinical trial (NCT05154240) involving 78 healthy participants. A separate phase I trial in China, CTR20221542, also demonstrated comparable safety and pharmacokinetic profiles. This work was completed in roughly 18 months from target discovery to preclinical candidate nomination and demonstrates the capabilities of our generative AI-driven drug-discovery pipeline.
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Affiliation(s)
- Feng Ren
- Insilico Medicine Shanghai Ltd., Shanghai, China
- Insilico Medicine AI Limited, Abu Dhabi, UAE
| | - Alex Aliper
- Insilico Medicine AI Limited, Abu Dhabi, UAE
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Jian Chen
- Department of Clinical Pharmacology, Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, China
| | - Heng Zhao
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Sujata Rao
- Insilico Medicine US Inc., New York, NY, USA
| | - Christoph Kuppe
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
- Department of Nephrology, University Clinic RWTH Aachen, Aachen, Germany
| | - Ivan V Ozerov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Man Zhang
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Klaus Witte
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Chris Kruse
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | | | - Yan Ivanenkov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | | | - Yanyun Fu
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | | | - Junwen Qiao
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Xing Liang
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Zhenzhen Mou
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Hui Wang
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Frank W Pun
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Pedro Torres Ayuso
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Temple University, PA, USA
| | | | - Dandan Song
- Department of Clinical Pharmacology, Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, China
| | - Sang Liu
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Bei Zhang
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Vladimir Naumov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Xiaoqiang Ding
- Division of Nephrology, Zhongshan Hospital Shanghai Medical College, Fudan University, Shanghai, China
| | - Andrey Kukharenko
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Evgeny Izumchenko
- Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Alex Zhavoronkov
- Insilico Medicine AI Limited, Abu Dhabi, UAE.
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China.
- Insilico Medicine US Inc., New York, NY, USA.
- Insilico Medicine Canada Inc, Montreal, Quebec, Canada.
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13
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Zhou E, Shen Q, Hou Y. Integrating artificial intelligence into the modernization of traditional Chinese medicine industry: a review. Front Pharmacol 2024; 15:1181183. [PMID: 38464717 PMCID: PMC10921893 DOI: 10.3389/fphar.2024.1181183] [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: 03/07/2023] [Accepted: 02/08/2024] [Indexed: 03/12/2024] Open
Abstract
Traditional Chinese medicine (TCM) is the practical experience and summary of the Chinese nation for thousands of years. It shows great potential in treating various chronic diseases, complex diseases and major infectious diseases, and has gradually attracted the attention of people all over the world. However, due to the complexity of prescription and action mechanism of TCM, the development of TCM industry is still in a relatively conservative stage. With the rise of artificial intelligence technology in various fields, many scholars began to apply artificial intelligence technology to traditional Chinese medicine industry and made remarkable progress. This paper comprehensively summarizes the important role of artificial intelligence in the development of traditional Chinese medicine industry from various aspects, including new drug discovery, data mining, quality standardization and industry technology of traditional Chinese medicine. The limitations of artificial intelligence in these applications are also emphasized, including the lack of pharmacological research, database quality problems and the challenges brought by human-computer interaction. Nevertheless, the development of artificial intelligence has brought new opportunities and innovations to the modernization of traditional Chinese medicine. Integrating artificial intelligence technology into the comprehensive application of Chinese medicine industry is expected to overcome the major problems faced by traditional Chinese medicine industry and further promote the modernization of the whole traditional Chinese medicine industry.
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Affiliation(s)
- E. Zhou
- Yuhu District Healthcare Security Administration, Xiangtan, China
| | - Qin Shen
- Department of Respiratory Medicine, Hunan Provincial People’s Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha, China
| | - Yang Hou
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
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14
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Abstract
Drug discovery is adapting to novel technologies such as data science, informatics, and artificial intelligence (AI) to accelerate effective treatment development while reducing costs and animal experiments. AI is transforming drug discovery, as indicated by increasing interest from investors, industrial and academic scientists, and legislators. Successful drug discovery requires optimizing properties related to pharmacodynamics, pharmacokinetics, and clinical outcomes. This review discusses the use of AI in the three pillars of drug discovery: diseases, targets, and therapeutic modalities, with a focus on small-molecule drugs. AI technologies, such as generative chemistry, machine learning, and multiproperty optimization, have enabled several compounds to enter clinical trials. The scientific community must carefully vet known information to address the reproducibility crisis. The full potential of AI in drug discovery can only be realized with sufficient ground truth and appropriate human intervention at later pipeline stages.
