1
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Puszkarska AM, Taddese B, Revell J, Davies G, Field J, Hornigold DC, Buchanan A, Vaughan TJ, Colwell LJ. Machine learning designs new GCGR/GLP-1R dual agonists with enhanced biological potency. Nat Chem 2024; 16:1436-1444. [PMID: 38755312 DOI: 10.1038/s41557-024-01532-x] [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: 12/26/2021] [Accepted: 04/08/2024] [Indexed: 05/18/2024]
Abstract
Several peptide dual agonists of the human glucagon receptor (GCGR) and the glucagon-like peptide-1 receptor (GLP-1R) are in development for the treatment of type 2 diabetes, obesity and their associated complications. Candidates must have high potency at both receptors, but it is unclear whether the limited experimental data available can be used to train models that accurately predict the activity at both receptors of new peptide variants. Here we use peptide sequence data labelled with in vitro potency at human GCGR and GLP-1R to train several models, including a deep multi-task neural-network model using multiple loss optimization. Model-guided sequence optimization was used to design three groups of peptide variants, with distinct ranges of predicted dual activity. We found that three of the model-designed sequences are potent dual agonists with superior biological activity. With our designs we were able to achieve up to sevenfold potency improvement at both receptors simultaneously compared to the best dual-agonist in the training set.
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Affiliation(s)
- Anna M Puszkarska
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Biologics Engineering, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Bruck Taddese
- Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
- Biologics Center (NBC) at the Novartis Institute for BioMedical Research (NIBR), Basel, Switzerland
| | | | - Graeme Davies
- Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Joss Field
- Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - David C Hornigold
- Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Andrew Buchanan
- Biologics Engineering, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Tristan J Vaughan
- Biologics Engineering, Oncology R&D, AstraZeneca, Cambridge, UK
- Immunocore Ltd., Abingdon, UK
| | - Lucy J Colwell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
- Google DeepMind, Cambridge, MA, USA.
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2
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Guo Y, Gao Y, Song J. MolCFL: A personalized and privacy-preserving drug discovery framework based on generative clustered federated learning. J Biomed Inform 2024; 157:104712. [PMID: 39182631 DOI: 10.1016/j.jbi.2024.104712] [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: 05/05/2024] [Revised: 08/16/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
In today's era of rapid development of large models, the traditional drug development process is undergoing a profound transformation. The vast demand for data and consumption of computational resources are making independent drug discovery increasingly difficult. By integrating federated learning technology into the drug discovery field, we have found a solution that both protects privacy and shares computational power. However, the differences in data held by various pharmaceutical institutions and the diversity in drug design objectives have exacerbated the issue of data heterogeneity, making traditional federated learning consensus models unable to meet the personalized needs of all parties. In this study, we introduce and evaluate an innovative drug discovery framework, MolCFL, which utilizes a multi-layer perceptron (MLP) as the generator and a graph convolutional network (GCN) as the discriminator in a generative adversarial network (GAN). By learning the graph structure of molecules, it generates new molecules in a highly personalized manner and then optimizes the learning process by clustering federated learning, grouping compound data with high similarity. MolCFL not only enhances the model's ability to protect privacy but also significantly improves the efficiency and personalization of molecular design. MolCFL exhibits superior performance when handling non-independently and identically distributed data compared to traditional models. Experimental results show that the framework demonstrates outstanding performance on two benchmark datasets, with the generated new molecules achieving over 90% in Uniqueness and close to 100% in Novelty. MolCFL not only improves the quality and efficiency of drug molecule design but also, through its highly customized clustered federated learning environment, promotes collaboration and specialization in the drug discovery process while ensuring data privacy. These features make MolCFL a powerful tool suitable for addressing the various challenges faced in the modern drug research and development field.
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Affiliation(s)
- Yan Guo
- Inner Mongolia University, College of Computer Science, Hohhot, 010000, China
| | - Yongqiang Gao
- Inner Mongolia University, College of Computer Science, Hohhot, 010000, China.
| | - Jiawei Song
- Inner Mongolia University, College of Computer Science, Hohhot, 010000, China
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3
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Kuldeep J, Chaturvedi N, Gupta D. Novel molecular inhibitor design for Plasmodium falciparum Lactate dehydrogenase enzyme using machine learning generated library of diverse compounds. Mol Divers 2024:10.1007/s11030-024-10960-3. [PMID: 39162960 DOI: 10.1007/s11030-024-10960-3] [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: 04/10/2024] [Accepted: 08/06/2024] [Indexed: 08/21/2024]
Abstract
Generative machine learning models offer a novel strategy for chemogenomics and de novo drug design, allowing researchers to streamline their exploration of the chemical space and concentrate on specific regions of interest. In cases with limited inhibitor data available for the target of interest, de novo drug design plays a crucial role. In this study, we utilized a package called 'mollib,' trained on ChEMBL data containing approximately 365,000 bioactive molecules. By leveraging transfer learning techniques with this package, we generated a series of compounds, starting from five initial compounds, which are potential Plasmodium falciparum (Pf) Lactate dehydrogenase inhibitors. The resulting compounds exhibit structural diversity and hold promise as potential novel Pf Lactate dehydrogenase inhibitors.
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Affiliation(s)
- Jitendra Kuldeep
- Translational Bioinformatics Group, International Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Neeraj Chaturvedi
- Translational Bioinformatics Group, International Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India.
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4
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Özçelik R, de Ruiter S, Criscuolo E, Grisoni F. Chemical language modeling with structured state space sequence models. Nat Commun 2024; 15:6176. [PMID: 39039051 PMCID: PMC11263548 DOI: 10.1038/s41467-024-50469-9] [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: 09/22/2023] [Accepted: 07/05/2024] [Indexed: 07/24/2024] Open
Abstract
Generative deep learning is reshaping drug design. Chemical language models (CLMs) - which generate molecules in the form of molecular strings - bear particular promise for this endeavor. Here, we introduce a recent deep learning architecture, termed Structured State Space Sequence (S4) model, into de novo drug design. In addition to its unprecedented performance in various fields, S4 has shown remarkable capabilities to learn the global properties of sequences. This aspect is intriguing in chemical language modeling, where complex molecular properties like bioactivity can 'emerge' from separated portions in the molecular string. This observation gives rise to the following question: Can S4 advance chemical language modeling for de novo design? To provide an answer, we systematically benchmark S4 with state-of-the-art CLMs on an array of drug discovery tasks, such as the identification of bioactive compounds, and the design of drug-like molecules and natural products. S4 shows a superior capacity to learn complex molecular properties, while at the same time exploring diverse scaffolds. Finally, when applied prospectively to kinase inhibition, S4 designs eight of out ten molecules that are predicted as highly active by molecular dynamics simulations. Taken together, these findings advocate for the introduction of S4 into chemical language modeling - uncovering its untapped potential in the molecular sciences.
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Affiliation(s)
- Rıza Özçelik
- Institute for Complex Molecular Systems and Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands
| | - Sarah de Ruiter
- Institute for Complex Molecular Systems and Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Emanuele Criscuolo
- Institute for Complex Molecular Systems and Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Francesca Grisoni
- Institute for Complex Molecular Systems and Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands.
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5
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Choudhary R, Mahadevan R. FOCUS on NOD2: Advancing IBD Drug Discovery with a User-Informed Machine Learning Framework. ACS Med Chem Lett 2024; 15:1057-1070. [PMID: 39015268 PMCID: PMC11247655 DOI: 10.1021/acsmedchemlett.4c00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/17/2024] [Accepted: 06/03/2024] [Indexed: 07/18/2024] Open
Abstract
In this study, we introduce the Framework for Optimized Customizable User-Informed Synthesis (FOCUS), a generative machine learning model tailored for drug discovery. FOCUS integrates domain expertise and uses Proximal Policy Optimization (PPO) to guide Monte Carlo Tree Search (MCTS) to efficiently explore chemical space. It generates SMILES representations of potential drug candidates, optimizing for druggability and binding efficacy to NOD2, PEP, and MCT1 receptors. The model is highly interpretive, allowing for user-feedback and expert-driven adjustments based on detailed cycle reports. Employing tools like SHAP and LIME, FOCUS provides a transparent analysis of decision-making processes, emphasizing features such as docking scores and interaction fingerprints. Comparative studies with Muramyl Dipeptide (MDP) demonstrate improved interaction profiles. FOCUS merges advanced machine learning with expert insight, accelerating the drug discovery pipeline.
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Affiliation(s)
- Ruhi Choudhary
- Department of Chemical Engineering
and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering
and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
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6
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Qin T, Wang Y, Kong M, Zhong H, Wu T, Xi Z, Qian Z, Li K, Cai Y, Wu J, Li W. Identification of potential PIM-2 inhibitors via ligand-based generative models, molecular docking and molecular dynamics simulations. Mol Divers 2024:10.1007/s11030-024-10916-7. [PMID: 38954072 DOI: 10.1007/s11030-024-10916-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/11/2024] [Indexed: 07/04/2024]
Abstract
Proviral Integrations of Moloney-2 (PIM-2) kinase is a promising target for various cancers and other diseases, and its inhibitors hold potential for treating related diseases. However, there is currently no clinically available PIM-2 inhibitor. In this study, we constructed a generative model for de novo PIM-2 inhibitor design based on artificial intelligence, performed molecular docking and molecular dynamics (MD) simulations to develop an efficient PIM-2 inhibitor generative model and discover potential PIM-2 inhibitors. First, we designed a generative model based on a Bi-directional Long Short-Term Memory (BiLSTM) framework combined with a transfer learning strategy and generated a new PIM-2 small molecule library using existing active drug databases. The generated compound library was then virtually screened by molecular docking and scaffold similarity comparison, identifying 10 initial hit compounds with better performance. Next, using the inhibitor in the crystal structure as a positive control, we performed two rounds of MD simulations, with lengths of 100 ns and 500 ns, respectively, to study the dynamic stability of the protein-ligand systems of the 10 compounds with PIM-2. Analyzed the interactions with key hinge region residues, binding free energies, and changes in the ATP pocket size. The generative model demonstrates good molecular generation capability and can generate efficient novel molecules with similar physicochemical properties as active PIM-2 drugs. Among the 10 initially selected hit compounds, 5 compounds C3 (- 29.69 kcal/mol), C4 (- 33.31 kcal/mol), C5 (- 28.59 kcal/mol), C8 (- 34.68 kcal/mol), and C9 (- 25.88 kcal/mol) have higher binding energies with PIM-2 than the positive drug 3YR (- 26.18 kcal/mol). The MD simulation results are consistent with the docking analysis, these compounds have lower and more stable RMSD values for the complex systems with the reported positive drug 3YR and PIM-2 complex system. They can form long-term stable interactions with active site and the hinge region of PIM-2, which suggests these compounds are likely to have potent inhibitory effects on PIM-2. This study provides an efficient generative model for PIM-2 inhibitor research and discovers 5 potential novel PIM-2 inhibitors.
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Affiliation(s)
- Tianli Qin
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Yijian Wang
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Miaomiao Kong
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Hongliang Zhong
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, 325000, Zhejiang, China
| | - Tao Wu
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Zixuan Xi
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Zhenyong Qian
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, 325000, Zhejiang, China
| | - Ke Li
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, 325000, Zhejiang, China
| | - Yuepiao Cai
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325000, China.
| | - Jianzhang Wu
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China.
