1
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Abou Hajal A, Bryce RA, Amor BB, Atatreh N, Ghattas MA. Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter. J Chem Inf Model 2024; 64:4991-5005. [PMID: 38920403 DOI: 10.1021/acs.jcim.4c00363] [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: 06/27/2024]
Abstract
The ability to conduct effective high throughput screening (HTS) campaigns in drug discovery is often hampered by the detection of false positives in these assays due to small colloidally aggregating molecules (SCAMs). SCAMs can produce artifactual hits in HTS by nonspecific inhibition of the protein target. In this work, we present a new computational prediction tool for detecting SCAMs based on their 2D chemical structure. The tool, called the boosted aggregation detection (BAD) molecule filter, employs decision tree ensemble methods, namely, the CatBoost classifier and the light gradient-boosting machine, to significantly improve the detection of SCAMs. In developing the filter, we explore models trained on individual data sets, a consensus approach using these models, and, third, a merged data set approach, each tailored for specific drug discovery needs. The individual data set method emerged as most effective, achieving 93% sensitivity and 90% specificity, outperforming existing state-of-the-art models by 20 and 5%, respectively. The consensus models offer broader chemical space coverage, exceeding 90% for all testing sets. This feature is an important aspect particularly for early stage medicinal chemistry projects, and provides information on applicability domain. Meanwhile, the merged data set models demonstrated robust performance, with a notable sensitivity of 79% in the comprehensive 10-fold cross-validation test set. A SHAP analysis of model features indicates the importance of hydrophobicity and molecular complexity as primary factors influencing the aggregation propensity. The BAD molecule filter is readily accessible for the public usage on https://molmodlab-aau.com/Tools.html. This filter provides a new, more robust tool for aggregate prediction in the early stages of drug discovery to optimize hit rates and reduce associated testing and validation overheads.
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Affiliation(s)
- Abdallah Abou Hajal
- College of Pharmacy, Al Ain University, Abu Dhabi 112612, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 112612, United Arab Emirates
| | - Richard A Bryce
- Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Boulbaba Ben Amor
- Core42, Inception/G42, Abu Dhabi 2282, United Arab Emirates
- IMT Nord Europe, Villeneuve D'Ascq 59650 France
| | - Noor Atatreh
- College of Pharmacy, Al Ain University, Abu Dhabi 112612, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 112612, United Arab Emirates
| | - Mohammad A Ghattas
- College of Pharmacy, Al Ain University, Abu Dhabi 112612, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 112612, United Arab Emirates
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2
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Shi S, Fu L, Yi J, Yang Z, Zhang X, Deng Y, Wang W, Wu C, Zhao W, Hou T, Zeng X, Lyu A, Cao D. ChemFH: an integrated tool for screening frequent false positives in chemical biology and drug discovery. Nucleic Acids Res 2024; 52:W439-W449. [PMID: 38783035 PMCID: PMC11223804 DOI: 10.1093/nar/gkae424] [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: 02/06/2024] [Revised: 04/25/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
High-throughput screening rapidly tests an extensive array of chemical compounds to identify hit compounds for specific biological targets in drug discovery. However, false-positive results disrupt hit compound screening, leading to wastage of time and resources. To address this, we propose ChemFH, an integrated online platform facilitating rapid virtual evaluation of potential false positives, including colloidal aggregators, spectroscopic interference compounds, firefly luciferase inhibitors, chemical reactive compounds, promiscuous compounds, and other assay interferences. By leveraging a dataset containing 823 391 compounds, we constructed high-quality prediction models using multi-task directed message-passing network (DMPNN) architectures combining uncertainty estimation, yielding an average AUC value of 0.91. Furthermore, ChemFH incorporated 1441 representative alert substructures derived from the collected data and ten commonly used frequent hitter screening rules. ChemFH was validated with an external set of 75 compounds. Subsequently, the virtual screening capability of ChemFH was successfully confirmed through its application to five virtual screening libraries. Furthermore, ChemFH underwent additional validation on two natural products and FDA-approved drugs, yielding reliable and accurate results. ChemFH is a comprehensive, reliable, and computationally efficient screening pipeline that facilitates the identification of true positive results in assays, contributing to enhanced efficiency and success rates in drug discovery. ChemFH is freely available via https://chemfh.scbdd.com/.
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Affiliation(s)
- Shaohua Shi
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, P.R. China
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, 999077, P.R. China
| | - Li Fu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, P.R. China
| | - Jiacai Yi
- School of Computer Science, National University of Defense Technology, Changsha, Hunan 410073, P.R. China
| | - Ziyi Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, P.R. China
| | - Xiaochen Zhang
- School of Information Technology, Shangqiu Normal University, Shangqiu, Henan 476000, P.R. China
| | - Youchao Deng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, P.R. China
| | - Wenxuan Wang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, P.R. China
| | - Chengkun Wu
- School of Computer Science, National University of Defense Technology, Changsha, Hunan 410073, P.R. China
| | - Wentao Zhao
- School of Computer Science, National University of Defense Technology, Changsha, Hunan 410073, P.R. China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
| | - Xiangxiang Zeng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan 410082, P.R. China
| | - Aiping Lyu
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, 999077, P.R. China
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, P.R. China
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3
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Kombo DC, Stepp JD, Lim S, Elshorst B, Li Y, Cato L, Shomali M, Fink D, LaMarche MJ. Predictions of Colloidal Molecular Aggregation Using AI/ML Models. ACS OMEGA 2024; 9:28691-28706. [PMID: 38973835 PMCID: PMC11223200 DOI: 10.1021/acsomega.4c02886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 07/09/2024]
Abstract
To facilitate the triage of hits from small molecule screens, we have used various AI/ML techniques and experimentally observed data sets to build models aimed at predicting colloidal aggregation of small organic molecules in aqueous solution. We have found that Naïve Bayesian and deep neural networks outperform logistic regression, recursive partitioning tree, support vector machine, and random forest techniques by having the lowest balanced error rate (BER) for the test set. Derived predictive classification models consistently and successfully discriminated aggregator molecules from nonaggregator hits. An analysis of molecular descriptors in favor of colloidal aggregation confirms previous observations (hydrophobicity, molecular weight, and solubility) in addition to undescribed molecular descriptors such as the fraction of sp3 carbon atoms (Fsp3), and electrotopological state of hydroxyl groups (ES_Sum_sOH). Naïve Bayesian modeling and scaffold tree analysis have revealed chemical features/scaffolds contributing the most to colloidal aggregation and nonaggregation, respectively. These results highlight the importance of scaffolds with high Fsp3 values in promoting nonaggregation. Matched molecular pair analysis (MMPA) has also deciphered context-dependent substitutions, which can be used to design nonaggregator molecules. We found that most matched molecular pairs have a neutral effect on aggregation propensity. We have prospectively applied our predictive models to assist in chemical library triage for optimal plate selection diversity and purchase for high throughput screening (HTS) in drug discovery projects.