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Affiliation(s)
- Catrin Hasselgren
- Safety Assessment, Genentech, Inc., South San Francisco, California, USA
| | - Tudor I Oprea
- Expert Systems Inc., San Diego, California, USA;
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
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15
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Wang Y, Wang C, Liu T, Qi H, Chen S, Cai X, Zhang M, Aliper A, Ren F, Ding X, Zhavoronkov A. Discovery of Tetrahydropyrazolopyrazine Derivatives as Potent and Selective MYT1 Inhibitors for the Treatment of Cancer. J Med Chem 2024; 67:420-432. [PMID: 38146659 DOI: 10.1021/acs.jmedchem.3c01476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Breast and gynecological cancers are among the leading causes of death in women worldwide, illustrating the urgent need for innovative treatment options. We identified MYT1 as a promising new therapeutic target for breast and gynecological cancer using PandaOmics, an AI-driven target discovery platform. The synthetic lethal relationship of MYT1 in tumor cell lines with CCNE1 amplification enhanced this rationale. Through structure-based drug design, we developed a series of novel, potent, and highly selective inhibitors specifically targeting MYT1. Importantly, our lead compound, featuring a tetrahydropyrazolopyrazine ring, exhibits remarkable selectivity over WEE1, a related kinase associated with bone marrow suppression upon inhibition. Optimization of potency and physical properties resulted in the discovery of compound 21, a novel MYT1 inhibitor, exhibiting optimal pharmacokinetic properties and promising in vivo antitumor efficacy.
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Affiliation(s)
- Yazhou Wang
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Chao Wang
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Tingting Liu
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Hongyun Qi
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Shan Chen
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Xin Cai
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Man Zhang
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Alex Aliper
- Insilico Medicine AI Limited, Masdar City 145748, Abu Dhabi, United Arab Emirates
| | - Feng Ren
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Xiao Ding
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Alex Zhavoronkov
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
- Insilico Medicine AI Limited, Masdar City 145748, Abu Dhabi, United Arab Emirates
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16
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Geraci J, Bhargava R, Qorri B, Leonchyk P, Cook D, Cook M, Sie F, Pani L. Machine learning hypothesis-generation for patient stratification and target discovery in rare disease: our experience with Open Science in ALS. Front Comput Neurosci 2024; 17:1199736. [PMID: 38260713 PMCID: PMC10801647 DOI: 10.3389/fncom.2023.1199736] [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: 04/03/2023] [Accepted: 11/20/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction Advances in machine learning (ML) methodologies, combined with multidisciplinary collaborations across biological and physical sciences, has the potential to propel drug discovery and development. Open Science fosters this collaboration by releasing datasets and methods into the public space; however, further education and widespread acceptance and adoption of Open Science approaches are necessary to tackle the plethora of known disease states. Motivation In addition to providing much needed insights into potential therapeutic protein targets, we also aim to demonstrate that small patient datasets have the potential to provide insights that usually require many samples (>5,000). There are many such datasets available and novel advancements in ML can provide valuable insights from these patient datasets. Problem statement Using a public dataset made available by patient advocacy group AnswerALS and a multidisciplinary Open Science approach with a systems biology augmented ML technology, we aim to validate previously reported drug targets in ALS and provide novel insights about ALS subpopulations and potential drug targets using a unique combination of ML methods and graph theory. Methodology We use NetraAI to generate hypotheses about specific patient subpopulations, which were then refined and validated through a combination of ML techniques, systems biology methods, and expert input. Results We extracted 8 target classes, each comprising of several genes that shed light into ALS pathophysiology and represent new avenues for treatment. These target classes are broadly categorized as inflammation, epigenetic, heat shock, neuromuscular junction, autophagy, apoptosis, axonal transport, and excitotoxicity. These findings are not mutually exclusive, and instead represent a systematic view of ALS pathophysiology. Based on these findings, we suggest that simultaneous targeting of ALS has the potential to mitigate ALS progression, with the plausibility of maintaining and sustaining an improved quality of life (QoL) for ALS patients. Even further, we identified subpopulations based on disease onset. Conclusion In the spirit of Open Science, this work aims to bridge the knowledge gap in ALS pathophysiology to aid in diagnostic, prognostic, and therapeutic strategies and pave the way for the development of personalized treatments tailored to the individual's needs.
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Affiliation(s)
- Joseph Geraci
- NetraMark Corp, Toronto, ON, Canada
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
- Centre for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States
- Arthur C. Clarke Center for Human Imagination, School of Physical Sciences, University of California San Diego, San Diego, CA, United States
| | - Ravi Bhargava
- Department of Biomedical and Molecular Science, Queens University, Kingston, ON, Canada
- Science and Research, Roche Integrated Informatics, F. Hoffmann La-Roche, Toronto, ON, Canada
| | | | | | - Douglas Cook
- NetraMark Corp, Toronto, ON, Canada
- Department of Surgery, Queen's University, Kingston, ON, Canada
| | - Moses Cook
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Fanny Sie
- Science and Research, Roche Integrated Informatics, F. Hoffmann La-Roche, Toronto, ON, Canada
| | - Luca Pani
- NetraMark Corp, Toronto, ON, Canada
- Department of Psychiatry and Behavioral Sciences, Leonard M. Miller School of Medicine, University of Miami, Coral Gables, FL, United States
- Department of Biomedical, Metabolic, and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
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17
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Bonde B. Edge, Fog, and Cloud Against Disease: The Potential of High-Performance Cloud Computing for Pharma Drug Discovery. Methods Mol Biol 2024; 2716:181-202. [PMID: 37702940 DOI: 10.1007/978-1-0716-3449-3_8] [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: 09/14/2023]
Abstract
The high-performance computing (HPC) platform for large-scale drug discovery simulation demands significant investment in speciality hardware, maintenance, resource management, and running costs. The rapid growth in computing hardware has made it possible to provide cost-effective, robust, secure, and scalable alternatives to the on-premise (on-prem) HPC via Cloud, Fog, and Edge computing. It has enabled recent state-of-the-art machine learning (ML) and artificial intelligence (AI)-based tools for drug discovery, such as BERT, BARD, AlphaFold2, and GPT. This chapter attempts to overview types of software architectures for developing scientific software or application with deployment agnostic (on-prem to cloud and hybrid) use cases. Furthermore, the chapter aims to outline how the innovation is disrupting the orthodox mindset of monolithic software running on on-prem HPC and provide the paradigm shift landscape to microservices driven application programming (API) and message parsing interface (MPI)-based scientific computing across the distributed, high-available infrastructure. This is coupled with agile DevOps, and good coding practices, low code and no-code application development frameworks for cost-efficient, secure, automated, and robust scientific application life cycle management.