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, 325000, Zhejiang, China.
| | - Wulan Li
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
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7
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Guo J, Schwaller P. Augmented Memory: Sample-Efficient Generative Molecular Design with Reinforcement Learning. JACS AU 2024; 4:2160-2172. [PMID: 38938817 PMCID: PMC11200228 DOI: 10.1021/jacsau.4c00066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 06/29/2024]
Abstract
Sample efficiency is a fundamental challenge in de novo molecular design. Ideally, molecular generative models should learn to satisfy a desired objective under minimal calls to oracles (computational property predictors). This problem becomes more apparent when using oracles that can provide increased predictive accuracy but impose significant computational cost. Consequently, designing molecules that are optimized for such oracles cannot be achieved under a practical computational budget. Molecular generative models based on simplified molecular-input line-entry system (SMILES) have shown remarkable sample efficiency when coupled with reinforcement learning, as demonstrated in the practical molecular optimization (PMO) benchmark. Here, we first show that experience replay drastically improves the performance of multiple previously proposed algorithms. Next, we propose a novel algorithm called Augmented Memory that combines data augmentation with experience replay. We show that scores obtained from oracle calls can be reused to update the model multiple times. We compare Augmented Memory to previously proposed algorithms and show significantly enhanced sample efficiency in an exploitation task, a drug discovery case study requiring both exploration and exploitation, and a materials design case study optimizing explicitly for quantum-mechanical properties. Our method achieves a new state-of-the-art in sample-efficient de novo molecular design, outperforming all of the previously reported methods. The code is available at https://github.com/schwallergroup/augmented_memory.
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Affiliation(s)
- Jeff Guo
- Laboratory
of Artificial Chemical Intelligence (LIAC), Institut des Sciences
et Ingénierie Chimiques, Ecole Polytechnique
Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Philippe Schwaller
- Laboratory
of Artificial Chemical Intelligence (LIAC), Institut des Sciences
et Ingénierie Chimiques, Ecole Polytechnique
Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
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8
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Gangwal A, Lavecchia A. Unleashing the power of generative AI in drug discovery. Drug Discov Today 2024; 29:103992. [PMID: 38663579 DOI: 10.1016/j.drudis.2024.103992] [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: 02/09/2024] [Revised: 03/22/2024] [Accepted: 04/18/2024] [Indexed: 05/04/2024]
Abstract
Artificial intelligence (AI) is revolutionizing drug discovery by enhancing precision, reducing timelines and costs, and enabling AI-driven computer-aided drug design. This review focuses on recent advancements in deep generative models (DGMs) for de novo drug design, exploring diverse algorithms and their profound impact. It critically analyses the challenges that are intricately interwoven into these technologies, proposing strategies to unlock their full potential. It features case studies of both successes and failures in advancing drugs to clinical trials with AI assistance. Last, it outlines a forward-looking plan for optimizing DGMs in de novo drug design, thereby fostering faster and more cost-effective drug development.
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Affiliation(s)
- Amit Gangwal
- Department of Natural Product Chemistry, Shri Vile Parle Kelavani Mandal's Institute of Pharmacy, Dhule 424001, Maharashtra, India
| | - Antonio Lavecchia
- "Drug Discovery" Laboratory, Department of Pharmacy, University of Naples Federico II, I-80131 Naples, Italy.
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9
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van Tilborg D, Brinkmann H, Criscuolo E, Rossen L, Özçelik R, Grisoni F. Deep learning for low-data drug discovery: Hurdles and opportunities. Curr Opin Struct Biol 2024; 86:102818. [PMID: 38669740 DOI: 10.1016/j.sbi.2024.102818] [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: 01/29/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024]
Abstract
Deep learning is becoming increasingly relevant in drug discovery, from de novo design to protein structure prediction and synthesis planning. However, it is often challenged by the small data regimes typical of certain drug discovery tasks. In such scenarios, deep learning approaches-which are notoriously 'data-hungry'-might fail to live up to their promise. Developing novel approaches to leverage the power of deep learning in low-data scenarios is sparking great attention, and future developments are expected to propel the field further. This mini-review provides an overview of recent low-data-learning approaches in drug discovery, analyzing their hurdles and advantages. Finally, we venture to provide a forecast of future research directions in low-data learning for drug discovery.
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Affiliation(s)
- Derek van Tilborg
- Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, the Netherlands; Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Princetonlaan 6, 3584 CB, Utrecht, the Netherlands. https://twitter.com/DerekvTilborg
| | - Helena Brinkmann
- Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, the Netherlands. https://twitter.com/hlnbrkmnn
| | - Emanuele Criscuolo
- Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, the Netherlands. https://twitter.com/emanuelecriscu9
| | - Luke Rossen
- Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, the Netherlands. https://twitter.com/molecular_ml
| | - Rıza Özçelik
- Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, the Netherlands; Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Princetonlaan 6, 3584 CB, Utrecht, the Netherlands. https://twitter.com/Rza_ozcelik
| | - Francesca Grisoni
- Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, the Netherlands; Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Princetonlaan 6, 3584 CB, Utrecht, the Netherlands.
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10
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Lim H. Development of scoring-assisted generative exploration (SAGE) and its application to dual inhibitor design for acetylcholinesterase and monoamine oxidase B. J Cheminform 2024; 16:59. [PMID: 38790018 PMCID: PMC11127438 DOI: 10.1186/s13321-024-00845-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
De novo molecular design is the process of searching chemical space for drug-like molecules with desired properties, and deep learning has been recognized as a promising solution. In this study, I developed an effective computational method called Scoring-Assisted Generative Exploration (SAGE) to enhance chemical diversity and property optimization through virtual synthesis simulation, the generation of bridged bicyclic rings, and multiple scoring models for drug-likeness. In six protein targets, SAGE generated molecules with high scores within reasonable numbers of steps by optimizing target specificity without a constraint and even with multiple constraints such as synthetic accessibility, solubility, and metabolic stability. Furthermore, I suggested a top-ranked molecule with SAGE as dual inhibitors of acetylcholinesterase and monoamine oxidase B through multiple desired property optimization. Therefore, SAGE can generate molecules with desired properties by optimizing multiple properties simultaneously, indicating the importance of de novo design strategies in the future of drug discovery and development. SCIENTIFIC CONTRIBUTION: The scientific contribution of this study lies in the development of the Scoring-Assisted Generative Exploration (SAGE) method, a novel computational approach that significantly enhances de novo molecular design. SAGE uniquely integrates virtual synthesis simulation, the generation of complex bridged bicyclic rings, and multiple scoring models to optimize drug-like properties comprehensively. By efficiently generating molecules that meet a broad spectrum of pharmacological criteria-including target specificity, synthetic accessibility, solubility, and metabolic stability-within a reasonable number of steps, SAGE represents a substantial advancement over traditional methods. Additionally, the application of SAGE to discover dual inhibitors for acetylcholinesterase and monoamine oxidase B not only demonstrates its potential to streamline and enhance the drug development process but also highlights its capacity to create more effective and precisely targeted therapies. This study emphasizes the critical and evolving role of de novo design strategies in reshaping the future of drug discovery and development, providing promising avenues for innovative therapeutic discoveries.
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Affiliation(s)
- Hocheol Lim
- Bioinformatics and Molecular Design Research Center (BMDRC), Incheon, Republic of Korea.
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11
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Atz K, Cotos L, Isert C, Håkansson M, Focht D, Hilleke M, Nippa DF, Iff M, Ledergerber J, Schiebroek CCG, Romeo V, Hiss JA, Merk D, Schneider P, Kuhn B, Grether U, Schneider G. Prospective de novo drug design with deep interactome learning. Nat Commun 2024; 15:3408. [PMID: 38649351 PMCID: PMC11035696 DOI: 10.1038/s41467-024-47613-w] [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: 09/13/2023] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
De novo drug design aims to generate molecules from scratch that possess specific chemical and pharmacological properties. We present a computational approach utilizing interactome-based deep learning for ligand- and structure-based generation of drug-like molecules. This method capitalizes on the unique strengths of both graph neural networks and chemical language models, offering an alternative to the need for application-specific reinforcement, transfer, or few-shot learning. It enables the "zero-shot" construction of compound libraries tailored to possess specific bioactivity, synthesizability, and structural novelty. In order to proactively evaluate the deep interactome learning framework for protein structure-based drug design, potential new ligands targeting the binding site of the human peroxisome proliferator-activated receptor (PPAR) subtype gamma are generated. The top-ranking designs are chemically synthesized and computationally, biophysically, and biochemically characterized. Potent PPAR partial agonists are identified, demonstrating favorable activity and the desired selectivity profiles for both nuclear receptors and off-target interactions. Crystal structure determination of the ligand-receptor complex confirms the anticipated binding mode. This successful outcome positively advocates interactome-based de novo design for application in bioorganic and medicinal chemistry, enabling the creation of innovative bioactive molecules.
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Affiliation(s)
- Kenneth Atz
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Leandro Cotos
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Clemens Isert
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Maria Håkansson
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Dorota Focht
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Mattis Hilleke
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - David F Nippa
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070, Basel, Switzerland
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstrasse 5, 81377, Munich, Germany
| | - Michael Iff
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Jann Ledergerber
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Carl C G Schiebroek
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Valentina Romeo
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070, Basel, Switzerland
| | - Jan A Hiss
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Daniel Merk
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstrasse 5, 81377, Munich, Germany
| | - Petra Schneider
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Bernd Kuhn
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070, Basel, Switzerland
| | - Uwe Grether
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070, Basel, Switzerland
| | - Gisbert Schneider
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland.
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12
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Grant-Jacob JA. Evolution of laughter from play. Commun Integr Biol 2024; 17:2338073. [PMID: 38601922 PMCID: PMC11005796 DOI: 10.1080/19420889.2024.2338073] [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: 01/29/2024] [Accepted: 03/28/2024] [Indexed: 04/12/2024] Open
Abstract
In this hypothesis, I discuss how laughter from physical play could have evolved to being induced via visual or even verbal stimuli, and serves as a signal to highlight incongruity that could potentially pose a threat to survival. I suggest how laughter's induction could have negated the need for physical contact in play, evolving from its use in tickling, to tickle-misses, and to taunting, and I discuss how the application of deep learning neural networks trained on images of spectra of a variety of laughter types from a variety of individuals or even species, could be used to determine such evolutionary pathways via the use of latent space exploration.
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Affiliation(s)
- James A. Grant-Jacob
- Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK
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13
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Pang C, Qiao J, Zeng X, Zou Q, Wei L. Deep Generative Models in De Novo Drug Molecule Generation. J Chem Inf Model 2024; 64:2174-2194. [PMID: 37934070 DOI: 10.1021/acs.jcim.3c01496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
The discovery of new drugs has important implications for human health. Traditional methods for drug discovery rely on experiments to optimize the structure of lead molecules, which are time-consuming and high-cost. Recently, artificial intelligence has exhibited promising and efficient performance for drug-like molecule generation. In particular, deep generative models achieve great success in de novo generation of drug-like molecules with desired properties, showing massive potential for novel drug discovery. In this study, we review the recent progress of molecule generation using deep generative models, mainly focusing on molecule representations, public databases, data processing tools, and advanced artificial intelligence based molecule generation frameworks. In particular, we present a comprehensive comparison of state-of-the-art deep generative models for molecule generation and a summary of commonly used molecular design strategies. We identify research gaps and challenges of molecule generation such as the need for better databases, missing 3D information in molecular representation, and the lack of high-precision evaluation metrics. We suggest future directions for molecular generation and drug discovery.