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Affiliation(s)
- David C. Kombo
- Integrated
Drug Discovery, Sanofi, 350 Water St., Cambridge, Massachusetts 02141, United States
| | - J. David Stepp
- Integrated
Drug Discovery, Sanofi, 350 Water St., Cambridge, Massachusetts 02141, United States
| | - Sungtaek Lim
- Integrated
Drug Discovery, Sanofi, 350 Water St., Cambridge, Massachusetts 02141, United States
| | - Bettina Elshorst
- CMC
Synthetics Early Development Analytics, Sanofi, Industriepark Hochst, Frankfurt 65926, Germany
| | - Yi Li
- Integrated
Drug Discovery, Sanofi, 350 Water St., Cambridge, Massachusetts 02141, United States
| | - Laura Cato
- Molecular
Oncology, Sanofi, 350
Water St., Cambridge, Massachusetts 02141, United States
| | - Maysoun Shomali
- Molecular
Oncology, Sanofi, 350
Water St., Cambridge, Massachusetts 02141, United States
| | - David Fink
- Integrated
Drug Discovery, Sanofi, 350 Water St., Cambridge, Massachusetts 02141, United States
| | - Matthew J. LaMarche
- Integrated
Drug Discovery, Sanofi, 350 Water St., Cambridge, Massachusetts 02141, United States
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4
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Glenn IS, Hall LN, Khalid MM, Ott M, Shoichet BK. Colloidal Aggregation Confounds Cell-Based Covid-19 Antiviral Screens. J Med Chem 2024; 67:10263-10274. [PMID: 38864383 PMCID: PMC11236530 DOI: 10.1021/acs.jmedchem.4c00597] [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] [Indexed: 06/13/2024]
Abstract
Colloidal aggregation is one of the largest contributors to false positives in early drug discovery. Here, we consider aggregation's role in cell-based infectivity assays in Covid-19 drug repurposing. We investigated the potential aggregation of 41 drug candidates reported as SARs-CoV-2 entry inhibitors. Of these, 17 formed colloidal particles by dynamic light scattering and exhibited detergent-dependent enzyme inhibition. To evaluate the impact of aggregation on antiviral efficacy in cells, we presaturated the colloidal drug suspensions with BSA or spun them down by centrifugation and measured the effects on spike pseudovirus infectivity. Antiviral potencies diminished by at least 10-fold following both BSA and centrifugation treatments, supporting a colloid-based mechanism. Aggregates induced puncta of the labeled spike protein in fluorescence microscopy, consistent with sequestration of the protein on the colloidal particles. These observations suggest that colloidal aggregation is common among cell-based antiviral drug repurposing and offers rapid counter-screens to detect and eliminate these artifacts.
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Affiliation(s)
- Isabella S Glenn
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, California 94143, United States
| | - Lauren N Hall
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, California 94143, United States
| | - Mir M Khalid
- Gladstone Institutes, San Francisco, California 94158, United States
- Department of Medicine, University of California, San Francisco, San Francisco, California 94158, United States
| | - Melanie Ott
- Gladstone Institutes, San Francisco, California 94158, United States
- Department of Medicine, University of California, San Francisco, San Francisco, California 94158, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, California 94143, United States
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5
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Li X, Zuo Y, Lin X, Guo B, Jiang H, Guan N, Zheng H, Huang Y, Gu X, Yu B, Wang X. Develop Targeted Protein Drug Carriers through a High-Throughput Screening Platform and Rational Design. Adv Healthc Mater 2024:e2401793. [PMID: 38804201 DOI: 10.1002/adhm.202401793] [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: 05/16/2024] [Revised: 05/24/2024] [Indexed: 05/29/2024]
Abstract
Protein-based drugs offer advantages, such as high specificity, low toxicity, and minimal side effects compared to small molecule drugs. However, delivery of proteins to target tissues or cells remains challenging due to the instability, diverse structures, charges, and molecular weights of proteins. Polymers have emerged as a leading choice for designing effective protein delivery systems, but identifying a suitable polymer for a given protein is complicated by the complexity of both proteins and polymers. To address this challenge, a fluorescence-based high-throughput screening platform called ProMatch to efficiently collect data on protein-polymer interactions, followed by in vivo and in vitro experiments with rational design is developed. Using this approach to streamline polymer selection for targeted protein delivery, candidate polymers from commercially available options are identified and a polyhexamethylene biguanide (PHMB)-based system for delivering proteins to white adipose tissue as a treatment for obesity is developed. A branched polyethylenimine (bPEI)-based system for neuron-specific protein delivery to stimulate optic nerve regeneration is also developed. The high-throughput screening methodology expedites identification of promising polymer candidates for tissue-specific protein delivery systems, thereby providing a platform to develop innovative protein-based therapeutics.
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Affiliation(s)
- Xiaodan Li
- Department of Neurobiology and Department of Rehabilitation Medicine, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, P. R. China
- Nanhu Brain-Computer Interface Institute, Hangzhou, 311100, China
- Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, State Key Laboratory of Brain-Machine Intelligence, Zhejiang University, 1369 West Wenyi Road, Hangzhou, 311121, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University, Hangzhou, 310058, China
| | - Yanming Zuo
- Department of Neurobiology and Department of Rehabilitation Medicine, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, P. R. China
- Nanhu Brain-Computer Interface Institute, Hangzhou, 311100, China
- Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, State Key Laboratory of Brain-Machine Intelligence, Zhejiang University, 1369 West Wenyi Road, Hangzhou, 311121, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University, Hangzhou, 310058, China
| | - Xurong Lin
- Department of Neurobiology and Department of Rehabilitation Medicine, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, P. R. China
- Lingang Laboratory, Shanghai, 200031, China
| | - Binjie Guo
- Department of Neurobiology and Department of Rehabilitation Medicine, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, P. R. China
- Lingang Laboratory, Shanghai, 200031, China
| | - Haohan Jiang
- Department of Neurobiology and Department of Rehabilitation Medicine, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, P. R. China
- Lingang Laboratory, Shanghai, 200031, China
| | - Naiyu Guan
- Department of Neurobiology and Department of Rehabilitation Medicine, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, P. R. China
- Nanhu Brain-Computer Interface Institute, Hangzhou, 311100, China
- Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, State Key Laboratory of Brain-Machine Intelligence, Zhejiang University, 1369 West Wenyi Road, Hangzhou, 311121, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University, Hangzhou, 310058, China
| | - Hanyu Zheng
- Department of Neurobiology and Department of Rehabilitation Medicine, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, P. R. China
- Lingang Laboratory, Shanghai, 200031, China
| | - Yan Huang
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Xiaosong Gu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Nantong University, Nantong, Jiangsu, 226001, P. R. China
| | - Bin Yu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Nantong University, Nantong, Jiangsu, 226001, P. R. China
| | - Xuhua Wang
- Department of Neurobiology and Department of Rehabilitation Medicine, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, P. R. China
- Nanhu Brain-Computer Interface Institute, Hangzhou, 311100, China
- Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, State Key Laboratory of Brain-Machine Intelligence, Zhejiang University, 1369 West Wenyi Road, Hangzhou, 311121, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University, Hangzhou, 310058, China
- Lingang Laboratory, Shanghai, 200031, China
- Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu, 226001, P. R. China
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6
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Lamens A, Bajorath J. Systematic generation and analysis of counterfactuals for compound activity predictions using multi-task models. RSC Med Chem 2024; 15:1547-1555. [PMID: 38784468 PMCID: PMC11110787 DOI: 10.1039/d4md00128a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/05/2024] [Indexed: 05/25/2024] Open
Abstract
Most machine learning (ML) methods produce predictions that are hard or impossible to understand. The black box nature of predictive models obscures potential learning bias and makes it difficult to recognize and trace problems. Moreover, the inability to rationalize model decisions causes reluctance to accept predictions for experimental design. For ML, limited trust in predictions presents a substantial problem and continues to limit its impact in interdisciplinary research, including early-phase drug discovery. As a desirable remedy, approaches from explainable artificial intelligence (XAI) are increasingly applied to shed light on the ML black box and help to rationalize predictions. Among these is the concept of counterfactuals (CFs), which are best understood as test cases with small modifications yielding opposing prediction outcomes (such as different class labels in object classification). For ML applications in medicinal chemistry, for example, compound activity predictions, CFs are particularly intuitive because these hypothetical molecules enable immediate comparisons with actual test compounds that do not require expert ML knowledge and are accessible to practicing chemists. Such comparisons often reveal structural moieties in compounds that determine their predictions and can be further investigated. Herein, we adapt and extend a recently introduced concept for the systematic generation of molecular CFs to multi-task predictions of different classes of protein kinase inhibitors, analyze CFs in detail, rationalize the origins of CF formation in multi-task modeling, and present exemplary explanations of predictions.