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Affiliation(s)
- Bhushan Bonde
- Evotec (UK) Ltd., Dorothy Crowfoot Hodgkin Campus, Abingdon, Oxfordshire, UK.
- Digital Futures Institute, University of Suffolk, Ipswich, United Kingdom.
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18
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Pun FW, Leung GHD, Leung HW, Rice J, Schmauck‐Medina T, Lautrup S, Long X, Liu BHM, Wong CW, Ozerov IV, Aliper A, Ren F, Rosenberg AJ, Agrawal N, Izumchenko E, Fang EF, Zhavoronkov A. A comprehensive AI-driven analysis of large-scale omic datasets reveals novel dual-purpose targets for the treatment of cancer and aging. Aging Cell 2023; 22:e14017. [PMID: 37888486 PMCID: PMC10726874 DOI: 10.1111/acel.14017] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023] Open
Abstract
As aging and tumorigenesis are tightly interconnected biological processes, targeting their common underlying driving pathways may induce dual-purpose anti-aging and anti-cancer effects. Our transcriptomic analyses of 16,740 healthy samples demonstrated tissue-specific age-associated gene expression, with most tumor suppressor genes downregulated during aging. Furthermore, a large-scale pan-cancer analysis of 11 solid tumor types (11,303 cases and 4431 control samples) revealed that many cellular processes, such as protein localization, DNA replication, DNA repair, cell cycle, and RNA metabolism, were upregulated in cancer but downregulated in healthy aging tissues, whereas pathways regulating cellular senescence were upregulated in both aging and cancer. Common cancer targets were identified by the AI-driven target discovery platform-PandaOmics. Age-associated cancer targets were selected and further classified into four groups based on their reported roles in lifespan. Among the 51 identified age-associated cancer targets with anti-aging experimental evidence, 22 were proposed as dual-purpose targets for anti-aging and anti-cancer treatment with the same therapeutic direction. Among age-associated cancer targets without known lifespan-regulating activity, 23 genes were selected based on predicted dual-purpose properties. Knockdown of histone demethylase KDM1A, one of these unexplored candidates, significantly extended lifespan in Caenorhabditis elegans. Given KDM1A's anti-cancer activities reported in both preclinical and clinical studies, our findings propose KDM1A as a promising dual-purpose target. This is the first study utilizing an innovative AI-driven approach to identify dual-purpose target candidates for anti-aging and anti-cancer treatment, supporting the value of AI-assisted target identification for drug discovery.
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Affiliation(s)
| | | | | | - Jared Rice
- Department of Clinical Molecular BiologyUniversity of Oslo and Akershus University HospitalLørenskogNorway
| | - Tomas Schmauck‐Medina
- Department of Clinical Molecular BiologyUniversity of Oslo and Akershus University HospitalLørenskogNorway
| | - Sofie Lautrup
- Department of Clinical Molecular BiologyUniversity of Oslo and Akershus University HospitalLørenskogNorway
| | - Xi Long
- Insilico Medicine Hong Kong Ltd.Hong KongChina
| | | | | | | | - Alex Aliper
- Insilico Medicine AI Ltd.Masdar CityUnited Arab Emirates
| | - Feng Ren
- Insilico Medicine Shanghai Ltd.ShanghaiChina
| | - Ari J. Rosenberg
- Department of Medicine, Section of Hematology and OncologyUniversity of ChicagoChicagoIllinoisUSA
| | - Nishant Agrawal
- Department of SurgeryUniversity of ChicagoChicagoIllinoisUSA
| | - Evgeny Izumchenko
- Department of Medicine, Section of Hematology and OncologyUniversity of ChicagoChicagoIllinoisUSA
| | - Evandro F. Fang
- Department of Clinical Molecular BiologyUniversity of Oslo and Akershus University HospitalLørenskogNorway
- The Norwegian Centre On Healthy Ageing (NO‐Age)OsloNorway
| | - Alex Zhavoronkov
- Insilico Medicine Hong Kong Ltd.Hong KongChina
- Insilico Medicine AI Ltd.Masdar CityUnited Arab Emirates
- Buck Institute for Research on AgingNovatoCaliforniaUSA
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19
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Blaudin de Thé FX, Baudier C, Andrade Pereira R, Lefebvre C, Moingeon P. Transforming drug discovery with a high-throughput AI-powered platform: A 5-year experience with Patrimony. Drug Discov Today 2023; 28:103772. [PMID: 37717933 DOI: 10.1016/j.drudis.2023.103772] [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] [Received: 07/26/2023] [Revised: 09/01/2023] [Accepted: 09/12/2023] [Indexed: 09/19/2023]
Abstract
High-throughput computational platforms are being established to accelerate drug discovery. Servier launched the Patrimony platform to harness computational sciences and artificial intelligence (AI) to integrate massive multimodal data from internal and external sources. Patrimony has enabled researchers to prioritize therapeutic targets based on a deep understanding of the pathophysiology of immuno-inflammatory diseases. Herein, we share our experience regarding main challenges and critical success factors faced when industrializing the platform and broadening its applications to neurological diseases. We emphasize the importance of integrating such platforms in an end-to-end drug discovery process and engaging human experts early on to ensure a transforming impact.