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Affiliation(s)
- Chao Pang
- School of Software, Shandong University, Jinan 250100, China
- Joint SDU-NTU Centre for Artificial Intelligence Research (C-FAIR), Shandong University, Jinan 250100, China
| | - Jianbo Qiao
- School of Software, Shandong University, Jinan 250100, China
- Joint SDU-NTU Centre for Artificial Intelligence Research (C-FAIR), Shandong University, Jinan 250100, China
| | - Xiangxiang Zeng
- College of Information Science and Engineering, Hunan University, Changsha 410082, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Leyi Wei
- School of Software, Shandong University, Jinan 250100, China
- Joint SDU-NTU Centre for Artificial Intelligence Research (C-FAIR), Shandong University, Jinan 250100, China
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14
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Li H, Shee Y, Allen B, Maschietto F, Morgunov A, Batista V. Kernel-elastic autoencoder for molecular design. PNAS NEXUS 2024; 3:pgae168. [PMID: 38689710 PMCID: PMC11059255 DOI: 10.1093/pnasnexus/pgae168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/04/2024] [Indexed: 05/02/2024]
Abstract
We introduce the kernel-elastic autoencoder (KAE), a self-supervised generative model based on the transformer architecture with enhanced performance for molecular design. KAE employs two innovative loss functions: modified maximum mean discrepancy (m-MMD) and weighted reconstruction (L WCEL ). The m-MMD loss has significantly improved the generative performance of KAE when compared to using the traditional Kullback-Leibler loss of VAE, or standard maximum mean discrepancy. Including the weighted reconstruction loss L WCEL , KAE achieves valid generation and accurate reconstruction at the same time, allowing for generative behavior that is intermediate between VAE and autoencoder not available in existing generative approaches. Further advancements in KAE include its integration with conditional generation, setting a new state-of-the-art benchmark in constrained optimizations. Moreover, KAE has demonstrated its capability to generate molecules with favorable binding affinities in docking applications, as evidenced by AutoDock Vina and Glide scores, outperforming all existing candidates from the training dataset. Beyond molecular design, KAE holds promise to solve problems by generation across a broad spectrum of applications.
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Affiliation(s)
- Haote Li
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Yu Shee
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Brandon Allen
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | | | - Anton Morgunov
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Victor Batista
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
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15
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Wang M, Wu Z, Wang J, Weng G, Kang Y, Pan P, Li D, Deng Y, Yao X, Bing Z, Hsieh CY, Hou T. Genetic Algorithm-Based Receptor Ligand: A Genetic Algorithm-Guided Generative Model to Boost the Novelty and Drug-Likeness of Molecules in a Sampling Chemical Space. J Chem Inf Model 2024; 64:1213-1228. [PMID: 38302422 DOI: 10.1021/acs.jcim.3c01964] [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: 02/03/2024]
Abstract
Deep learning-based de novo molecular design has recently gained significant attention. While numerous DL-based generative models have been successfully developed for designing novel compounds, the majority of the generated molecules lack sufficiently novel scaffolds or high drug-like profiles. The aforementioned issues may not be fully captured by commonly used metrics for the assessment of molecular generative models, such as novelty, diversity, and quantitative estimation of the drug-likeness score. To address these limitations, we proposed a genetic algorithm-guided generative model called GARel (genetic algorithm-based receptor-ligand interaction generator), a novel framework for training a DL-based generative model to produce drug-like molecules with novel scaffolds. To efficiently train the GARel model, we utilized dense net to update the parameters based on molecules with novel scaffolds and drug-like features. To demonstrate the capability of the GARel model, we used it to design inhibitors for three targets: AA2AR, EGFR, and SARS-Cov2. The results indicate that GARel-generated molecules feature more diverse and novel scaffolds and possess more desirable physicochemical properties and favorable docking scores. Compared with other generative models, GARel makes significant progress in balancing novelty and drug-likeness, providing a promising direction for the further development of DL-based de novo design methodology with potential impacts on drug discovery.
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Affiliation(s)
- Mingyang Wang
- College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang ,China
- CarbonSilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang ,China
| | - Zhengjian Wu
- College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang ,China
- School of Computer Science, Wuhan University, Wuhan 430072, Hubei ,China
| | - Jike Wang
- College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang ,China
- CarbonSilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang ,China
| | - Gaoqi Weng
- College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang ,China
| | - Yu Kang
- College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang ,China
| | - Peichen Pan
- College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang ,China
| | - Dan Li
- College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang ,China
| | - Yafeng Deng
- CarbonSilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang ,China
| | - Xiaojun Yao
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery Macau Institute for Applied Research in Medicine and Health State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Zhitong Bing
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, Gansu 730000, China
| | - Chang-Yu Hsieh
- College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang ,China
| | - Tingjun Hou
- College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang ,China
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16
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Horne R, Wilson-Godber J, González Díaz A, Brotzakis ZF, Seal S, Gregory RC, Possenti A, Chia S, Vendruscolo M. Using Generative Modeling to Endow with Potency Initially Inert Compounds with Good Bioavailability and Low Toxicity. J Chem Inf Model 2024; 64:590-596. [PMID: 38261763 PMCID: PMC10865343 DOI: 10.1021/acs.jcim.3c01777] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024]
Abstract
In the early stages of drug development, large chemical libraries are typically screened to identify compounds of promising potency against the chosen targets. Often, however, the resulting hit compounds tend to have poor drug metabolism and pharmacokinetics (DMPK), with negative developability features that may be difficult to eliminate. Therefore, starting the drug discovery process with a "null library", compounds that have highly desirable DMPK properties but no potency against the chosen targets, could be advantageous. Here, we explore the opportunities offered by machine learning to realize this strategy in the case of the inhibition of α-synuclein aggregation, a process associated with Parkinson's disease. We apply MolDQN, a generative machine learning method, to build an inhibitory activity against α-synuclein aggregation into an initial inactive compound with good DMPK properties. Our results illustrate how generative modeling can be used to endow initially inert compounds with desirable developability properties.
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Affiliation(s)
- Robert
I. Horne
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United
Kingdom
| | - Jared Wilson-Godber
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United
Kingdom
| | - Alicia González Díaz
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United
Kingdom
| | - Z. Faidon Brotzakis
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United
Kingdom
| | - Srijit Seal
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United
Kingdom
- Imaging
Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Rebecca C. Gregory
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United
Kingdom
| | - Andrea Possenti
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United
Kingdom
| | - Sean Chia
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United
Kingdom
- Bioprocessing
Technology Institute, Agency for Science, Technology and Research (A*STAR), 138668 Singapore, Singapore
| | - Michele Vendruscolo
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United
Kingdom
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17
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Kyro GW, Morgunov A, Brent RI, Batista VS. ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation. J Chem Inf Model 2024; 64:653-665. [PMID: 38287889 DOI: 10.1021/acs.jcim.3c01456] [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: 01/31/2024]
Abstract
The incredible capabilities of generative artificial intelligence models have inevitably led to their application in the domain of drug discovery. Within this domain, the vastness of chemical space motivates the development of more efficient methods for identifying regions with molecules that exhibit desired characteristics. In this work, we present a computationally efficient active learning methodology and demonstrate its applicability to targeted molecular generation. When applied to c-Abl kinase, a protein with FDA-approved small-molecule inhibitors, the model learns to generate molecules similar to the inhibitors without prior knowledge of their existence and even reproduces two of them exactly. We also show that the methodology is effective for a protein without any commercially available small-molecule inhibitors, the HNH domain of the CRISPR-associated protein 9 (Cas9) enzyme. To facilitate implementation and reproducibility, we made all of our software available through the open-source ChemSpaceAL Python package.
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Affiliation(s)
- Gregory W Kyro
- Department of Chemistry, Yale University, New Haven, Connecticut 06511-8499, United States
| | - Anton Morgunov
- Department of Chemistry, Yale University, New Haven, Connecticut 06511-8499, United States
| | - Rafael I Brent
- Department of Chemistry, Yale University, New Haven, Connecticut 06511-8499, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06511-8499, United States
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18
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Shen T, Guo J, Han Z, Zhang G, Liu Q, Si X, Wang D, Wu S, Xia J. AutoMolDesigner for Antibiotic Discovery: An AI-Based Open-Source Software for Automated Design of Small-Molecule Antibiotics. J Chem Inf Model 2024; 64:575-583. [PMID: 38265916 DOI: 10.1021/acs.jcim.3c01562] [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: 01/26/2024]
Abstract
Discovery of small-molecule antibiotics with novel chemotypes serves as one of the essential strategies to address antibiotic resistance. Although a considerable number of computational tools committed to molecular design have been reported, there is a deficit in holistic and efficient tools specifically developed for small-molecule antibiotic discovery. To address this issue, we report AutoMolDesigner, a computational modeling software dedicated to small-molecule antibiotic design. It is a generalized framework comprising two functional modules, i.e., generative-deep-learning-enabled molecular generation and automated machine-learning-based antibacterial activity/property prediction, wherein individually trained models and curated datasets are out-of-the-box for whole-cell-based antibiotic screening and design. It is open-source, thus allowing for the incorporation of new features for flexible use. Unlike most software programs based on Linux and command lines, this application equipped with a Qt-based graphical user interface can be run on personal computers with multiple operating systems, making it much easier to use for experimental scientists. The software and related materials are freely available at GitHub (https://github.com/taoshen99/AutoMolDesigner) and Zenodo (https://zenodo.org/record/10097899).
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Affiliation(s)
- Tao Shen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jiale Guo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zunsheng Han
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Gao Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Qingxin Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- School of Pharmacy, Jiangsu Ocean University, Lianyungang, Jiangsu 222005, China
| | - Xinxin Si
- School of Pharmacy, Jiangsu Ocean University, Lianyungang, Jiangsu 222005, China
| | - Dongmei Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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19
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Bo W, Duan Y, Zou Y, Ma Z, Yang T, Wang P, Guo T, Fu Z, Wang J, Fan L, Liu J, Wang T, Chen L. Local Scaffold Diversity-Contributed Generator for Discovering Potential NLRP3 Inhibitors. J Chem Inf Model 2024; 64:737-748. [PMID: 38258981 DOI: 10.1021/acs.jcim.3c01818] [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: 01/24/2024]
Abstract
Deep generative models have become crucial tools in de novo drug design. In current models for multiobjective optimization in molecular generation, the scaffold diversity is limited when multiple constraints are introduced. To enhance scaffold diversity, we herein propose a local scaffold diversity-contributed generator (LSDC), which can be utilized to generate diverse lead compounds capable of satisfying multiple constraints. Compared to the state-of-the-art methods, molecules generated by LSDC exhibit greater diversity when applied to the generation of inhibitors targeting the NOD-like receptor (NLR) family, pyrin domain-containing protein 3 (NLRP3). We present 12 molecules, some of which feature previously unreported scaffolds, and demonstrate their reasonable docking binding modes. Consequently, the modification of selected scaffolds and subsequent bioactivity evaluation lead to the discovery of two potent NLRP3 inhibitors, A22 and A14, with IC50 values of 38.1 nM and 44.43 nM, respectively. And the oral bioavailability of compound A14 is very high (F is 83.09% in mice). This work contributes to the discovery of novel NLRP3 inhibitors and provides a reference for integrating AI-based generation with wet experiments.