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Affiliation(s)
- Alec Lamens
- Department of Life Science Informatics and Data Science, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität Friedrich-Hirzebruch-Allee 5/6 D-53115 Bonn Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics and Data Science, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität Friedrich-Hirzebruch-Allee 5/6 D-53115 Bonn Germany
- Lamarr Institute for Machine Learning and Artificial Intelligence, Rheinische Friedrich-Wilhelms-Universität Bonn Friedrich-Hirzebruch-Allee 5/6 D-53115 Bonn Germany
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7
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Tan L, Hirte S, Palmacci V, Stork C, Kirchmair J. Tackling assay interference associated with small molecules. Nat Rev Chem 2024; 8:319-339. [PMID: 38622244 DOI: 10.1038/s41570-024-00593-3] [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: 02/29/2024] [Indexed: 04/17/2024]
Abstract
Biochemical and cell-based assays are essential to discovering and optimizing efficacious and safe drugs, agrochemicals and cosmetics. However, false assay readouts stemming from colloidal aggregation, chemical reactivity, chelation, light signal attenuation and emission, membrane disruption, and other interference mechanisms remain a considerable challenge in screening synthetic compounds and natural products. To address assay interference, a range of powerful experimental approaches are available and in silico methods are now gaining traction. This Review begins with an overview of the scope and limitations of experimental approaches for tackling assay interference. It then focuses on theoretical methods, discusses strategies for their integration with experimental approaches, and provides recommendations for best practices. The Review closes with a summary of the critical facts and an outlook on potential future developments.
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Affiliation(s)
- Lu Tan
- Drug Discovery Sciences, Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Steffen Hirte
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Pharmaceutical, Nutritional and Sport Sciences (PhaNuSpo), University of Vienna, Vienna, Austria
| | - Vincenzo Palmacci
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Pharmaceutical, Nutritional and Sport Sciences (PhaNuSpo), University of Vienna, Vienna, Austria
| | - Conrad Stork
- Department of Informatics, Center for Bioinformatics, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Hamburg, Germany
- BASF SE, Ludwigshafen am Rhein, Germany
| | - Johannes Kirchmair
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
- Christian Doppler Laboratory for Molecular Informatics in the Biosciences, Department for Pharmaceutical Sciences, University of Vienna, Vienna, Austria.
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8
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Boldini D, Friedrich L, Kuhn D, Sieber SA. Machine Learning Assisted Hit Prioritization for High Throughput Screening in Drug Discovery. ACS CENTRAL SCIENCE 2024; 10:823-832. [PMID: 38680560 PMCID: PMC11046457 DOI: 10.1021/acscentsci.3c01517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 05/01/2024]
Abstract
Efficient prioritization of bioactive compounds from high throughput screening campaigns is a fundamental challenge for accelerating drug development efforts. In this study, we present the first data-driven approach to simultaneously detect assay interferents and prioritize true bioactive compounds. By analyzing the learning dynamics during training of a gradient boosting model on noisy high throughput screening data using a novel formulation of sample influence, we are able to distinguish between compounds exhibiting the desired biological response and those producing assay artifacts. Therefore, our method enables false positive and true positive detection without relying on prior screens or assay interference mechanisms, making it applicable to any high throughput screening campaign. We demonstrate that our approach consistently excludes assay interferents with different mechanisms and prioritizes biologically relevant compounds more efficiently than all tested baselines, including a retrospective case study simulating its use in a real drug discovery campaign. Finally, our tool is extremely computationally efficient, requiring less than 30 s per assay on low-resource hardware. As such, our findings show that our method is an ideal addition to existing false positive detection tools and can be used to guide further pharmacological optimization after high throughput screening campaigns.
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Affiliation(s)
- Davide Boldini
- TUM
School of Natural Sciences, Department of Bioscience, Center for Functional
Protein Assemblies (CPA), Technical University
of Munich, 85748 Garching bei München, Germany
| | - Lukas Friedrich
- The
Healthcare business of Merck KGaA, 64293 Darmstadt, Germany
| | - Daniel Kuhn
- The
Healthcare business of Merck KGaA, 64293 Darmstadt, Germany
| | - Stephan A. Sieber
- TUM
School of Natural Sciences, Department of Bioscience, Center for Functional
Protein Assemblies (CPA), Technical University
of Munich, 85748 Garching bei München, Germany
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9
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Nesabi A, Kalayan J, Al-Rawashdeh S, Ghattas MA, Bryce RA. Molecular dynamics simulations as a guide for modulating small molecule aggregation. J Comput Aided Mol Des 2024; 38:11. [PMID: 38470532 PMCID: PMC10933209 DOI: 10.1007/s10822-024-00557-1] [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: 02/02/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024]
Abstract
Small colloidally aggregating molecules (SCAMs) can be problematic for biological assays in drug discovery campaigns. However, the self-associating properties of SCAMs have potential applications in drug delivery and analytical biochemistry. Consequently, the ability to predict the aggregation propensity of a small organic molecule is of considerable interest. Chemoinformatics-based filters such as ChemAGG and Aggregator Advisor offer rapid assessment but are limited by the assay quality and structural diversity of their training set data. Complementary to these tools, we explore here the ability of molecular dynamics (MD) simulations as a physics-based method capable of predicting the aggregation propensity of diverse chemical structures. For a set of 32 molecules, using simulations of 100 ns in explicit solvent, we find a success rate of 97% (one molecule misclassified) as opposed to 75% by Aggregator Advisor and 72% by ChemAGG. These short timescale MD simulations are representative of longer microsecond trajectories and yield an informative spectrum of aggregation propensities across the set of solutes, capturing the dynamic behaviour of weakly aggregating compounds. Implicit solvent simulations using the generalized Born model were less successful in predicting aggregation propensity. MD simulations were also performed to explore structure-aggregation relationships for selected molecules, identifying chemical modifications that reversed the predicted behaviour of a given aggregator/non-aggregator compound. While lower throughput than rapid cheminformatics-based SCAM filters, MD-based prediction of aggregation has potential to be deployed on the scale of focused subsets of moderate size, and, depending on the target application, provide guidance on removing or optimizing a compound's aggregation propensity.