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20
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Shiammala PN, Duraimutharasan NKB, Vaseeharan B, Alothaim AS, Al-Malki ES, Snekaa B, Safi SZ, Singh SK, Velmurugan D, Selvaraj C. Exploring the artificial intelligence and machine learning models in the context of drug design difficulties and future potential for the pharmaceutical sectors. Methods 2023; 219:82-94. [PMID: 37778659 DOI: 10.1016/j.ymeth.2023.09.010] [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] [Received: 08/07/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023] Open
Abstract
Artificial intelligence (AI), particularly deep learning as a subcategory of AI, provides opportunities to accelerate and improve the process of discovering and developing new drugs. The use of AI in drug discovery is still in its early stages, but it has the potential to revolutionize the way new drugs are discovered and developed. As AI technology continues to evolve, it is likely that AI will play an even greater role in the future of drug discovery. AI is used to identify new drug targets, design new molecules, and predict the efficacy and safety of potential drugs. The inclusion of AI in drug discovery can screen millions of compounds in a matter of hours, identifying potential drug candidates that would have taken years to find using traditional methods. AI is highly utilized in the pharmaceutical industry by optimizing processes, reducing waste, and ensuring quality control. This review covers much-needed topics, including the different types of machine-learning techniques, their applications in drug discovery, and the challenges and limitations of using machine learning in this field. The state-of-the-art of AI-assisted pharmaceutical discovery is described, covering applications in structure and ligand-based virtual screening, de novo drug creation, prediction of physicochemical and pharmacokinetic properties, drug repurposing, and related topics. Finally, many obstacles and limits of present approaches are outlined, with an eye on potential future avenues for AI-assisted drug discovery and design.
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Affiliation(s)
| | | | - Baskaralingam Vaseeharan
- Department of Animal Health and Management, Science Block, Alagappa University, Karaikudi, Tamil Nadu 630 003, India
| | - Abdulaziz S Alothaim
- Department of Biology, College of Science in Zulfi, Majmaah University, Al-Majmaah 11952, Saudi Arabia
| | - Esam S Al-Malki
- Department of Biology, College of Science in Zulfi, Majmaah University, Al-Majmaah 11952, Saudi Arabia
| | - Babu Snekaa
- Laboratory for Artificial Intelligence and Molecular Modelling, Department of Pharmacology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu 600077, India
| | - Sher Zaman Safi
- Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
| | - Devadasan Velmurugan
- Department of Biotechnology, College of Engineering & Technology, SRM Institute of Science & Technology, Kattankulathur, Chennai, Tamil Nadu 603203, India
| | - Chandrabose Selvaraj
- Laboratory for Artificial Intelligence and Molecular Modelling, Department of Pharmacology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu 600077, India; Laboratory for Artificial Intelligence and Molecular Modelling, Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha Nagar, Thandalam, Chennai, Tamil Nadu 602105, India.
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21
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Zagirova D, Pushkov S, Leung GHD, Liu BHM, Urban A, Sidorenko D, Kalashnikov A, Kozlova E, Naumov V, Pun FW, Ozerov IV, Aliper A, Zhavoronkov A. Biomedical generative pre-trained based transformer language model for age-related disease target discovery. Aging (Albany NY) 2023; 15:9293-9309. [PMID: 37742294 PMCID: PMC10564439 DOI: 10.18632/aging.205055] [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] [Received: 06/15/2023] [Accepted: 08/20/2023] [Indexed: 09/26/2023]
Abstract
Target discovery is crucial for the development of innovative therapeutics and diagnostics. However, current approaches often face limitations in efficiency, specificity, and scalability, necessitating the exploration of novel strategies for identifying and validating disease-relevant targets. Advances in natural language processing have provided new avenues for predicting potential therapeutic targets for various diseases. Here, we present a novel approach for predicting therapeutic targets using a large language model (LLM). We trained a domain-specific BioGPT model on a large corpus of biomedical literature consisting of grant text and developed a pipeline for generating target prediction. Our study demonstrates that pre-training of the LLM model with task-specific texts improves its performance. Applying the developed pipeline, we retrieved prospective aging and age-related disease targets and showed that these proteins are in correspondence with the database data. Moreover, we propose CCR5 and PTH as potential novel dual-purpose anti-aging and disease targets which were not previously identified as age-related but were highly ranked in our approach. Overall, our work highlights the high potential of transformer models in novel target prediction and provides a roadmap for future integration of AI approaches for addressing the intricate challenges presented in the biomedical field.