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Affiliation(s)
- Weichen Bo
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yangqin Duan
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yurong Zou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ziyan Ma
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tao Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Peng Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tao Guo
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhiyuan Fu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jianmin Wang
- The Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea
| | - Linchuan Fan
- College of Automation, Chongqing University, Chongqing 40000, China
| | - Jie Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Taijin Wang
- Chengdu Zenitar Biomedical Technology Co., Ltd, Chengdu 610041, China
| | - Lijuan Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Chengdu Zenitar Biomedical Technology Co., Ltd, Chengdu 610041, China
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20
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Tropsha A, Isayev O, Varnek A, Schneider G, Cherkasov A. Integrating QSAR modelling and deep learning in drug discovery: the emergence of deep QSAR. Nat Rev Drug Discov 2024; 23:141-155. [PMID: 38066301 DOI: 10.1038/s41573-023-00832-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2023] [Indexed: 02/08/2024]
Abstract
Quantitative structure-activity relationship (QSAR) modelling, an approach that was introduced 60 years ago, is widely used in computer-aided drug design. In recent years, progress in artificial intelligence techniques, such as deep learning, the rapid growth of databases of molecules for virtual screening and dramatic improvements in computational power have supported the emergence of a new field of QSAR applications that we term 'deep QSAR'. Marking a decade from the pioneering applications of deep QSAR to tasks involved in small-molecule drug discovery, we herein describe key advances in the field, including deep generative and reinforcement learning approaches in molecular design, deep learning models for synthetic planning and the application of deep QSAR models in structure-based virtual screening. We also reflect on the emergence of quantum computing, which promises to further accelerate deep QSAR applications and the need for open-source and democratized resources to support computer-aided drug design.
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Affiliation(s)
| | | | | | | | - Artem Cherkasov
- University of British Columbia, Vancouver, BC, Canada.
- Photonic Inc., Coquitlam, BC, Canada.
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21
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Du W, Ma F, Zhang B, Zhang J, Wu D, Sharman E, Jiang J, Wang Y. Spectroscopy-Guided Deep Learning Predicts Solid-Liquid Surface Adsorbate Properties in Unseen Solvents. J Am Chem Soc 2024; 146:811-823. [PMID: 38157302 PMCID: PMC10785802 DOI: 10.1021/jacs.3c10921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024]
Abstract
Accurately and rapidly acquiring the microscopic properties of a material is crucial for catalysis and electrochemistry. Characterization tools, such as spectroscopy, can be a valuable tool to infer these properties, and when combined with machine learning tools, they can theoretically achieve fast and accurate prediction results. However, on the path to practical applications, training a reliable machine learning model is faced with the challenge of uneven data distribution in a vast array of non-negligible solvent types. Herein, we employ a combination of the first-principles-based approach and data-driven model. Specifically, we utilize density functional theory (DFT) to calculate theoretical spectral data of CO-Ag adsorption in 23 different solvent systems as a data source. Subsequently, we propose a hierarchical knowledge extraction multiexpert neural network (HMNN) to bridge the knowledge gaps among different solvent systems. HMNN undergoes two training tiers: in tier I, it learns fundamental quantitative spectra-property relationships (QSPRs), and in tier II, it inherits the fundamental QSPR knowledge from previous steps through a dynamic integration of expert modules and subsequently captures the solvent differences. The results demonstrate HMNN's superiority in estimating a range of molecular adsorbate properties, with an error range of less than 0.008 eV for zero-shot predictions on unseen solvents. The findings underscore the usability, reliability, and convenience of HMNN and could pave the way for real-time access to microscopic properties by exploiting QSPR.
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Affiliation(s)
- Wenjie Du
- Key
Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
- School
of Software Engineering, University of Science
and Technology of China, Hefei, Anhui 230026, China
- Suzhou
Institute for Advanced Research, University
of Science and Technology of China, Suzhou, Jiangsu 215123, China
| | - Fenfen Ma
- Key
Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
- School
of Chemistry and Materials Science, University
of Science and Technology of China, Hefei, Anhui 230026, China
- Gusu
Laboratory of Materials, Suzhou, Jiangsu 215123, China
| | - Baicheng Zhang
- Key
Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
- School
of Chemistry and Materials Science, University
of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jiahui Zhang
- School
of Software Engineering, University of Science
and Technology of China, Hefei, Anhui 230026, China
- Suzhou
Institute for Advanced Research, University
of Science and Technology of China, Suzhou, Jiangsu 215123, China
| | - Di Wu
- School
of Software Engineering, University of Science
and Technology of China, Hefei, Anhui 230026, China
- Suzhou
Institute for Advanced Research, University
of Science and Technology of China, Suzhou, Jiangsu 215123, China
| | - Edward Sharman
- Department
of Neurology, University of California, Irvine, California 92697, United States
| | - Jun Jiang
- Key
Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
- School
of Chemistry and Materials Science, University
of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yang Wang
- Key
Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
- School
of Software Engineering, University of Science
and Technology of China, Hefei, Anhui 230026, China
- Suzhou
Institute for Advanced Research, University
of Science and Technology of China, Suzhou, Jiangsu 215123, China
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22
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Qin R, Zhang H, Huang W, Shao Z, Lei J. Deep learning-based design and screening of benzimidazole-pyrazine derivatives as adenosine A 2B receptor antagonists. J Biomol Struct Dyn 2023:1-17. [PMID: 38133953 DOI: 10.1080/07391102.2023.2295974] [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: 09/16/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023]
Abstract
The Adenosine A2B receptor (A2BAR) is considered a novel potential target for the immunotherapy of cancer, and A2BAR antagonists have an inhibitory effect on tumor growth, proliferation, and metastasis. In our previous studies, we identified a class of benzimidazole-pyrazine scaffolds whose derivatives exhibited the antagonistic effect but lacked subtype selectivity towards A2BAR. In this work, we developed a scaffold-based protocol that incorporates a deep generative model and multilayer virtual screening to design benzimidazole-pyrazine derivatives as potential selective A2BAR antagonists. By utilizing a generative model with reported A2BAR antagonists as the training set, we built up a scaffold-focused library of benzimidazole-pyrazine derivatives and processed a virtual screening protocol to discover potential A2BAR antagonists. Finally, five molecules with different Bemis-Murcko scaffolds were identified and exhibited higher binding free energies than the reference molecule 12o. Further computational analysis revealed that the 3-benzyl derivative ABA-1266 presented high selectivity toward A2BAR and showed preferred draggability, providing future potent development of selective A2BAR antagonists.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rui Qin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Hao Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Weifeng Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhenglin Shao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jinping Lei
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
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23
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Hu J, Li Z, Lin J, Zhang L. Prediction and Interpretability of Glass Transition Temperature of Homopolymers by Data-Augmented Graph Convolutional Neural Networks. ACS APPLIED MATERIALS & INTERFACES 2023; 15:54006-54017. [PMID: 37934171 DOI: 10.1021/acsami.3c13698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Establishing the structure-property relationship by machine learning (ML) models is extremely valuable for accelerating the molecular design of polymers. However, existing ML models for the polymers are subject to scarcity issues of training data and fewer variations of graph structures of molecules. In addition, limited works have explored the interpretability of ML models to infer the latent knowledge in the field of polymer science that could inspire ML-assisted molecular design. In this contribution, we integrate graph convolutional neural networks (GCNs) with data augmentation strategy to predict the glass transition temperature Tg of polymers. It is demonstrated that the data-augmented GCN model outperforms the conventional models and achieves a higher accuracy for the prediction of Tg despite a small amount of training data. Furthermore, taking advantage of molecular graph representations, the data-augmented GCN model has the capability to infer the importance of atoms or substructures from the understanding of Tg, which generally agrees with the experimental findings in the field of polymer science. The inferred knowledge of the GCN model is used to advise on the design of functional polymers with specific Tg. The data-augmented GCN model possesses prominent superiorities in the establishment of structure-property relationship and also provides an efficient way for accelerating the rational design of polymer molecules.
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Affiliation(s)
- Junyang Hu
- Shanghai Key Laboratory of Advanced Polymeric Materials, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zean Li
- Shanghai Key Laboratory of Advanced Polymeric Materials, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jiaping Lin
- Shanghai Key Laboratory of Advanced Polymeric Materials, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Liangshun Zhang
- Shanghai Key Laboratory of Advanced Polymeric Materials, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
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24
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Wang Q, Wei Z, Hu X, Wang Z, Dong Y, Liu H. Molecular generation strategy and optimization based on A2C reinforcement learning in de novo drug design. Bioinformatics 2023; 39:btad693. [PMID: 37971970 PMCID: PMC10689670 DOI: 10.1093/bioinformatics/btad693] [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] [Received: 08/22/2023] [Revised: 10/08/2023] [Accepted: 11/15/2023] [Indexed: 11/19/2023] Open
Abstract
MOTIVATION In the field of pharmacochemistry, it is a time-consuming and expensive process for the new drug development. The existing drug design methods face a significant challenge in terms of generation efficiency and quality. RESULTS In this paper, we proposed a novel molecular generation strategy and optimization based on A2C reinforcement learning. In molecular generation strategy, we adopted transformer-DNN to retain the scaffolds advantages, while accounting for the generated molecules' similarity and internal diversity by dynamic parameter adjustment, further improving the overall quality of molecule generation. In molecular optimization, we introduced heterogeneous parallel supercomputing for large-scale molecular docking based on message passing interface communication technology to rapidly obtain bioactive information, thereby enhancing the efficiency of drug design. Experiments show that our model can generate high-quality molecules with multi-objective properties at a high generation efficiency, with effectiveness and novelty close to 100%. Moreover, we used our method to assist shandong university school of pharmacy to find several candidate drugs molecules of anti-PEDV. AVAILABILITY AND IMPLEMENTATION The datasets involved in this method and the source code are freely available to academic users at https://github.com/wq-sunshine/MomdTDSRL.git.
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Affiliation(s)
- Qian Wang
- College of Computer Science and Technology, Ocean University of China, Qingdao, Shandong 266100, China
| | - Zhiqiang Wei
- College of Computer Science and Technology, Ocean University of China, Qingdao, Shandong 266100, China
| | - Xiaotong Hu
- College of Computer Science and Technology, Ocean University of China, Qingdao, Shandong 266100, China
| | - Zhuoya Wang
- Center for High Performance Computing and System Simulation, National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Yujie Dong
- Marine Big Data Center of Institute for Advanced Ocean Study, Ocean University of China, Qingdao, Shandong 266100, China
| | - Hao Liu
- College of Computer Science and Technology, Ocean University of China, Qingdao, Shandong 266100, China
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25
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Mullowney MW, Duncan KR, Elsayed SS, Garg N, van der Hooft JJJ, Martin NI, Meijer D, Terlouw BR, Biermann F, Blin K, Durairaj J, Gorostiola González M, Helfrich EJN, Huber F, Leopold-Messer S, Rajan K, de Rond T, van Santen JA, Sorokina M, Balunas MJ, Beniddir MA, van Bergeijk DA, Carroll LM, Clark CM, Clevert DA, Dejong CA, Du C, Ferrinho S, Grisoni F, Hofstetter A, Jespers W, Kalinina OV, Kautsar SA, Kim H, Leao TF, Masschelein J, Rees ER, Reher R, Reker D, Schwaller P, Segler M, Skinnider MA, Walker AS, Willighagen EL, Zdrazil B, Ziemert N, Goss RJM, Guyomard P, Volkamer A, Gerwick WH, Kim HU, Müller R, van Wezel GP, van Westen GJP, Hirsch AKH, Linington RG, Robinson SL, Medema MH. Artificial intelligence for natural product drug discovery. Nat Rev Drug Discov 2023; 22:895-916. [PMID: 37697042 DOI: 10.1038/s41573-023-00774-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2023] [Indexed: 09/13/2023]
Abstract
Developments in computational omics technologies have provided new means to access the hidden diversity of natural products, unearthing new potential for drug discovery. In parallel, artificial intelligence approaches such as machine learning have led to exciting developments in the computational drug design field, facilitating biological activity prediction and de novo drug design for molecular targets of interest. Here, we describe current and future synergies between these developments to effectively identify drug candidates from the plethora of molecules produced by nature. We also discuss how to address key challenges in realizing the potential of these synergies, such as the need for high-quality datasets to train deep learning algorithms and appropriate strategies for algorithm validation.