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Affiliation(s)
- Azam Nesabi
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Jas Kalayan
- Daresbury Laboratory, Science and Technologies Facilities Council (STFC), Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK
| | - Sara Al-Rawashdeh
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | | | - Richard A Bryce
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
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10
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van Vlijmen H, Pannifer AD, Cochrane P, Basting D, Li VM, Engkvist O, Ortholand JY, Wagener M, Duffy J, Finsinger D, Davis J, van Helden SP, de Vlieger JSB. The European Lead Factory: Results from a decade of collaborative, public-private, drug discovery programs. Drug Discov Today 2024; 29:103886. [PMID: 38244673 DOI: 10.1016/j.drudis.2024.103886] [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: 10/31/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 01/22/2024]
Abstract
The European Lead Factory (ELF) is a consortium of universities and small and medium-sized enterprises (SMEs) dedicated to drug discovery, and the pharmaceutical industry. This unprecedented consortium provides high-throughput screening, triage, and hit validation, including to non-consortium members. The ELF library was created through a novel compound-sharing model between nine pharmaceutical companies and expanded through library synthesis by chemistry-specialized SMEs. The library has been screened against ∼270 different targets and 15 phenotypic assays, and hits have been developed to form the basis of patents and spin-off companies. Here, we review the outcome of screening campaigns of the ELF, including the performance and physicochemical properties of the library, identification of possible frequent hitter compounds, and the effectiveness of the compound-sharing model.
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Affiliation(s)
| | | | | | | | - Volkhart M Li
- Bayer AG, Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Ola Engkvist
- AstraZeneca Discovery Sciences, Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | | | | | - James Duffy
- Medicines for Malaria Venture, ICC 20, Rte de Pré-Bois, 1215 Geneva, Switzerland
| | - Dirk Finsinger
- Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Jeremy Davis
- UCB Biopharma UK, 216 Bath Road, Slough, SL1 3WE, UK
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11
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Mahgoub RE, Mohamed FE, Ali BR, Ferreira J, Rabeh WM, Atatreh N, Ghattas MA. Discovery of pyrimidoindol and benzylpyrrolyl inhibitors targeting SARS-CoV-2 main protease (M pro) through pharmacophore modelling, covalent docking, and biological evaluation. J Mol Graph Model 2024; 127:108672. [PMID: 37992552 DOI: 10.1016/j.jmgm.2023.108672] [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: 09/15/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
The main protease (Mpro) enzyme has an imperative function in disease progression and the life cycle of the SARS-CoV-2 virus. Although the orally active drug nirmatrelvir (co-administered with ritonavir as paxlovid) has been approved for emergency use as the frontline antiviral agent, there are a number of limitations that necessitate the discovery of new drug scaffolds, such as poor pharmacokinetics and susceptibility to proteolytic degradation due to its peptidomimetic nature. This study utilized a novel virtual screening workflow that combines pharmacophore modelling, multiple-receptor covalent docking, and biological evaluation in order to find new Mpro inhibitors. After filtering and analysing ∼66,000 ligands from three different electrophilic libraries, 29 compounds were shortlisted for experimental testing, and two of them exhibited ≥20% inhibition at 100 μM. Our top candidate, GF04, is a benzylpyrrolyl compound that exhibited the highest inhibition activity of 38.3%, with a relatively small size (<350 Da) and leadlike character. Interestingly, our approach also identified another hit, DR07, a pyrimidoindol with a non-peptide character, and a molecular weight of 438.9 Da, reporting an inhibition of 26.3%. The established approach detailed in this study, in conjunction with the discovered inhibitors, has the capacity to yield novel perspectives for devising covalent inhibitors targeting the COVID-19 Mpro enzyme and other comparable targets.
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Affiliation(s)
- Radwa E Mahgoub
- College of Pharmacy, Al Ain University, Abu Dhabi, 112612, United Arab Emirates; AAU Health and Biomedical Research Centre, Al Ain University, Abu Dhabi, 112612, United Arab Emirates
| | - Feda E Mohamed
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, 15551, United Arab Emirates; Zayed Centre for Health Sciences, United Arab Emirates University, Al-Ain, 15551, United Arab Emirates
| | - Juliana Ferreira
- Science Division, New York University Abu Dhabi, Abu Dhabi, 129188, United Arab Emirates
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, Abu Dhabi, 129188, United Arab Emirates
| | - Noor Atatreh
- College of Pharmacy, Al Ain University, Abu Dhabi, 112612, United Arab Emirates; AAU Health and Biomedical Research Centre, Al Ain University, Abu Dhabi, 112612, United Arab Emirates
| | - Mohammad A Ghattas
- College of Pharmacy, Al Ain University, Abu Dhabi, 112612, United Arab Emirates; AAU Health and Biomedical Research Centre, Al Ain University, Abu Dhabi, 112612, United Arab Emirates.
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12
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Wang Q, Fu X, Yan Y, Liu T, Xie Y, Song X, Zhou Y, Xu M, Wang P, Fu P, Huang J, Huang N. Structure-Based Identification of Organoruthenium Compounds as Nanomolar Antagonists of Cannabinoid Receptors. J Chem Inf Model 2024; 64:761-774. [PMID: 38215394 DOI: 10.1021/acs.jcim.3c01282] [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: 01/14/2024]
Abstract
Metal complexes exhibit a diverse range of coordination geometries, representing novel privileged scaffolds with convenient click types of preparation inaccessible for typical carbon-centered organic compounds. Herein, we explored the opportunity to identify biologically active organometallic complexes by reverse docking of a rigid, minimum-size octahedral organoruthenium scaffold against thousands of protein-binding pockets. Interestingly, cannabinoid receptor type 1 (CB1) was identified based on the docking scores and the degree of overlap between the docked organoruthenium scaffold and the hydrophobic scaffold of the cocrystallized ligand. Further structure-based optimization led to the discovery of organoruthenium complexes with nanomolar binding affinities and high selectivity toward CB2. Our work indicates that octahedral organoruthenium scaffolds may be advantageous for targeting the large and hydrophobic binding pockets and that the reverse docking approach may facilitate the discovery of novel privileged scaffolds, such as organometallic complexes, for exploring chemical space in lead discovery.
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Affiliation(s)
- Qing Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Xuegang Fu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yuting Yan
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Tao Liu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Yuting Xie
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Xiaoqing Song
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yu Zhou
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Min Xu
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Ping Wang
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Peng Fu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Jianhui Huang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Niu Huang
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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13
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Lamens A, Bajorath J. Generation of Molecular Counterfactuals for Explainable Machine Learning Based on Core-Substituent Recombination. ChemMedChem 2024; 19:e202300586. [PMID: 37983655 DOI: 10.1002/cmdc.202300586] [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: 10/27/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 11/22/2023]
Abstract
The use of black box machine learning models whose decisions cannot be understood limits the acceptance of predictions in interdisciplinary research and camouflages artificial learning characteristics leading to predictions for other than anticipated reasons. Consequently, there is increasing interest in explainable artificial intelligence to rationalize predictions and uncover potential pitfalls. Among others, relevant approaches include feature attribution methods to identify molecular structures determining predictions and counterfactuals (CFs) or contrastive explanations. CFs are defined as variants of test instances with minimal modifications leading to opposing predictions. In medicinal chemistry, CFs have thus far only been little investigated although they are particularly intuitive from a chemical perspective. We introduce a new methodology for the systematic generation of CFs that is centered on well-defined structural analogues of test compounds. The approach is transparent, computationally straightforward, and shown to provide a wealth of CFs for test sets. The method is made freely available.