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Affiliation(s)
- Diana Zagirova
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Stefan Pushkov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Geoffrey Ho Duen Leung
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Bonnie Hei Man Liu
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Anatoly Urban
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Denis Sidorenko
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Aleksandr Kalashnikov
- Insilico Medicine AI Limited, Level 6, Unit 08, Block A, IRENA HQ Building, Masdar City, Abu Dhabi, UAE
| | - Ekaterina Kozlova
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Vladimir Naumov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Frank W. Pun
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Ivan V. Ozerov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Alex Aliper
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
- Insilico Medicine AI Limited, Level 6, Unit 08, Block A, IRENA HQ Building, Masdar City, Abu Dhabi, UAE
| | - Alex Zhavoronkov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
- Insilico Medicine AI Limited, Level 6, Unit 08, Block A, IRENA HQ Building, Masdar City, Abu Dhabi, UAE
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22
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Pun FW, Ozerov IV, Zhavoronkov A. AI-powered therapeutic target discovery. Trends Pharmacol Sci 2023; 44:561-572. [PMID: 37479540 DOI: 10.1016/j.tips.2023.06.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/23/2023]
Abstract
Disease modeling and target identification are the most crucial initial steps in drug discovery, and influence the probability of success at every step of drug development. Traditional target identification is a time-consuming process that takes years to decades and usually starts in an academic setting. Given its advantages of analyzing large datasets and intricate biological networks, artificial intelligence (AI) is playing a growing role in modern drug target identification. We review recent advances in target discovery, focusing on breakthroughs in AI-driven therapeutic target exploration. We also discuss the importance of striking a balance between novelty and confidence in target selection. An increasing number of AI-identified targets are being validated through experiments and several AI-derived drugs are entering clinical trials; we highlight current limitations and potential pathways for moving forward.
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Affiliation(s)
- Frank W Pun
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong
| | - Ivan V Ozerov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong
| | - Alex Zhavoronkov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong; Insilico Medicine MENA, 6F IRENA Building, Abu Dhabi, United Arab Emirates; Buck Institute for Research on Aging, Novato, CA, USA.
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23
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Berquez M, Chen Z, Festa BP, Krohn P, Keller SA, Parolo S, Korzinkin M, Gaponova A, Laczko E, Domenici E, Devuyst O, Luciani A. Lysosomal cystine export regulates mTORC1 signaling to guide kidney epithelial cell fate specialization. Nat Commun 2023; 14:3994. [PMID: 37452023 PMCID: PMC10349091 DOI: 10.1038/s41467-023-39261-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 06/06/2023] [Indexed: 07/18/2023] Open
Abstract
Differentiation is critical for cell fate decisions, but the signals involved remain unclear. The kidney proximal tubule (PT) cells reabsorb disulphide-rich proteins through endocytosis, generating cystine via lysosomal proteolysis. Here we report that defective cystine mobilization from lysosomes through cystinosin (CTNS), which is mutated in cystinosis, diverts PT cells towards growth and proliferation, disrupting their functions. Mechanistically, cystine storage stimulates Ragulator-Rag GTPase-dependent recruitment of mechanistic target of rapamycin complex 1 (mTORC1) and its constitutive activation. Re-introduction of CTNS restores nutrient-dependent regulation of mTORC1 in knockout cells, whereas cell-permeant analogues of L-cystine, accumulating within lysosomes, render wild-type cells resistant to nutrient withdrawal. Therapeutic mTORC1 inhibition corrects lysosome and differentiation downstream of cystine storage, and phenotypes in preclinical models of cystinosis. Thus, cystine serves as a lysosomal signal that tailors mTORC1 and metabolism to direct epithelial cell fate decisions. These results identify mechanisms and therapeutic targets for dysregulated homeostasis in cystinosis.
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Affiliation(s)
- Marine Berquez
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland
| | - Zhiyong Chen
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland
| | | | - Patrick Krohn
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland
| | | | - Silvia Parolo
- Fondazione The Microsoft Research University of Trento-Centre for Computational and Systems Biology (COSBI), 38068, Rovereto, Italy
| | - Mikhail Korzinkin
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Anna Gaponova
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Endre Laczko
- Functional Genomics Center Zurich, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Enrico Domenici
- Fondazione The Microsoft Research University of Trento-Centre for Computational and Systems Biology (COSBI), 38068, Rovereto, Italy
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Olivier Devuyst
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland.