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Affiliation(s)
| | - Katherine R Duncan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Somayah S Elsayed
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Neha Garg
- School of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - David Meijer
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Barbara R Terlouw
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Friederike Biermann
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Institute of Molecular Bio Science, Goethe-University Frankfurt, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Marina Gorostiola González
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
- ONCODE institute, Leiden, The Netherlands
| | - Eric J N Helfrich
- Institute of Molecular Bio Science, Goethe-University Frankfurt, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
| | - Florian Huber
- Center for Digitalization and Digitality, Hochschule Düsseldorf, Düsseldorf, Germany
| | - Stefan Leopold-Messer
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Kohulan Rajan
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Jena, Germany
| | - Tristan de Rond
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Jeffrey A van Santen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Jena, Germany
- Pharmaceuticals R&D, Bayer AG, Berlin, Germany
| | - Marcy J Balunas
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Mehdi A Beniddir
- Équipe "Chimie des Substances Naturelles", Université Paris-Saclay, CNRS, BioCIS, Orsay, France
| | - Doris A van Bergeijk
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Laura M Carroll
- Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Chase M Clark
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Chao Du
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | - Francesca Grisoni
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands
| | | | - Willem Jespers
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Olga V Kalinina
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
- Drug Bioinformatics, Medical Faculty, Saarland University, Homburg, Germany
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | | | - Hyunwoo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University Seoul, Goyang-si, Republic of Korea
| | - Tiago F Leao
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Joleen Masschelein
- Center for Microbiology, VIB-KU Leuven, Heverlee, Belgium
- Department of Biology, KU Leuven, Heverlee, Belgium
| | - Evan R Rees
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Raphael Reher
- Institute of Pharmaceutical Biology and Biotechnology, University of Marburg, Marburg, Germany
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Daniel Reker
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Philippe Schwaller
- Laboratory of Artificial Chemical Intelligence, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Michael A Skinnider
- Adapsyn Bioscience, Hamilton, Ontario, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Allison S Walker
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Egon L Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Barbara Zdrazil
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridgeshire, UK
| | - Nadine Ziemert
- Interfaculty Institute for Microbiology and Infection Medicine Tuebingen (IMIT), Institute for Bioinformatics and Medical Informatics (IBMI), University of Tuebingen, Tuebingen, Germany
| | | | - Pierre Guyomard
- Bonsai team, CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, Université de Lille, Villeneuve d'Ascq Cedex, France
| | - Andrea Volkamer
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
- In silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - William H Gerwick
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- German Center for infection research (DZIF), Braunschweig, Germany
- Helmholtz International Lab for Anti-Infectives, Saarbrücken, Germany
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
- Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, The Netherlands
| | - Gerard J P van Westen
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands.
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany.
- Department of Pharmacy, Saarland University, Saarbrücken, Germany.
- German Center for infection research (DZIF), Braunschweig, Germany.
- Helmholtz International Lab for Anti-Infectives, Saarbrücken, Germany.
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
| | - Serina L Robinson
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute for Aquatic Science and Technology, Dübendorf, Switzerland.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Institute of Biology, Leiden University, Leiden, The Netherlands.
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26
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Bustillo L, Laino T, Rodrigues T. The rise of automated curiosity-driven discoveries in chemistry. Chem Sci 2023; 14:10378-10384. [PMID: 37799997 PMCID: PMC10548516 DOI: 10.1039/d3sc03367h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 09/07/2023] [Indexed: 10/07/2023] Open
Abstract
The quest for generating novel chemistry knowledge is critical in scientific advancement, and machine learning (ML) has emerged as an asset in this pursuit. Through interpolation among learned patterns, ML can tackle tasks that were previously deemed demanding to machines. This distinctive capacity of ML provides invaluable aid to bench chemists in their daily work. However, current ML tools are typically designed to prioritize experiments with the highest likelihood of success, i.e., higher predictive confidence. In this perspective, we build on current trends that suggest a future in which ML could be just as beneficial in exploring uncharted search spaces through simulated curiosity. We discuss how low and 'negative' data can catalyse one-/few-shot learning, and how the broader use of curious ML and novelty detection algorithms can propel the next wave of chemical discoveries. We anticipate that ML for curiosity-driven research will help the community overcome potentially biased assumptions and uncover unexpected findings in the chemical sciences at an accelerated pace.
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Affiliation(s)
- Latimah Bustillo
- Research Institute for Medicines (iMed), Faculdade de Farmácia, Universidade de Lisboa Lisbon Portugal
| | - Teodoro Laino
- IBM Research Europe Säumerstrasse 4 8803 Rüschlikon Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis) Zurich Switzerland
| | - Tiago Rodrigues
- Research Institute for Medicines (iMed), Faculdade de Farmácia, Universidade de Lisboa Lisbon Portugal
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27
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Diao Y, Liu D, Ge H, Zhang R, Jiang K, Bao R, Zhu X, Bi H, Liao W, Chen Z, Zhang K, Wang R, Zhu L, Zhao Z, Hu Q, Li H. Macrocyclization of linear molecules by deep learning to facilitate macrocyclic drug candidates discovery. Nat Commun 2023; 14:4552. [PMID: 37507402 PMCID: PMC10382584 DOI: 10.1038/s41467-023-40219-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Interest in macrocycles as potential therapeutic agents has increased rapidly. Macrocyclization of bioactive acyclic molecules provides a potential avenue to yield novel chemical scaffolds, which can contribute to the improvement of the biological activity and physicochemical properties of these molecules. In this study, we propose a computational macrocyclization method based on Transformer architecture (which we name Macformer). Leveraging deep learning, Macformer explores the vast chemical space of macrocyclic analogues of a given acyclic molecule by adding diverse linkers compatible with the acyclic molecule. Macformer can efficiently learn the implicit relationships between acyclic and macrocyclic structures represented as SMILES strings and generate plenty of macrocycles with chemical diversity and structural novelty. In data augmentation scenarios using both internal ChEMBL and external ZINC test datasets, Macformer display excellent performance and generalisability. We showcase the utility of Macformer when combined with molecular docking simulations and wet lab based experimental validation, by applying it to the prospective design of macrocyclic JAK2 inhibitors.
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Affiliation(s)
- Yanyan Diao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Dandan Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Huan Ge
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Rongrong Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Kexin Jiang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Runhui Bao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Xiaoqian Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Hongjie Bi
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Wenjie Liao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Ziqi Chen
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Kai Zhang
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai, 200062, China
| | - Rui Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Zhenjiang Zhao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Qiaoyu Hu
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai, 200062, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China.
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai, 200062, China.
- Lingang Laboratory, Shanghai, 200031, China.
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28
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Niazi SK, Mariam Z. Recent Advances in Machine-Learning-Based Chemoinformatics: A Comprehensive Review. Int J Mol Sci 2023; 24:11488. [PMID: 37511247 PMCID: PMC10380192 DOI: 10.3390/ijms241411488] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/30/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
In modern drug discovery, the combination of chemoinformatics and quantitative structure-activity relationship (QSAR) modeling has emerged as a formidable alliance, enabling researchers to harness the vast potential of machine learning (ML) techniques for predictive molecular design and analysis. This review delves into the fundamental aspects of chemoinformatics, elucidating the intricate nature of chemical data and the crucial role of molecular descriptors in unveiling the underlying molecular properties. Molecular descriptors, including 2D fingerprints and topological indices, in conjunction with the structure-activity relationships (SARs), are pivotal in unlocking the pathway to small-molecule drug discovery. Technical intricacies of developing robust ML-QSAR models, including feature selection, model validation, and performance evaluation, are discussed herewith. Various ML algorithms, such as regression analysis and support vector machines, are showcased in the text for their ability to predict and comprehend the relationships between molecular structures and biological activities. This review serves as a comprehensive guide for researchers, providing an understanding of the synergy between chemoinformatics, QSAR, and ML. Due to embracing these cutting-edge technologies, predictive molecular analysis holds promise for expediting the discovery of novel therapeutic agents in the pharmaceutical sciences.
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Affiliation(s)
- Sarfaraz K Niazi
- College of Pharmacy, University of Illinois, Chicago, IL 61820, USA
| | - Zamara Mariam
- Zamara Mariam, School of Interdisciplinary Engineering & Sciences (SINES), National University of Sciences & Technology (NUST), Islamabad 24090, Pakistan
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29
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Zhang J, Du W, Yang X, Wu D, Li J, Wang K, Wang Y. SMG-BERT: integrating stereoscopic information and chemical representation for molecular property prediction. Front Mol Biosci 2023; 10:1216765. [PMID: 37457837 PMCID: PMC10348360 DOI: 10.3389/fmolb.2023.1216765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/15/2023] [Indexed: 07/18/2023] Open
Abstract
Molecular property prediction is a crucial task in various fields and has recently garnered significant attention. To achieve accurate and fast prediction of molecular properties, machine learning (ML) models have been widely employed due to their superior performance compared to traditional methods by trial and error. However, most of the existing ML models that do not incorporate 3D molecular information are still in need of improvement, as they are mostly poor at differentiating stereoisomers of certain types, particularly chiral ones. Also,routine featurization methods using only incomplete features are hard to obtain explicable molecular representations. In this paper, we propose the Stereo Molecular Graph BERT (SMG-BERT) by integrating the 3D space geometric parameters, 2D topological information, and 1D SMILES string into the self-attention-based BERT model. In addition, nuclear magnetic resonance (NMR) spectroscopy results and bond dissociation energy (BDE) are integrated as extra atomic and bond features to improve the model's performance and interpretability analysis. The comprehensive integration of 1D, 2D, and 3D information could establish a unified and unambiguous molecular characterization system to distinguish conformations, such as chiral molecules. Intuitively integrated chemical information enables the model to possess interpretability that is consistent with chemical logic. Experimental results on 12 benchmark molecular datasets show that SMG-BERT consistently outperforms existing methods. At the same time, the experimental results demonstrate that SMG-BERT is generalizable and reliable.
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Affiliation(s)
- Jiahui Zhang
- School of Software Engineering, University of Science and Technology of China, Hefei, China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu, China
| | - Wenjie Du
- School of Software Engineering, University of Science and Technology of China, Hefei, China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu, China
| | - Xiaoting Yang
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu, China
- School of Computer Science and Technology, University of Science and Technology of China, Hefei, China
| | - Di Wu
- School of Software Engineering, University of Science and Technology of China, Hefei, China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu, China
| | - Jiahe Li
- School of Software Engineering, University of Science and Technology of China, Hefei, China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu, China
| | - Kun Wang
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu, China
| | - Yang Wang
- School of Software Engineering, University of Science and Technology of China, Hefei, China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu, China
- School of Computer Science and Technology, University of Science and Technology of China, Hefei, China
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30
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Ballarotto M, Willems S, Stiller T, Nawa F, Marschner JA, Grisoni F, Merk D. De Novo Design of Nurr1 Agonists via Fragment-Augmented Generative Deep Learning in Low-Data Regime. J Med Chem 2023. [PMID: 37256819 DOI: 10.1021/acs.jmedchem.3c00485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Generative neural networks trained on SMILES can design innovative bioactive molecules de novo. These so-called chemical language models (CLMs) have typically been trained on tens of template molecules for fine-tuning. However, it is challenging to apply CLM to orphan targets with few known ligands. We have fine-tuned a CLM with a single potent Nurr1 agonist as template in a fragment-augmented fashion and obtained novel Nurr1 agonists using sampling frequency for design prioritization. Nanomolar potency and binding affinity of the top-ranking design and its structural novelty compared to available Nurr1 ligands highlight its value as an early chemical tool and as a lead for Nurr1 agonist development, as well as the applicability of CLM in very low-data scenarios.