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Affiliation(s)
- Alec Lamens
- Department of Life Science Informatics and Data Science B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 5/6, 53115, Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics and Data Science B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 5/6, 53115, Bonn, Germany
- Lamarr Institute for Machine Learning and Artificial Intelligence, Rheinische Friedrich-Wilhelms-Universität Bonn, Friedrich-Hirzebruch-Allee 5/6, 53115, Bonn, Germany
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14
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Kralj S, Jukič M, Bahun M, Kranjc L, Kolarič A, Hodošček M, Ulrih NP, Bren U. Identification of Triazolopyrimidinyl Scaffold SARS-CoV-2 Papain-Like Protease (PL pro) Inhibitor. Pharmaceutics 2024; 16:169. [PMID: 38399230 PMCID: PMC10893172 DOI: 10.3390/pharmaceutics16020169] [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: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
The global impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its companion disease, COVID-19, has reminded us of the importance of basic coronaviral research. In this study, a comprehensive approach using molecular docking, in vitro assays, and molecular dynamics simulations was applied to identify potential inhibitors for SARS-CoV-2 papain-like protease (PLpro), a key and underexplored viral enzyme target. A focused protease inhibitor library was initially created and molecular docking was performed using CmDock software (v0.2.0), resulting in the selection of hit compounds for in vitro testing on the isolated enzyme. Among them, compound 372 exhibited promising inhibitory properties against PLpro, with an IC50 value of 82 ± 34 μM. The compound also displayed a new triazolopyrimidinyl scaffold not yet represented within protease inhibitors. Molecular dynamics simulations demonstrated the favorable binding properties of compound 372. Structural analysis highlighted its key interactions with PLpro, and we stress its potential for further optimization. Moreover, besides compound 372 as a candidate for PLpro inhibitor development, this study elaborates on the PLpro binding site dynamics and provides a valuable contribution for further efforts in pan-coronaviral PLpro inhibitor development.
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Affiliation(s)
- Sebastjan Kralj
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, SI-2000 Maribor, Slovenia
| | - Marko Jukič
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, SI-2000 Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška Ulica 8, SI-6000 Koper, Slovenia
- Institute of Enviormental Protection and Sensors, Beloruska Ulica 7, SI-2000 Maribor, Slovenia
| | - Miha Bahun
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Luka Kranjc
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
- National Institute of Biology, Večna Pot 111, SI-1000 Ljubljana, Slovenia
| | - Anja Kolarič
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, SI-2000 Maribor, Slovenia
| | - Milan Hodošček
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Nataša Poklar Ulrih
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Urban Bren
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, SI-2000 Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška Ulica 8, SI-6000 Koper, Slovenia
- Institute of Enviormental Protection and Sensors, Beloruska Ulica 7, SI-2000 Maribor, Slovenia
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15
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Chen C, Wu Y, Wang ST, Berisha N, Manzari MT, Vogt K, Gang O, Heller DA. Fragment-based drug nanoaggregation reveals drivers of self-assembly. Nat Commun 2023; 14:8340. [PMID: 38097573 PMCID: PMC10721832 DOI: 10.1038/s41467-023-43560-0] [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: 03/23/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
Drug nanoaggregates are particles that can deleteriously cause false positive results during drug screening efforts, but alternatively, they may be used to improve pharmacokinetics when developed for drug delivery purposes. The structural features of molecules that drive nanoaggregate formation remain elusive, however, and the prediction of intracellular aggregation and rational design of nanoaggregate-based carriers are still challenging. We investigate nanoaggregate self-assembly mechanisms using small molecule fragments to identify the critical molecular forces that contribute to self-assembly. We find that aromatic groups and hydrogen bond acceptors/donors are essential for nanoaggregate formation, suggesting that both π-π stacking and hydrogen bonding are drivers of nanoaggregation. We apply structure-assembly-relationship analysis to the drug sorafenib and discover that nanoaggregate formation can be predicted entirely using drug fragment substructures. We also find that drug nanoaggregates are stabilized in an amorphous core-shell structure. These findings demonstrate that rational design can address intracellular aggregation and pharmacologic/delivery challenges in conventional and fragment-based drug development processes.
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Affiliation(s)
- Chen Chen
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, 10065, USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - You Wu
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, 10065, USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Shih-Ting Wang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Naxhije Berisha
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- The Graduate Center of the City University of New York, New York, NY, 10016, USA
- Department of Chemistry, Hunter College, City University of New York, New York, 10065, USA
| | - Mandana T Manzari
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Kaleidoscope Technologies, Inc., New York, NY, 10003, USA
| | - Kristen Vogt
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, 10065, USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Oleg Gang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, 10027, USA
| | - Daniel A Heller
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, 10065, USA.
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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16
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Janela T, Bajorath J. Anatomy of Potency Predictions Focusing on Structural Analogues with Increasing Potency Differences Including Activity Cliffs. J Chem Inf Model 2023; 63:7032-7044. [PMID: 37943257 DOI: 10.1021/acs.jcim.3c01530] [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: 11/10/2023]
Abstract
Potency predictions are popular in compound design and optimization but are complicated by intrinsic limitations. Moreover, even for nonlinear methods, activity cliffs (ACs, formed by structural analogues with large potency differences) represent challenging test cases for compound potency predictions. We have devised a new test system for potency predictions, including AC compounds, that is based on partitioned matched molecular pairs (MMP) and makes it possible to monitor prediction accuracy at the level of analogue pairs with increasing potency differences. The results of systematic predictions using different machine learning and control methods on MMP-based data sets revealed increasing prediction errors when potency differences between corresponding training and test compounds increased, including large prediction errors for AC compounds. At the global level, these prediction errors were not apparent due to the statistical dominance of analogue pairs with small potency differences. Test compounds from such pairs were accurately predicted and determined the observed global prediction accuracy. Shapley value analysis, an explainable artificial intelligence approach, was applied to identify structural features determining potency predictions using different methods. The analysis revealed that numerical predictions of different regression models were determined by features that were shared by MMP partner compounds or absent in these compounds, with opposing effects. These findings provided another rationale for accurate predictions of similar potency values for structural analogues and failures in predicting the potency of AC compounds.