- Institute for Rare Diseases, UCLouvain Medical School, 1200, Brussels, Belgium.
| | - Alessandro Luciani
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland.
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24
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Long E, Wan P, Chen Q, Lu Z, Choi J. From function to translation: Decoding genetic susceptibility to human diseases via artificial intelligence. CELL GENOMICS 2023; 3:100320. [PMID: 37388909 PMCID: PMC10300605 DOI: 10.1016/j.xgen.2023.100320] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
While genome-wide association studies (GWAS) have discovered thousands of disease-associated loci, molecular mechanisms for a considerable fraction of the loci remain to be explored. The logical next steps for post-GWAS are interpreting these genetic associations to understand disease etiology (GWAS functional studies) and translating this knowledge into clinical benefits for the patients (GWAS translational studies). Although various datasets and approaches using functional genomics have been developed to facilitate these studies, significant challenges remain due to data heterogeneity, multiplicity, and high dimensionality. To address these challenges, artificial intelligence (AI) technology has demonstrated considerable promise in decoding complex functional datasets and providing novel biological insights into GWAS findings. This perspective first describes the landmark progress driven by AI in interpreting and translating GWAS findings and then outlines specific challenges followed by actionable recommendations related to data availability, model optimization, and interpretation, as well as ethical concerns.
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Affiliation(s)
- Erping Long
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peixing Wan
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Qingyu Chen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Zhiyong Lu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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25
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Fatoki TH, Chukwuejim S, Udenigwe CC, Aluko RE. In Silico Exploration of Metabolically Active Peptides as Potential Therapeutic Agents against Amyotrophic Lateral Sclerosis. Int J Mol Sci 2023; 24:5828. [PMID: 36982902 PMCID: PMC10058213 DOI: 10.3390/ijms24065828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/11/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is regarded as a fatal neurodegenerative disease that is featured by progressive damage of the upper and lower motor neurons. To date, over 45 genes have been found to be connected with ALS pathology. The aim of this work was to computationally identify unique sets of protein hydrolysate peptides that could serve as therapeutic agents against ALS. Computational methods which include target prediction, protein-protein interaction, and peptide-protein molecular docking were used. The results showed that the network of critical ALS-associated genes consists of ATG16L2, SCFD1, VAC15, VEGFA, KEAP1, KIF5A, FIG4, TUBA4A, SIGMAR1, SETX, ANXA11, HNRNPL, NEK1, C9orf72, VCP, RPSA, ATP5B, and SOD1 together with predicted kinases such as AKT1, CDK4, DNAPK, MAPK14, and ERK2 in addition to transcription factors such as MYC, RELA, ZMIZ1, EGR1, TRIM28, and FOXA2. The identified molecular targets of the peptides that support multi-metabolic components in ALS pathogenesis include cyclooxygenase-2, angiotensin I-converting enzyme, dipeptidyl peptidase IV, X-linked inhibitor of apoptosis protein 3, and endothelin receptor ET-A. Overall, the results showed that AGL, APL, AVK, IIW, PVI, and VAY peptides are promising candidates for further study. Future work would be needed to validate the therapeutic properties of these hydrolysate peptides by in vitro and in vivo approaches.
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Affiliation(s)
- Toluwase Hezekiah Fatoki
- Department of Biochemistry, Federal University Oye-Ekiti, PMB 373, Oye 371104, Nigeria; (T.H.F.); (S.C.)
| | - Stanley Chukwuejim
- Department of Biochemistry, Federal University Oye-Ekiti, PMB 373, Oye 371104, Nigeria; (T.H.F.); (S.C.)
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Chibuike C. Udenigwe
- Faculty of Health Sciences, School of Nutrition Sciences, University of Ottawa, Ottawa, ON K1H 8M5, Canada;
- Department of Chemistry and Biomolecular Sciences, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Rotimi E. Aluko
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Richardson Centre for Food Technology and Research, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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26
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Ren F, Ding X, Zheng M, Korzinkin M, Cai X, Zhu W, Mantsyzov A, Aliper A, Aladinskiy V, Cao Z, Kong S, Long X, Man Liu BH, Liu Y, Naumov V, Shneyderman A, Ozerov IV, Wang J, Pun FW, Polykovskiy DA, Sun C, Levitt M, Aspuru-Guzik A, Zhavoronkov A. AlphaFold accelerates artificial intelligence powered drug discovery: efficient discovery of a novel CDK20 small molecule inhibitor. Chem Sci 2023; 14:1443-1452. [PMID: 36794205 PMCID: PMC9906638 DOI: 10.1039/d2sc05709c] [Citation(s) in RCA: 85] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
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.