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Affiliation(s)
- Marco Ballarotto
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
- Department of Pharmaceutical Sciences, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Sabine Willems
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Tanja Stiller
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Felix Nawa
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Julian A Marschner
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Francesca Grisoni
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584CB Utrecht, The Netherlands
| | - Daniel Merk
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
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31
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Tay DWP, Yeo NZX, Adaikkappan K, Lim YH, Ang SJ. 67 million natural product-like compound database generated via molecular language processing. Sci Data 2023; 10:296. [PMID: 37208372 DOI: 10.1038/s41597-023-02207-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/21/2023] [Indexed: 05/21/2023] Open
Abstract
Natural products are a rich resource of bioactive compounds for valuable applications across multiple fields such as food, agriculture, and medicine. For natural product discovery, high throughput in silico screening offers a cost-effective alternative to traditional resource-heavy assay-guided exploration of structurally novel chemical space. In this data descriptor, we report a characterized database of 67,064,204 natural product-like molecules generated using a recurrent neural network trained on known natural products, demonstrating a significant 165-fold expansion in library size over the approximately 400,000 known natural products. This study highlights the potential of using deep generative models to explore novel natural product chemical space for high throughput in silico discovery.
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Affiliation(s)
- Dillon W P Tay
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore.
| | - Naythan Z X Yeo
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore
- Hwa Chong Institution, 661 Bukit Timah Road, Singapore, 269734, Republic of Singapore
| | - Krishnan Adaikkappan
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore
- National Junior College, 37 Hillcrest Road, Singapore, 288913, Republic of Singapore
| | - Yee Hwee Lim
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore
- Synthetic Biology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore, 117597, Republic of Singapore
| | - Shi Jun Ang
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore.
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore, 138632, Republic of Singapore.
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32
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Bustillo L, Rodrigues T. A focus on the use of real-world datasets for yield prediction. Chem Sci 2023; 14:4958-4960. [PMID: 37206402 PMCID: PMC10189867 DOI: 10.1039/d3sc90069j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023] Open
Abstract
The prediction of reaction yields remains a challenging task for machine learning (ML), given the vast search spaces and absence of robust training data. Wiest, Chawla et al. (https://doi.org/10.1039/D2SC06041H) show that a deep learning algorithm performs well on high-throughput experimentation data but surprisingly poorly on real-world, historical data from a pharmaceutical company. The result suggests that there is considerable room for improvement when coupling ML to electronic laboratory notebook data.
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Affiliation(s)
- Latimah Bustillo
- Research Institute for Medicines (iMed), Faculty of Pharmacy, University of Lisbon Av Prof Gama Pinto 1649-003 Lisbon Portugal
| | - Tiago Rodrigues
- Research Institute for Medicines (iMed), Faculty of Pharmacy, University of Lisbon Av Prof Gama Pinto 1649-003 Lisbon Portugal
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33
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Yang Y, Hsieh CY, Kang Y, Hou T, Liu H, Yao X. Deep Generation Model Guided by the Docking Score for Active Molecular Design. J Chem Inf Model 2023; 63:2983-2991. [PMID: 37163364 DOI: 10.1021/acs.jcim.3c00572] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A deep generation model, as a novel drug design and discovery tool, shows obvious advantages in generating compounds with novel backbones and has been applied successfully in the field of drug discovery. However, it is still a challenge to generate molecules with expected properties, especially high activity. Here, to obtain compounds both with novelty and high activity to a target, we proposed a conditional molecular generation model COMG by considering the docking score and 3D pharmacophore matching during molecular generation. The proposed model was based on the conditional variational autoencoder architecture constrained by the pharmacophore matching score. During Bayesian optimization, the docking score was applied to enhance the target relevance of generated compounds. Furthermore, to overcome the problem of high structural similarity caused by Bayesian optimization, the idea of the scaffold memory unit was also introduced. The evaluation results of COMG show that our model not only can improve the structural diversity of generated molecules but also can effectively improve the proportion of target-related drug-active molecules. The obtained results indicate that our proposed model COMG is a useful drug design tool.
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Affiliation(s)
- Yuwei Yang
- Faculty of Applied Sciences, Macao Polytechnic University, Macao (SAR) 999078, P. R. China
- School of Pharmacy, Lanzhou University, Lanzhou 730000, Gansu, P. R. China
| | - Chang-Yu Hsieh
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Huanxiang Liu
- Faculty of Applied Sciences, Macao Polytechnic University, Macao (SAR) 999078, P. R. China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, 999078 Macau (SAR), P. R. China
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34
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Ji C, Zheng Y, Wang R, Cai Y, Wu H. Graph Polish: A Novel Graph Generation Paradigm for Molecular Optimization. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2023; 34:2323-2337. [PMID: 34520363 DOI: 10.1109/tnnls.2021.3106392] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Molecular optimization, which transforms a given input molecule X into another Y with desired properties, is essential in molecular drug discovery. The traditional approaches either suffer from sample-inefficient learning or ignore information that can be captured with the supervised learning of optimized molecule pairs. In this study, we present a novel molecular optimization paradigm, Graph Polish. In this paradigm, with the guidance of the source and target molecule pairs of the desired properties, a heuristic optimization solution can be derived: given an input molecule, we first predict which atom can be viewed as the optimization center, and then the nearby regions are optimized around this center. We then propose an effective and efficient learning framework, Teacher and Student polish, to capture the dependencies in the optimization steps. A teacher component automatically identifies and annotates the optimization centers and the preservation, removal, and addition of some parts of the molecules; a student component learns these knowledges and applies them to a new molecule. The proposed paradigm can offer an intuitive interpretation for the molecular optimization result. Experiments with multiple optimization tasks are conducted on several benchmark datasets. The proposed approach achieves a significant advantage over the six state-of-the-art baseline methods. Also, extensive studies are conducted to validate the effectiveness, explainability, and time savings of the novel optimization paradigm.
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35
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Grisoni F. Chemical language models for de novo drug design: Challenges and opportunities. Curr Opin Struct Biol 2023; 79:102527. [PMID: 36738564 DOI: 10.1016/j.sbi.2023.102527] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 02/05/2023]
Abstract
Generative deep learning is accelerating de novo drug design, by allowing the generation of molecules with desired properties on demand. Chemical language models - which generate new molecules in the form of strings using deep learning - have been particularly successful in this endeavour. Thanks to advances in natural language processing methods and interdisciplinary collaborations, chemical language models are expected to become increasingly relevant in drug discovery. This minireview provides an overview of the current state-of-the-art of chemical language models for de novo design, and analyses current limitations, challenges, and advantages. Finally, a perspective on future opportunities is provided.
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Affiliation(s)
- Francesca Grisoni
- Eindhoven University of Technology, Institute for Complex Molecular Systems and Dept. Biomedical Engineering, Eindhoven, Netherlands; Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Netherlands.
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36
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Horne RI, Murtada MH, Huo D, Brotzakis ZF, Gregory RC, Possenti A, Chia S, Vendruscolo M. Exploration and Exploitation Approaches Based on Generative Machine Learning to Identify Potent Small Molecule Inhibitors of α-Synuclein Secondary Nucleation. J Chem Theory Comput 2023. [PMID: 36939645 PMCID: PMC10373478 DOI: 10.1021/acs.jctc.2c01303] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
The high attrition rate in drug discovery pipelines is an especially pressing issue for Parkinson's disease, for which no disease-modifying drugs have yet been approved. Numerous clinical trials targeting α-synuclein aggregation have failed, at least in part due to the challenges in identifying potent compounds in preclinical investigations. To address this problem, we present a machine learning approach that combines generative modeling and reinforcement learning to identify small molecules that perturb the kinetics of aggregation in a manner that reduces the production of oligomeric species. Training data were obtained by an assay reporting on the degree of inhibition of secondary nucleation, which is the most important mechanism of α-synuclein oligomer production. This approach resulted in the identification of small molecules with high potency against secondary nucleation.
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Affiliation(s)
- Robert I Horne
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Mhd Hussein Murtada
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Donghui Huo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Z Faidon Brotzakis
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Rebecca C Gregory
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Andrea Possenti
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Sean Chia
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.,Bioprocessing Technology Institute, Agency of Science, Technology and Research (A*STAR), Singapore 138668, Singapore
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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37
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Seo S, Lim J, Kim WY. Molecular Generative Model via Retrosynthetically Prepared Chemical Building Block Assembly. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206674. [PMID: 36596675 PMCID: PMC10015872 DOI: 10.1002/advs.202206674] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Deep generative models are attracting attention as a smart molecular design strategy. However, previous models often render molecules with low synthesizability, hindering their real-world applications. Here, a novel graph-based conditional generative model which makes molecules by tailoring retrosynthetically prepared chemical building blocks until achieving target properties in an auto-regressive fashion is proposed. This strategy improves the synthesizability and property control of the resulting molecules and also helps learn how to select appropriate building blocks and bind them together to achieve target properties. By applying a negative sampling method to the selection process of building blocks, this model overcame a critical limitation of previous fragment-based models, which can only use molecules from the training set during generation. As a result, the model works equally well with unseen building blocks without sacrificing computational efficiency. It is demonstrated that the model can generate potential inhibitors with high docking scores against the 3CL protease of SARS-COV-2.
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Affiliation(s)
- Seonghwan Seo
- HITS Incorporation124 Teheran‐ro, Gangnam‐guSeoul06234Republic of Korea
- Department of ChemistryKAIST, 291 Daehak‐ro, Yuseong‐guDaejeon34141Republic of Korea
| | - Jaechang Lim
- HITS Incorporation124 Teheran‐ro, Gangnam‐guSeoul06234Republic of Korea
| | - Woo Youn Kim
- HITS Incorporation124 Teheran‐ro, Gangnam‐guSeoul06234Republic of Korea
- Department of ChemistryKAIST, 291 Daehak‐ro, Yuseong‐guDaejeon34141Republic of Korea
- AI InstituteKAIST, 291 Daehak‐ro, Yuseong‐guDaejeon34141Republic of Korea
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38
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Wang L, Song Y, Wang H, Zhang X, Wang M, He J, Li S, Zhang L, Li K, Cao L. Advances of Artificial Intelligence in Anti-Cancer Drug Design: A Review of the Past Decade. Pharmaceuticals (Basel) 2023; 16:253. [PMID: 37259400 PMCID: PMC9963982 DOI: 10.3390/ph16020253] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/25/2023] [Accepted: 02/06/2023] [Indexed: 10/13/2023] Open
Abstract
Anti-cancer drug design has been acknowledged as a complicated, expensive, time-consuming, and challenging task. How to reduce the research costs and speed up the development process of anti-cancer drug designs has become a challenging and urgent question for the pharmaceutical industry. Computer-aided drug design methods have played a major role in the development of cancer treatments for over three decades. Recently, artificial intelligence has emerged as a powerful and promising technology for faster, cheaper, and more effective anti-cancer drug designs. This study is a narrative review that reviews a wide range of applications of artificial intelligence-based methods in anti-cancer drug design. We further clarify the fundamental principles of these methods, along with their advantages and disadvantages. Furthermore, we collate a large number of databases, including the omics database, the epigenomics database, the chemical compound database, and drug databases. Other researchers can consider them and adapt them to their own requirements.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Kang Li
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin 150081, China
| | - Lei Cao
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin 150081, China
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39
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Danel T, Łęski J, Podlewska S, Podolak IT. Docking-based generative approaches in the search for new drug candidates. Drug Discov Today 2023; 28:103439. [PMID: 36372330 DOI: 10.1016/j.drudis.2022.103439] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/08/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Despite the popularity of virtual screening (VS) of existing compound libraries, the search for new potential drug candidates also takes advantage of generative protocols, where new compound suggestions are enumerated using various algorithms. To increase the activity potency of generative approaches, they have recently been coupled with molecular docking, a leading methodology of structure-based drug design (SBDD). In this review, we summarize progress since docking-based generative models emerged. We propose a new taxonomy for these methods and discuss their importance for the field of computer-aided drug design (CADD). In addition, we discuss the most promising directions for the further development of generative protocols coupled with docking.