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Affiliation(s)
- Tiago Janela
- Department of Life Science Informatics and Data Science, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 5/6, D-53115 Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics and Data Science, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 5/6, D-53115 Bonn, Germany
- Lamarr Institute for Machine Learning and Artificial Intelligence, Rheinische Friedrich-Wilhelms-Universität Bonn, Friedrich-Hirzebruch-Allee 5/6, D-53115 Bonn, Germany
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17
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Subakaeva E, Zelenikhin P, Sokolova E, Pergat A, Aleksandrova Y, Shurpik D, Stoikov I. The Synthesis and Antibacterial Properties of Pillar[5]arene with Streptocide Fragments. Pharmaceutics 2023; 15:2660. [PMID: 38140001 PMCID: PMC10747162 DOI: 10.3390/pharmaceutics15122660] [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: 10/12/2023] [Revised: 11/07/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
The growing problem of bacterial resistance to antimicrobials actualizes the development of new approaches to solve this challenge. Supramolecular chemistry tools can overcome the limited bacterial resistance and side effects of classical sulfonamides that hinder their use in therapy. Here, we synthesized a number of pillar[5]arenes functionalized with different substituents, determined their ability to self-association using DLS, and characterized antimicrobial properties against S. typhimurium, K. pneumoniae, P. aeruginosa, S. epidermidis, S. aureus via a resazurin test. Biofilm prevention concentration was calculated for an agent with established antimicrobial activity by the crystal-violet staining method. We evaluated the mutagenicity of the macrocycle using the Ames test and its ability to affect the viability of A549 and LEK cells in the MTT-test. It was shown that macrocycle functionalized with sulfonamide residues exhibited antimicrobial activity an order higher than pure streptocide and also revealed the ability to prevent biofilm formation of S. aureus and P. aeruginosa. The compound did not show mutagenic activity and exhibited low toxicity to eukaryotic cells. The obtained results allow considering modification of the macrocyclic platforms with classic antimicrobials as an opportunity to give them a "second life" and return to practice with improved properties.
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Affiliation(s)
- Evgenia Subakaeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya, 18, 420008 Kazan, Russia; (E.S.); (E.S.)
| | - Pavel Zelenikhin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya, 18, 420008 Kazan, Russia; (E.S.); (E.S.)
| | - Evgenia Sokolova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya, 18, 420008 Kazan, Russia; (E.S.); (E.S.)
| | - Arina Pergat
- A.M. Butlerov Chemical Institute, Kazan Federal University, Kremlevskaya, 29, 420008 Kazan, Russia; (A.P.); (Y.A.); (D.S.)
| | - Yulia Aleksandrova
- A.M. Butlerov Chemical Institute, Kazan Federal University, Kremlevskaya, 29, 420008 Kazan, Russia; (A.P.); (Y.A.); (D.S.)
| | - Dmitriy Shurpik
- A.M. Butlerov Chemical Institute, Kazan Federal University, Kremlevskaya, 29, 420008 Kazan, Russia; (A.P.); (Y.A.); (D.S.)
| | - Ivan Stoikov
- A.M. Butlerov Chemical Institute, Kazan Federal University, Kremlevskaya, 29, 420008 Kazan, Russia; (A.P.); (Y.A.); (D.S.)
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18
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Glenn IS, Hall LN, Khalid MM, Ott M, Shoichet BK. Colloidal aggregation confounds cell-based Covid-19 antiviral screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.27.564435. [PMID: 37961552 PMCID: PMC10634915 DOI: 10.1101/2023.10.27.564435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Colloidal aggregation is one of the largest contributors to false-positives in early drug discovery and chemical biology. Much work has focused on its impact on pure-protein screens; here we consider aggregations role in cell-based infectivity assays in Covid-19 drug repurposing. We began by investigating the potential aggregation of 41 drug candidates reported as SARs-CoV-2 entry inhibitors. Of these, 17 formed colloidal-particles by dynamic light scattering and exhibited detergent-dependent enzyme inhibition. To evaluate antiviral efficacy of the drugs in cells we used spike pseudotyped lentivirus and pre-saturation of the colloids with BSA. The antiviral potency of the aggregators was diminished by at least 10-fold and often entirely eliminated in the presence of BSA, suggesting antiviral activity can be attributed to the non-specific nature of the colloids. In confocal microscopy, the aggregates induced fluorescent puncta of labeled spike protein, consistent with sequestration of the protein on the colloidal particles. Addition of either non-ionic detergent or of BSA disrupted these puncta. These observations suggest that colloidal aggregation is common among cell-based anti-viral drug repurposing, and perhaps cell-based assays more broadly, and offers rapid counter-screens to detect and eliminate these artifacts, allowing the community invest resources in compounds with true potential as a Covid-19 therapeutic.
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Affiliation(s)
- Isabella S Glenn
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Lauren N Hall
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Mir M Khalid
- Gladstone Institutes, San Francisco, California, United States
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States
| | - Melanie Ott
- Gladstone Institutes, San Francisco, California, United States
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States
- Chan Zuckerberg Biohub, San Francisco, California, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, CA, USA
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19
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Ahmed DM, Sanders DAR. Unraveling the unexpected aggregation behavior of Pyrazole-Based compounds Targeting Mycobacterium tuberculosis UDP-Galactopyranose mutase. Bioorg Med Chem 2023; 94:117466. [PMID: 37722298 DOI: 10.1016/j.bmc.2023.117466] [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: 05/16/2023] [Revised: 07/24/2023] [Accepted: 09/04/2023] [Indexed: 09/20/2023]
Abstract
A pyrazole-based compound, MS208, was previously identified as an inhibitor of UDP-Galactopyranose Mutase from Mycobacterium tuberculosis (MtUGM). Targeting this enzyme is a novel therapeutic strategy for the development of new antituberculosis agents because MtUGM is an essential enzyme for the bacterial cell wall synthesis and it is not present in human. It was proposed that MS208 targets an allosteric site in MtUGM as MS208 followed a mixed inhibition model. DA10, an MS208 analogue, showed competitive inhibition rather than mixed inhibition. In this paper, we have used an integrated biophysical approach, including thermal shift assays, dynamic light scattering and nuclear magnetic resonance experiments, to show that MS208 and many analogues displayed unexpected aggregation behavior against MtUGM.
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Affiliation(s)
- Dalia M Ahmed
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan, S7N 5C9, Canada; Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia 11566, Cairo, Egypt
| | - David A R Sanders
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan, S7N 5C9, Canada.
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20
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Eastman RT, Rusinova R, Herold KF, Huang XP, Dranchak P, Voss TC, Rana S, Shrimp JH, White AD, Hemmings HC, Roth BL, Inglese J, Andersen OS, Dahlin JL. Nonspecific membrane bilayer perturbations by ivermectin underlie SARS-CoV-2 in vitro activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563088. [PMID: 37961094 PMCID: PMC10634736 DOI: 10.1101/2023.10.23.563088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Since it was proposed as a potential host-directed antiviral agent for SARS-CoV-2, the antiparasitic drug ivermectin has been investigated thoroughly in clinical trials, which have provided insufficient support for its clinical efficacy. To examine the potential for ivermectin to be repurposed as an antiviral agent, we therefore undertook a series of preclinical studies. Consistent with early reports, ivermectin decreased SARS-CoV-2 viral burden in in vitro models at low micromolar concentrations, five- to ten-fold higher than the reported toxic clinical concentration. At similar concentrations, ivermectin also decreased cell viability and increased biomarkers of cytotoxicity and apoptosis. Further mechanistic and profiling studies revealed that ivermectin nonspecifically perturbs membrane bilayers at the same concentrations where it decreases the SARS-CoV-2 viral burden, resulting in nonspecific modulation of membrane-based targets such as G-protein coupled receptors and ion channels. These results suggest that a primary molecular mechanism for the in vitro antiviral activity of ivermectin may be nonspecific membrane perturbation, indicating that ivermectin is unlikely to be translatable into a safe and effective antiviral agent. These results and experimental workflow provide a useful paradigm for performing preclinical studies on (pandemic-related) drug repurposing candidates.