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Affiliation(s)
- Feng Ren
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
| | - Xiao Ding
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
| | - Min Zheng
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
| | - Mikhail Korzinkin
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Xin Cai
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
| | - Wei Zhu
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
| | - Alexey Mantsyzov
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Alex Aliper
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Vladimir Aladinskiy
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Zhongying Cao
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
| | - Shanshan Kong
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
| | - Xi Long
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Bonnie Hei Man Liu
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Yingtao Liu
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
| | - Vladimir Naumov
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Anastasia Shneyderman
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Ivan V Ozerov
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Ju Wang
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
| | - Frank W Pun
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Daniil A Polykovskiy
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Chong Sun
- Department of Chemistry, Department of Computer Science, University of Toronto, Vector Institute for Artificial Intelligence, Canadian Institute for Advanced Research Toronto Ontario Canada
| | - Michael Levitt
- Department of Structural Biology, Stanford University Palo Alto CA USA
| | - Alán Aspuru-Guzik
- Department of Chemistry, Department of Computer Science, University of Toronto, Vector Institute for Artificial Intelligence, Canadian Institute for Advanced Research Toronto Ontario Canada
| | - Alex Zhavoronkov
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
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27
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Huber RG, Pandey S, Chhangani D, Rincon-Limas DE, Staff NP, Yeo CJJ. Identification of potential pathways and biomarkers linked to progression in ALS. Ann Clin Transl Neurol 2023; 10:150-165. [PMID: 36533811 PMCID: PMC9930436 DOI: 10.1002/acn3.51697] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/24/2022] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE To identify potential diagnostic and prognostic biomarkers for clinical management and clinical trials in amyotrophic lateral sclerosis. METHODS We analysed proteomics data of ALS patient-induced pluripotent stem cell-derived motor neurons available through the AnswerALS consortium. After stratifying patients using clinical ALSFRS-R and ALS-CBS scales, we identified differentially expressed proteins indicative of ALS disease severity and progression rate as candidate ALS-related and prognostic biomarkers. Pathway analysis for identified proteins was performed using STITCH. Protein sets were correlated with the effects of drugs using the Connectivity Map tool to identify compounds likely to affect similar pathways. RNAi screening was performed in a Drosophila TDP-43 ALS model to validate pathological relevance. A statistical classification machine learning model was constructed using ridge regression that uses proteomics data to differentiate ALS patients from controls. RESULTS We identified 76, 21, 71 and 1 candidate ALS-related biomarkers and 22, 41, 27 and 64 candidate prognostic biomarkers from patients stratified by ALSFRS-R baseline, ALSFRS-R progression slope, ALS-CBS baseline and ALS-CBS progression slope, respectively. Nineteen proteins enhanced or suppressed pathogenic eye phenotypes in the ALS fly model. Nutraceuticals, dopamine pathway modulators, statins, anti-inflammatories and antimicrobials were predicted starting points for drug repurposing using the connectivity map tool. Ten diagnostic biomarker proteins were predicted by machine learning to identify ALS patients with high accuracy and sensitivity. INTERPRETATION This study showcases the powerful approach of iPSC-motor neuron proteomics combined with machine learning and biological confirmation in the prediction of novel mechanisms and diagnostic and predictive biomarkers in ALS.
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Affiliation(s)
- Roland G Huber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Matrix #07-01, 30 Biopolis Street, Singapore, 138671, Singapore
| | - Swapnil Pandey
- Department of Neurology, McKnight Brain Institute, and Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, Florida, 32611, USA
| | - Deepak Chhangani
- Department of Neurology, McKnight Brain Institute, and Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, Florida, 32611, USA
| | - Diego E Rincon-Limas
- Department of Neurology, McKnight Brain Institute, and Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, Florida, 32611, USA
| | - Nathan P Staff
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, 55905, USA
| | - Crystal Jing Jing Yeo
- Agency for Science, Technology and Research (A*STAR), IMCB, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611, USA
- Lee Kong Chian School of Medicine, Imperial College London and NTU Singapore, Singapore, 308232, Singapore
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB243FX, Scotland, UK
- National Neuroscience Institute, TTSH Campus, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore
- Duke NUS Medical School, 8 College Road, Singapore, 169857, Singapore
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28
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Founta K, Dafou D, Kanata E, Sklaviadis T, Zanos TP, Gounaris A, Xanthopoulos K. Gene targeting in amyotrophic lateral sclerosis using causality-based feature selection and machine learning. Mol Med 2023; 29:12. [PMID: 36694130 PMCID: PMC9872307 DOI: 10.1186/s10020-023-00603-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a rare progressive neurodegenerative disease that affects upper and lower motor neurons. As the molecular basis of the disease is still elusive, the development of high-throughput sequencing technologies, combined with data mining techniques and machine learning methods, could provide remarkable results in identifying pathogenetic mechanisms. High dimensionality is a major problem when applying machine learning techniques in biomedical data analysis, since a huge number of features is available for a limited number of samples. The aim of this study was to develop a methodology for training interpretable machine learning models in the classification of ALS and ALS-subtypes samples, using gene expression datasets. METHODS We performed dimensionality reduction in gene expression data using a semi-automated preprocessing systematic gene selection procedure using Statistically Equivalent Signature (SES), a causality-based feature selection algorithm, followed by Boosted Regression Trees (XGBoost) and Random Forest to train the machine learning classifiers. The SHapley Additive exPlanations (SHAP values) were used for interpretation of the machine learning classifiers. The methodology was developed and tested using two distinct publicly available ALS RNA-seq datasets. We evaluated the performance of SES as a dimensionality reduction method against: (a) Least Absolute Shrinkage and Selection Operator (LASSO), and (b) Local Outlier Factor (LOF). RESULTS The proposed methodology achieved 85.18% accuracy for the classification of cerebellum or frontal cortex samples as C9orf72-related familial ALS, sporadic ALS or healthy samples. Importantly, the genes identified as the most determinative have also been reported as disease-associated in ALS literature. When tested in the evaluation dataset, the methodology achieved 88.89% accuracy for the classification of sporadic ALS motor neuron samples. When LASSO was used as feature selection method instead of SES, the accuracy of the machine learning classifiers ranged from 74.07 to 96.30%, depending on tissue assessed, while LOF underperformed significantly (77.78% accuracy for the classification of pooled cerebellum and frontal cortex samples). CONCLUSIONS Using SES, we addressed the challenge of high dimensionality in gene expression data analysis, and we trained accurate machine learning ALS classifiers, specific for the gene expression patterns of different disease subtypes and tissue samples, while identifying disease-associated genes.