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Affiliation(s)
- Tomasz Danel
- Faculty of Mathematics and Computer Science, Jagiellonian University, 6 Łojasiewicza Street, 30-348 Kraków, Poland.
| | - Jan Łęski
- Faculty of Mathematics and Computer Science, Jagiellonian University, 6 Łojasiewicza Street, 30-348 Kraków, Poland
| | - Sabina Podlewska
- Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Medicinal Chemistry, 31-343 Kraków, Smętna Street 12, Poland
| | - Igor T Podolak
- Faculty of Mathematics and Computer Science, Jagiellonian University, 6 Łojasiewicza Street, 30-348 Kraków, Poland
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40
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Duran-Frigola M, Cigler M, Winter GE. Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence. J Am Chem Soc 2023; 145:2711-2732. [PMID: 36706315 PMCID: PMC9912273 DOI: 10.1021/jacs.2c11098] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Only around 20% of the human proteome is considered to be druggable with small-molecule antagonists. This leaves some of the most compelling therapeutic targets outside the reach of ligand discovery. The concept of targeted protein degradation (TPD) promises to overcome some of these limitations. In brief, TPD is dependent on small molecules that induce the proximity between a protein of interest (POI) and an E3 ubiquitin ligase, causing ubiquitination and degradation of the POI. In this perspective, we want to reflect on current challenges in the field, and discuss how advances in multiomics profiling, artificial intelligence, and machine learning (AI/ML) will be vital in overcoming them. The presented roadmap is discussed in the context of small-molecule degraders but is equally applicable for other emerging proximity-inducing modalities.
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Affiliation(s)
- Miquel Duran-Frigola
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria,Ersilia
Open Source Initiative, 28 Belgrave Road, CB1 3DE, Cambridge, United Kingdom,
| | - Marko Cigler
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Georg E. Winter
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria,
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41
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Moret M, Pachon Angona I, Cotos L, Yan S, Atz K, Brunner C, Baumgartner M, Grisoni F, Schneider G. Leveraging molecular structure and bioactivity with chemical language models for de novo drug design. Nat Commun 2023; 14:114. [PMID: 36611029 PMCID: PMC9825622 DOI: 10.1038/s41467-022-35692-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
Generative chemical language models (CLMs) can be used for de novo molecular structure generation by learning from a textual representation of molecules. Here, we show that hybrid CLMs can additionally leverage the bioactivity information available for the training compounds. To computationally design ligands of phosphoinositide 3-kinase gamma (PI3Kγ), a collection of virtual molecules was created with a generative CLM. This virtual compound library was refined using a CLM-based classifier for bioactivity prediction. This second hybrid CLM was pretrained with patented molecular structures and fine-tuned with known PI3Kγ ligands. Several of the computer-generated molecular designs were commercially available, enabling fast prescreening and preliminary experimental validation. A new PI3Kγ ligand with sub-micromolar activity was identified, highlighting the method's scaffold-hopping potential. Chemical synthesis and biochemical testing of two of the top-ranked de novo designed molecules and their derivatives corroborated the model's ability to generate PI3Kγ ligands with medium to low nanomolar activity for hit-to-lead expansion. The most potent compounds led to pronounced inhibition of PI3K-dependent Akt phosphorylation in a medulloblastoma cell model, demonstrating efficacy of PI3Kγ ligands in PI3K/Akt pathway repression in human tumor cells. The results positively advocate hybrid CLMs for virtual compound screening and activity-focused molecular design.
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Affiliation(s)
- Michael Moret
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Irene Pachon Angona
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Leandro Cotos
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Shen Yan
- University of Zurich, University Children's Hospital, Children's Research Center, Pediatric Molecular Neuro-Oncology Research, Lengghalde 5, 8008, Zurich, Switzerland
| | - Kenneth Atz
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Cyrill Brunner
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Martin Baumgartner
- University of Zurich, University Children's Hospital, Children's Research Center, Pediatric Molecular Neuro-Oncology Research, Lengghalde 5, 8008, Zurich, Switzerland
| | - Francesca Grisoni
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland. .,Eindhoven University of Technology, Institute for Complex Molecular Systems and Eindhoven Artificial Intelligence Systems Institute, Department of Biomedical Engineering, Groene Loper 7, 5612AZ, Eindhoven, The Netherlands. .,Center for 393 Living Technologies, Alliance TU/e, WUR, UU, UMC 394 Utrecht, Utrecht, 3584 CB, The Netherlands.
| | - Gisbert Schneider
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland. .,ETH Singapore SEC Ltd, 1 CREATE Way, #06-01 CREATE Tower, Singapore, 138602, Singapore.
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42
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Zang X, Zhou X, Bian H, Jin W, Pan X, Jiang J, Koroleva MY, Shen R. Prediction and Construction of Energetic Materials Based on Machine Learning Methods. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010322. [PMID: 36615516 PMCID: PMC9821915 DOI: 10.3390/molecules28010322] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/18/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023]
Abstract
Energetic materials (EMs) are the core materials of weapons and equipment. Achieving precise molecular design and efficient green synthesis of EMs has long been one of the primary concerns of researchers around the world. Traditionally, advanced materials were discovered through a trial-and-error processes, which required long research and development (R&D) cycles and high costs. In recent years, the machine learning (ML) method has matured into a tool that compliments and aids experimental studies for predicting and designing advanced EMs. This paper reviews the critical process of ML methods to discover and predict EMs, including data preparation, feature extraction, model construction, and model performance evaluation. The main ideas and basic steps of applying ML methods are analyzed and outlined. The state-of-the-art research about ML applications in property prediction and inverse material design of EMs is further summarized. Finally, the existing challenges and the strategies for coping with challenges in the further applications of the ML methods are proposed.
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Affiliation(s)
- Xiaowei Zang
- College of Safety Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Xiang Zhou
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Haitao Bian
- College of Safety Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Weiping Jin
- Jiangxi Xinyu Guoke Technology Co., Ltd., Xinyu 338018, China
| | - Xuhai Pan
- College of Safety Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Juncheng Jiang
- College of Safety Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - M. Yu. Koroleva
- Institute of Modern Energetics and Nanomaterials, D. Mendeleev University of Chemical Technology of Russia, Moscow 125047, Russia
| | - Ruiqi Shen
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Micro-Nano Energetic Devices Key Laboratory of MIIT, Nanjing 210094, China
- Institute of Space Propulsion, Nanjing University of Science and Technology, Nanjing 210094, China
- Correspondence:
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43
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Du W, Yang X, Wu D, Ma F, Zhang B, Bao C, Huo Y, Jiang J, Chen X, Wang Y. Fusing 2D and 3D molecular graphs as unambiguous molecular descriptors for conformational and chiral stereoisomers. Brief Bioinform 2022; 24:6931719. [PMID: 36528804 PMCID: PMC9851338 DOI: 10.1093/bib/bbac560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/28/2022] [Accepted: 11/15/2022] [Indexed: 12/23/2022] Open
Abstract
The rapid progress of machine learning (ML) in predicting molecular properties enables high-precision predictions being routinely achieved. However, many ML models, such as conventional molecular graph, cannot differentiate stereoisomers of certain types, particularly conformational and chiral ones that share the same bonding connectivity but differ in spatial arrangement. Here, we designed a hybrid molecular graph network, Chemical Feature Fusion Network (CFFN), to address the issue by integrating planar and stereo information of molecules in an interweaved fashion. The three-dimensional (3D, i.e., stereo) modality guarantees precision and completeness by providing unabridged information, while the two-dimensional (2D, i.e., planar) modality brings in chemical intuitions as prior knowledge for guidance. The zipper-like arrangement of 2D and 3D information processing promotes cooperativity between them, and their synergy is the key to our model's success. Experiments on various molecules or conformational datasets including a special newly created chiral molecule dataset comprised of various configurations and conformations demonstrate the superior performance of CFFN. The advantage of CFFN is even more significant in datasets made of small samples. Ablation experiments confirm that fusing 2D and 3D molecular graphs as unambiguous molecular descriptors can not only effectively distinguish molecules and their conformations, but also achieve more accurate and robust prediction of quantum chemical properties.
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Affiliation(s)
- Wenjie Du
- School of Software Engineering, University of Science and Technology of China, Hefei 230026, China,Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, China
| | - Xiaoting Yang
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, China,School of Computer Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Di Wu
- School of Software Engineering, University of Science and Technology of China, Hefei 230026, China,Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, China
| | - FenFen Ma
- Suzhou Laboratory , Suzhou 215123, Jiangsu, China
| | - Baicheng Zhang
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Chaochao Bao
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, China
| | - Yaoyuan Huo
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, China
| | - Jun Jiang
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Xin Chen
- Corresponding authors: Yang Wang, School of Software Engineering, University of Science and Technology of China, Hefei 230026, China. E-mail: ; Xin Chen, Suzhou Laboratory, Suzhou 215123, Jiangsu, China. E-mail:
| | - Yang Wang
- Corresponding authors: Yang Wang, School of Software Engineering, University of Science and Technology of China, Hefei 230026, China. E-mail: ; Xin Chen, Suzhou Laboratory, Suzhou 215123, Jiangsu, China. E-mail:
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44
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Wang M, Wang J, Weng G, Kang Y, Pan P, Li D, Deng Y, Li H, Hsieh CY, Hou T. ReMODE: a deep learning-based web server for target-specific drug design. J Cheminform 2022; 14:84. [PMID: 36510307 PMCID: PMC9743675 DOI: 10.1186/s13321-022-00665-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022] Open
Abstract
Deep learning (DL) and machine learning contribute significantly to basic biology research and drug discovery in the past few decades. Recent advances in DL-based generative models have led to superior developments in de novo drug design. However, data availability, deep data processing, and the lack of user-friendly DL tools and interfaces make it difficult to apply these DL techniques to drug design. We hereby present ReMODE (Receptor-based MOlecular DEsign), a new web server based on DL algorithm for target-specific ligand design, which integrates different functional modules to enable users to develop customizable drug design tasks. As designed, the ReMODE sever can construct the target-specific tasks toward the protein targets selected by users. Meanwhile, the server also provides some extensions: users can optimize the drug-likeness or synthetic accessibility of the generated molecules, and control other physicochemical properties; users can also choose a sub-structure/scaffold as a starting point for fragment-based drug design. The ReMODE server also enables users to optimize the pharmacophore matching and docking conformations of the generated molecules. We believe that the ReMODE server will benefit researchers for drug discovery. ReMODE is publicly available at http://cadd.zju.edu.cn/relation/remode/ .