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Affiliation(s)
- Richard T. Eastman
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Radda Rusinova
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Karl F. Herold
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Patricia Dranchak
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Ty C. Voss
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Sandeep Rana
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Jonathan H. Shrimp
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Alex D. White
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Hugh C. Hemmings
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Bryan L. Roth
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Division of Chemical Biology and Medicinal Chemistry, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - James Inglese
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
- Metabolic Medicine Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Olaf S. Andersen
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Jayme L. Dahlin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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21
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Janela T, Bajorath J. Rationalizing general limitations in assessing and comparing methods for compound potency prediction. Sci Rep 2023; 13:17816. [PMID: 37857835 PMCID: PMC10587074 DOI: 10.1038/s41598-023-45086-3] [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: 07/07/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023] Open
Abstract
Compound potency predictions play a major role in computational drug discovery. Predictive methods are typically evaluated and compared in benchmark calculations that are widely applied. Previous studies have revealed intrinsic limitations of potency prediction benchmarks including very similar performance of increasingly complex machine learning methods and simple controls and narrow error margins separating machine learning from randomized predictions. However, origins of these limitations are currently unknown. We have carried out an in-depth analysis of potential reasons leading to artificial outcomes of potency predictions using different methods. Potency predictions on activity classes typically used in benchmark settings were found to be determined by compounds with intermediate potency close to median values of the compound data sets. The potency of these compounds was consistently predicted with high accuracy, without the need for learning, which dominated the results of benchmark calculations, regardless of the activity classes used. Taken together, our findings provide a clear rationale for general limitations of compound potency benchmark predictions and a basis for the design of alternative test systems for methodological comparisons.
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Affiliation(s)
- Tiago Janela
- B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Department of Life Science Informatics and Data Science, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 5/6, 53115, Bonn, Germany
| | - Jürgen Bajorath
- B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Department of Life Science Informatics and Data Science, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 5/6, 53115, Bonn, Germany.
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22
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Tian Y, Zhang Z, Yan A. Discovering the Active Ingredients of Medicine and Food Homologous Substances for Inhibiting the Cyclooxygenase-2 Metabolic Pathway by Machine Learning Algorithms. Molecules 2023; 28:6782. [PMID: 37836625 PMCID: PMC10574661 DOI: 10.3390/molecules28196782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Cyclooxygenase-2 (COX-2) and microsomal prostaglandin E2 synthase (mPGES-1) are two key targets in anti-inflammatory therapy. Medicine and food homology (MFH) substances have both edible and medicinal properties, providing a valuable resource for the development of novel, safe, and efficient COX-2 and mPGES-1 inhibitors. In this study, we collected active ingredients from 503 MFH substances and constructed the first comprehensive MFH database containing 27,319 molecules. Subsequently, we performed Murcko scaffold analysis and K-means clustering to deeply analyze the composition of the constructed database and evaluate its structural diversity. Furthermore, we employed four supervised machine learning algorithms, including support vector machine (SVM), random forest (RF), deep neural networks (DNNs), and eXtreme Gradient Boosting (XGBoost), as well as ensemble learning, to establish 640 classification models and 160 regression models for COX-2 and mPGES-1 inhibitors. Among them, ModelA_ensemble_RF_1 emerged as the optimal classification model for COX-2 inhibitors, achieving predicted Matthews correlation coefficient (MCC) values of 0.802 and 0.603 on the test set and external validation set, respectively. ModelC_RDKIT_SVM_2 was identified as the best regression model based on COX-2 inhibitors, with root mean squared error (RMSE) values of 0.419 and 0.513 on the test set and external validation set, respectively. ModelD_ECFP_SVM_4 stood out as the top classification model for mPGES-1 inhibitors, attaining MCC values of 0.832 and 0.584 on the test set and external validation set, respectively. The optimal regression model for mPGES-1 inhibitors, ModelF_3D_SVM_1, exhibited predictive RMSE values of 0.253 and 0.35 on the test set and external validation set, respectively. Finally, we proposed a ligand-based cascade virtual screening strategy, which integrated the well-performing supervised machine learning models with unsupervised learning: the self-organized map (SOM) and molecular scaffold analysis. Using this virtual screening workflow, we discovered 10 potential COX-2 inhibitors and 15 potential mPGES-1 inhibitors from the MFH database. We further verified candidates by molecular docking, investigated the interaction of the candidate molecules upon binding to COX-2 or mPGES-1. The constructed comprehensive MFH database has laid a solid foundation for the further research and utilization of the MFH substances. The series of well-performing machine learning models can be employed to predict the COX-2 and mPGES-1 inhibitory capabilities of unknown compounds, thereby aiding in the discovery of anti-inflammatory medications. The COX-2 and mPGES-1 potential inhibitor molecules identified through the cascade virtual screening approach provide insights and references for the design of highly effective and safe novel anti-inflammatory drugs.
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Affiliation(s)
- Yujia Tian
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Beijing 100029, China; (Y.T.); (Z.Z.)
| | - Zhixing Zhang
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Beijing 100029, China; (Y.T.); (Z.Z.)
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Aixia Yan
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Beijing 100029, China; (Y.T.); (Z.Z.)
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23
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Santos LH, Rocha REO, Dias DL, Ribeiro BMRM, Serafim MSM, Abrahão JS, Ferreira RS. Evaluating Known Zika Virus NS2B-NS3 Protease Inhibitor Scaffolds via In Silico Screening and Biochemical Assays. Pharmaceuticals (Basel) 2023; 16:1319. [PMID: 37765127 PMCID: PMC10537087 DOI: 10.3390/ph16091319] [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: 08/04/2023] [Revised: 09/04/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
The NS2B-NS3 protease (NS2B-NS3pro) is regarded as an interesting molecular target for drug design, discovery, and development because of its essential role in the Zika virus (ZIKV) cycle. Although no NS2B-NS3pro inhibitors have reached clinical trials, the employment of drug-like scaffolds can facilitate the screening process for new compounds. In this study, we performed a combination of ligand-based and structure-based in silico methods targeting two known non-peptide small-molecule scaffolds with micromolar inhibitory activity against ZIKV NS2B-NS3pro by a virtual screening (VS) of promising compounds. Based on these two scaffolds, we selected 13 compounds from an initial library of 509 compounds from ZINC15's similarity search. These compounds exhibited structural modifications that are distinct from previously known compounds yet keep pertinent features for binding. Despite promising outcomes from molecular docking and initial enzymatic assays against NS2B-NS3pro, confirmatory assays with a counter-screening enzyme revealed an artifactual inhibition of the assessed compounds. However, we report two compounds, 9 and 11, that exhibited antiviral properties at a concentration of 50 μM in cellular-based assays. Overall, this study provides valuable insights into the ongoing research on anti-ZIKV compounds to facilitate and improve the development of new inhibitors.