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Affiliation(s)
- Kyriaki Founta
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY, 11549, USA
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, 11030, USA
- Laboratory of Pharmacology, School of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Dimitra Dafou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Eirini Kanata
- Laboratory of Pharmacology, School of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Theodoros Sklaviadis
- Laboratory of Pharmacology, School of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Theodoros P Zanos
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY, 11549, USA
- Feinstein Institutes for Medical Research, Institute of Health Systems Science, Northwell Health, Manhasset, NY, 11030, USA
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, 11030, USA
| | - Anastasios Gounaris
- School of Informatics, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Konstantinos Xanthopoulos
- Laboratory of Pharmacology, School of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, 57001, Thermi, Greece.
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Chisholm O, Critchley H. Future directions in regulatory affairs. Front Med (Lausanne) 2023; 9:1082384. [PMID: 36698838 PMCID: PMC9868628 DOI: 10.3389/fmed.2022.1082384] [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: 10/28/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
The field of regulatory affairs deals with the regulatory requirements for marketing authorization of therapeutic products. This field is facing a myriad of forces impacting all aspects of the development, regulation and value proposition of new therapeutic products. Changes in global megatrends, such as geopolitical shifts and the rise of the green economy, have emphasized the importance of manufacturing and supply chain security, and reducing the environmental impacts of product development. Rapid changes due to advances in science, digital disruption, a renewed focus on the centrality of the patient in all stages of therapeutic product development and greater collaboration between national regulatory authorities have been accelerated by the COVID-19 pandemic. This article will discuss the various trends that are impacting the development of new therapies for alleviating disease and how these trends therefore impact on the role of the regulatory affairs professional. We discuss some of the challenges and provide insights for the regulatory professional to remain at the forefront of these trends and prepare for their impacts on their work.
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Affiliation(s)
- Orin Chisholm
- Faculty of Medicine and Health, Sydney Pharmacy School, The University of Sydney, Sydney, NSW, Australia
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30
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Mkrtchyan GV, Veviorskiy A, Izumchenko E, Shneyderman A, Pun FW, Ozerov IV, Aliper A, Zhavoronkov A, Scheibye-Knudsen M. High-confidence cancer patient stratification through multiomics investigation of DNA repair disorders. Cell Death Dis 2022; 13:999. [PMID: 36435816 PMCID: PMC9701218 DOI: 10.1038/s41419-022-05437-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/28/2022]
Abstract
Multiple cancer types have limited targeted therapeutic options, in part due to incomplete understanding of the molecular processes underlying tumorigenesis and significant intra- and inter-tumor heterogeneity. Identification of novel molecular biomarkers stratifying cancer patients with different survival outcomes may provide new opportunities for target discovery and subsequent development of tailored therapies. Here, we applied the artificial intelligence-driven PandaOmics platform ( https://pandaomics.com/ ) to explore gene expression changes in rare DNA repair-deficient disorders and identify novel cancer targets. Our analysis revealed that CEP135, a scaffolding protein associated with early centriole biogenesis, is commonly downregulated in DNA repair diseases with high cancer predisposition. Further screening of survival data in 33 cancers available at TCGA database identified sarcoma as a cancer type where lower survival was significantly associated with high CEP135 expression. Stratification of cancer patients based on CEP135 expression enabled us to examine therapeutic targets that could be used for the improvement of existing therapies against sarcoma. The latter was based on application of the PandaOmics target-ID algorithm coupled with in vitro studies that revealed polo-like kinase 1 (PLK1) as a potential therapeutic candidate in sarcoma patients with high CEP135 levels and poor survival. While further target validation is required, this study demonstrated the potential of in silico-based studies for a rapid biomarker discovery and target characterization.
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Affiliation(s)
- Garik V Mkrtchyan
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Evgeny Izumchenko
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | | | | | | | | | | | - Morten Scheibye-Knudsen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
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