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Affiliation(s)
- Mingyang Wang
- grid.13402.340000 0004 1759 700XInnovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou, 310058 Zhejiang People’s Republic of China ,CarbonSilicon AI Technology Co., Ltd, Hangzhou, 310018 Zhejiang People’s Republic of China
| | - Jike Wang
- grid.13402.340000 0004 1759 700XInnovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou, 310058 Zhejiang People’s Republic of China ,CarbonSilicon AI Technology Co., Ltd, Hangzhou, 310018 Zhejiang People’s Republic of China
| | - Gaoqi Weng
- grid.13402.340000 0004 1759 700XInnovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou, 310058 Zhejiang People’s Republic of China ,CarbonSilicon AI Technology Co., Ltd, Hangzhou, 310018 Zhejiang People’s Republic of China
| | - Yu Kang
- grid.13402.340000 0004 1759 700XInnovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou, 310058 Zhejiang People’s Republic of China
| | - Peichen Pan
- grid.13402.340000 0004 1759 700XInnovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou, 310058 Zhejiang People’s Republic of China
| | - Dan Li
- grid.13402.340000 0004 1759 700XInnovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou, 310058 Zhejiang People’s Republic of China
| | - Yafeng Deng
- CarbonSilicon AI Technology Co., Ltd, Hangzhou, 310018 Zhejiang People’s Republic of China
| | - Honglin Li
- grid.28056.390000 0001 2163 4895Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237 People’s Republic of China
| | - Chang-Yu Hsieh
- grid.13402.340000 0004 1759 700XInnovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou, 310058 Zhejiang People’s Republic of China
| | - Tingjun Hou
- grid.13402.340000 0004 1759 700XInnovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou, 310058 Zhejiang People’s Republic of China
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45
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Noguchi S, Inoue J. Exploration of Chemical Space Guided by PixelCNN for Fragment-Based De Novo Drug Discovery. J Chem Inf Model 2022; 62:5988-6001. [PMID: 36454646 DOI: 10.1021/acs.jcim.2c01345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
We report a novel framework for achieving fragment-based molecular design using pixel convolutional neural network (PixelCNN) combined with the simplified molecular input line entry system (SMILES) as molecular representation. While a widely used recurrent neural network (RNN) assumes monotonically decaying correlations in strings, PixelCNN captures a periodicity among characters of SMILES. Thus, PixelCNN provides us with a novel solution for the analysis of chemical space by extracting the periodicity of molecular structures that will be buried in SMILES. Moreover, this characteristic enables us to generate molecules by combining several simple building blocks, such as a benzene ring and side-chain structures, which contributes to the effective exploration of chemical space by step-by-step searching for molecules from a target fragment. In conclusion, PixelCNN could be a powerful approach focusing on the periodicity of molecules to explore chemical space for the fragment-based molecular design.
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Affiliation(s)
- Satoshi Noguchi
- Department of Advanced Interdisciplinary Studies, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo153-8904, Japan
| | - Junya Inoue
- Institute for Industrial Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba277-0082, Japan.,Department of Materials Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo113-8656, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo153-8904, Japan
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46
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Zhang Y, Jiang Q, Li L, Li Z, Xu Z, Chen Y, Sun Y, Liu C, Mao Z, Chen F, Li H, Cao Y, Pian C. Predicting the structure of unexplored novel fentanyl analogues by deep learning model. Brief Bioinform 2022; 23:6741166. [PMID: 36184256 DOI: 10.1093/bib/bbac418] [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: 06/01/2022] [Revised: 08/21/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022] Open
Abstract
Fentanyl and its analogues are psychoactive substances and the concern of fentanyl abuse has been existed in decades. Because the structure of fentanyl is easy to be modified, criminals may synthesize new fentanyl analogues to avoid supervision. The drug supervision is based on the structure matching to the database and too few kinds of fentanyl analogues are included in the database, so it is necessary to find out more potential fentanyl analogues and expand the sample space of fentanyl analogues. In this study, we introduced two deep generative models (SeqGAN and MolGPT) to generate potential fentanyl analogues, and a total of 11 041 valid molecules were obtained. The results showed that not only can we generate molecules with similar property distribution of original data, but the generated molecules also contain potential fentanyl analogues that are not pretty similar to any of original data. Ten molecules based on the rules of fentanyl analogues were selected for NMR, MS and IR validation. The results indicated that these molecules are all unreported fentanyl analogues. Furthermore, this study is the first to apply the deep learning to the generation of fentanyl analogues, greatly expands the exploring space of fentanyl analogues and provides help for the supervision of fentanyl.
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Affiliation(s)
| | | | | | - Zutan Li
- Bioinformatics Doctoral Student at Nanjing Agricultural University, China
| | - Zhihui Xu
- Researcher in Simcere Diagnostics Co., Ltd, China
| | - Yuanyuan Chen
- College of Sciences at Nanjing Agricultural University, China
| | - Yang Sun
- Nanjing Medical University, China
| | - Cheng Liu
- Department of Forensic Medicine, College of Basic Medical Science at Nanjing Medical University, China
| | - Zhengsheng Mao
- Forensic Science Department at Nanjing Medical University, China
| | | | - Hualan Li
- Bioinformatics Master Student at Nanjing Agricultural University, China
| | - Yue Cao
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Cong Pian
- College of Sciences, Nanjing Agricultural University, Nanjing, JiangsuChina
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47
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Li Y, Zhang L, Wang Y, Zou J, Yang R, Luo X, Wu C, Yang W, Tian C, Xu H, Wang F, Yang X, Li L, Yang S. Generative deep learning enables the discovery of a potent and selective RIPK1 inhibitor. Nat Commun 2022; 13:6891. [PMID: 36371441 PMCID: PMC9653409 DOI: 10.1038/s41467-022-34692-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/03/2022] [Indexed: 11/13/2022] Open
Abstract
The retrieval of hit/lead compounds with novel scaffolds during early drug development is an important but challenging task. Various generative models have been proposed to create drug-like molecules. However, the capacity of these generative models to design wet-lab-validated and target-specific molecules with novel scaffolds has hardly been verified. We herein propose a generative deep learning (GDL) model, a distribution-learning conditional recurrent neural network (cRNN), to generate tailor-made virtual compound libraries for given biological targets. The GDL model is then applied to RIPK1. Virtual screening against the generated tailor-made compound library and subsequent bioactivity evaluation lead to the discovery of a potent and selective RIPK1 inhibitor with a previously unreported scaffold, RI-962. This compound displays potent in vitro activity in protecting cells from necroptosis, and good in vivo efficacy in two inflammatory models. Collectively, the findings prove the capacity of our GDL model in generating hit/lead compounds with unreported scaffolds, highlighting a great potential of deep learning in drug discovery.
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Affiliation(s)
- Yueshan Li
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Liting Zhang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Yifei Wang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Jun Zou
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Ruicheng Yang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Xinling Luo
- grid.13291.380000 0001 0807 1581Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, 610041 Chengdu, Sichuan China
| | - Chengyong Wu
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Wei Yang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Chenyu Tian
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Haixing Xu
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Falu Wang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Xin Yang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Linli Li
- grid.13291.380000 0001 0807 1581Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, 610041 Chengdu, Sichuan China
| | - Shengyong Yang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
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48
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Korshunova M, Huang N, Capuzzi S, Radchenko DS, Savych O, Moroz YS, Wells CI, Willson TM, Tropsha A, Isayev O. Generative and reinforcement learning approaches for the automated de novo design of bioactive compounds. Commun Chem 2022; 5:129. [PMID: 36697952 PMCID: PMC9814657 DOI: 10.1038/s42004-022-00733-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 09/12/2022] [Indexed: 01/28/2023] Open
Abstract
Deep generative neural networks have been used increasingly in computational chemistry for de novo design of molecules with desired properties. Many deep learning approaches employ reinforcement learning for optimizing the target properties of the generated molecules. However, the success of this approach is often hampered by the problem of sparse rewards as the majority of the generated molecules are expectedly predicted as inactives. We propose several technical innovations to address this problem and improve the balance between exploration and exploitation modes in reinforcement learning. In a proof-of-concept study, we demonstrate the application of the deep generative recurrent neural network architecture enhanced by several proposed technical tricks to design inhibitors of the epidermal growth factor (EGFR) and further experimentally validate their potency. The proposed technical solutions are expected to substantially improve the success rate of finding novel bioactive compounds for specific biological targets using generative and reinforcement learning approaches.
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Affiliation(s)
- Maria Korshunova
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA, USA. .,Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Niles Huang
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Stephen Capuzzi
- Laboratory for Molecular Modeling, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dmytro S Radchenko
- Enamine Ltd, 78 Chervonotkatska Street, Kyiv, 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
| | - Olena Savych
- Enamine Ltd, 78 Chervonotkatska Street, Kyiv, 02094, Ukraine
| | - Yuriy S Moroz
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine.,Chemspace LLC, Chervonotkatska Street 85, Suite 1, Kyiv, 02094, Ukraine
| | - Carrow I Wells
- Structual Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Timothy M Willson
- Structual Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Olexandr Isayev
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA, USA. .,Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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49
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Atance SR, Diez JV, Engkvist O, Olsson S, Mercado R. De Novo Drug Design Using Reinforcement Learning with Graph-Based Deep Generative Models. J Chem Inf Model 2022; 62:4863-4872. [PMID: 36219571 DOI: 10.1021/acs.jcim.2c00838] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Machine learning provides effective computational tools for exploring the chemical space via deep generative models. Here, we propose a new reinforcement learning scheme to fine-tune graph-based deep generative models for de novo molecular design tasks. We show how our computational framework can successfully guide a pretrained generative model toward the generation of molecules with a specific property profile, even when such molecules are not present in the training set and unlikely to be generated by the pretrained model. We explored the following tasks: generating molecules of decreasing/increasing size, increasing drug-likeness, and increasing bioactivity. Using the proposed approach, we achieve a model which generates diverse compounds with predicted DRD2 activity for 95% of sampled molecules, outperforming previously reported methods on this metric.
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Affiliation(s)
- Sara Romeo Atance
- Molecular AI, Discovery Sciences, R&D, AstraZeneca Gothenburg, Pepparedsleden 1, 431 50Mölndal, Sweden.,Department of Computer Science and Engineering, Chalmers University of Technology, Rännvägen 6, 412 58Göteborg, Sweden
| | - Juan Viguera Diez
- Molecular AI, Discovery Sciences, R&D, AstraZeneca Gothenburg, Pepparedsleden 1, 431 50Mölndal, Sweden.,Department of Computer Science and Engineering, Chalmers University of Technology, Rännvägen 6, 412 58Göteborg, Sweden
| | - Ola Engkvist
- Molecular AI, Discovery Sciences, R&D, AstraZeneca Gothenburg, Pepparedsleden 1, 431 50Mölndal, Sweden.,Department of Computer Science and Engineering, Chalmers University of Technology, Rännvägen 6, 412 58Göteborg, Sweden
| | - Simon Olsson
- Department of Computer Science and Engineering, Chalmers University of Technology, Rännvägen 6, 412 58Göteborg, Sweden
| | - Rocío Mercado
- Molecular AI, Discovery Sciences, R&D, AstraZeneca Gothenburg, Pepparedsleden 1, 431 50Mölndal, Sweden
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50
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Uludoğan G, Ozkirimli E, Ulgen KO, Karalı N, Özgür A. Exploiting pretrained biochemical language models for targeted drug design. Bioinformatics 2022; 38:ii155-ii161. [PMID: 36124801 DOI: 10.1093/bioinformatics/btac482] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
MOTIVATION The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabelled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation and (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target-specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. RESULTS The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. AVAILABILITY AND IMPLEMENTATION The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials (i.e., data, models, and outputs) are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gökçe Uludoğan
- Department of Computer Engineering, Boğaziçi University, İstanbul 34342, Turkey
| | - Elif Ozkirimli
- Data and Analytics Chapter, Pharma International Informatics, F. Hoffmann-La Roche AG 4303, Switzerland
| | - Kutlu O Ulgen
- Department of Chemical Engineering, Boğaziçi University, İstanbul 34342, Turkey
| | - Nilgün Karalı
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, İstanbul University, İstanbul 34116, Turkey
| | - Arzucan Özgür
- Department of Computer Engineering, Boğaziçi University, İstanbul 34342, Turkey
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