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Affiliation(s)
- Lucianna H. Santos
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| | - Rafael E. O. Rocha
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| | - Diego L. Dias
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil (M.S.M.S.)
| | - Beatriz M. R. M. Ribeiro
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| | - Mateus Sá M. Serafim
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil (M.S.M.S.)
| | - Jônatas S. Abrahão
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil (M.S.M.S.)
| | - Rafaela S. Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
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24
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Guedes RA, Grilo JH, Carvalho AN, Fernandes PMP, Ressurreição AS, Brito V, Santos AO, Silvestre S, Gallerani E, Gama MJ, Gavioli R, Salvador JAR, Guedes RC. New Scaffolds of Proteasome Inhibitors: Boosting Anticancer Potential by Exploiting the Synergy of In Silico and In Vitro Methodologies. Pharmaceuticals (Basel) 2023; 16:1096. [PMID: 37631011 PMCID: PMC10458307 DOI: 10.3390/ph16081096] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
Cancer is a complex multifactorial disease whose pathophysiology involves multiple metabolic pathways, including the ubiquitin-proteasome system, for which several proteasome inhibitors have already been approved for clinical use. However, the resistance to existing therapies and the occurrence of severe adverse effects is still a concern. The purpose of this study was the discovery of novel scaffolds of proteasome inhibitors with anticancer activity, aiming to overcome the limitations of the existing proteasome inhibitors. Thus, a structure-based virtual screening protocol was developed using the structure of the human 20S proteasome, and 246 compounds from virtual databases were selected for in vitro evaluation, namely proteasome inhibition assays and cell viability assays. Compound 4 (JHG58) was shortlisted as the best hit compound based on its potential in terms of proteasome inhibitory activity and its ability to induce cell death (both with IC50 values in the low micromolar range). Molecular docking studies revealed that compound 4 interacts with key residues, namely with the catalytic Thr1, Ala20, Thr21, Lys33, and Asp125 at the chymotrypsin-like catalytic active site. The hit compound is a good candidate for additional optimization through a hit-to-lead campaign.
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Affiliation(s)
- Romina A. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Jorge H. Grilo
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
| | - Andreia N. Carvalho
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
| | - Pedro M. P. Fernandes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Ana S. Ressurreição
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
| | - Vanessa Brito
- Health Sciences Research Centre (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal; (V.B.); (A.O.S.); (S.S.)
| | - Adriana O. Santos
- Health Sciences Research Centre (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal; (V.B.); (A.O.S.); (S.S.)
| | - Samuel Silvestre
- Health Sciences Research Centre (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal; (V.B.); (A.O.S.); (S.S.)
| | - Eleonora Gallerani
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy;
| | - Maria João Gama
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
| | - Riccardo Gavioli
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy;
| | - Jorge A. R. Salvador
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
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25
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Azagury DM, Gluck BF, Harris Y, Avrutin Y, Niezni D, Sason H, Shamay Y. Prediction of cancer nanomedicines self-assembled from meta-synergistic drug pairs. J Control Release 2023; 360:418-432. [PMID: 37406821 DOI: 10.1016/j.jconrel.2023.06.040] [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: 10/27/2022] [Revised: 06/07/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023]
Abstract
Combination therapy is widely used in cancer medicine due to the benefits of drug synergy and the reduction of acquired resistance. To minimize emergent toxicities, nanomedicines containing drug combinations are being developed, and they have shown encouraging results. However, developing multi-drug loaded nanoparticles is highly complex and lacks predictability. Previously, it was shown that single drugs can self-assemble with near-infrared dye, IR783, to form cancer-targeted nanoparticles. A structure-based predictive model showed that only 4% of the drug space self-assembles with IR783. Here, we mapped the self-assembly outcomes of 77 small molecule drugs and drug pairs with IR783. We found that the small molecule drug space can be divided into five types, and type-1 drugs self-assemble with three out of four possible drug types that do not form stable nanoparticles. To predict the self-assembly outcome of any drug pair, we developed a machine learning model based on decision trees, which was trained and tested with F1-scores of 89.3% and 87.2%, respectively. We used literature text mining to capture drug pairs with biological synergy together with synergistic chemical self-assembly and generated a database with 1985 drug pairs for 70 cancers. We developed an online search tool to identify cancer-specific, meta-synergistic drug pairs (both chemical and biological synergism) and validated three different pairs in vitro. Lastly, we discovered a novel meta-synergistic pair, bortezomib-cabozantinib, which formed stable nanoparticles with improved biodistribution, efficacy, and reduced toxicity, even over single drugs, in an in vivo model of head and neck cancer.
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Affiliation(s)
- Dana Meron Azagury
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Ben Friedmann Gluck
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel; Faculty of Electrical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yuval Harris
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yulia Avrutin
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Danna Niezni
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Hagit Sason
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yosi Shamay
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel.
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26
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Kerber PJ, Nuñez R, Jensen DR, Zhou AL, Peterson FC, Hill RB, Volkman BF, Smith BC. Fragment-based screening by protein-detected NMR spectroscopy. Methods Enzymol 2023; 690:285-310. [PMID: 37858532 PMCID: PMC10657026 DOI: 10.1016/bs.mie.2023.06.018] [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] [Indexed: 10/21/2023]
Abstract
Fragment-based drug discovery (FBDD) identifies low molecular weight compounds that can be developed into ligands with high affinity and selectivity for therapeutic targets. Screening fragment libraries (<10,000 molecules) with biophysical techniques against macromolecules provides information about novel chemical spaces that bind the macromolecule and scaffolds that can be modified to increase potency. A fragment-screening pipeline requires a standardized protocol for target selection, library assembly and maintenance, library screening, and hit validation to ensure hit integrity. Herein, the fundamental aspects of a fragment screening pipeline-focusing on protein-detected NMR data collection and analysis-are discussed in detail for researchers to use as a resource in their FBDD projects. Selected screening targets must undergo rigorous stability and buffer testing by NMR spectroscopy to ensure the protein structure is stable for the entire screen. Biophysical instrumentation that rapidly measures protein thermostability is helpful in buffer screening. Molecules in fragment libraries are analyzed computationally and physically, stored at appropriate temperatures, and multiplexed in well plates for library conservation. The screening protocol is streamlined using liquid handling robotics for sample preparation and customized Python scripts for protein-detected NMR data analysis. Molecules identified from the screen are titrated to determine their binding site(s) and Kd values and confirmed with an orthogonal biophysical assay. This detailed FBDD screening pipeline developed by the Program in Chemical Biology at the Medical College of Wisconsin has successfully screened many unrelated target proteins to identified novel molecules that selectively bind to these target proteins.
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Affiliation(s)
- Paul J Kerber
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - Raymundo Nuñez
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - Davin R Jensen
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - Angela L Zhou
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - R Blake Hill
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States.
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States.
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27
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Lamens A, Bajorath J. Explaining Multiclass Compound Activity Predictions Using Counterfactuals and Shapley Values. Molecules 2023; 28:5601. [PMID: 37513472 PMCID: PMC10383571 DOI: 10.3390/molecules28145601] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Most machine learning (ML) models produce black box predictions that are difficult, if not impossible, to understand. In pharmaceutical research, black box predictions work against the acceptance of ML models for guiding experimental work. Hence, there is increasing interest in approaches for explainable ML, which is a part of explainable artificial intelligence (XAI), to better understand prediction outcomes. Herein, we have devised a test system for the rationalization of multiclass compound activity prediction models that combines two approaches from XAI for feature relevance or importance analysis, including counterfactuals (CFs) and Shapley additive explanations (SHAP). For compounds with different single- and dual-target activities, we identified small compound modifications that induce feature changes inverting class label predictions. In combination with feature mapping, CFs and SHAP value calculations provide chemically intuitive explanations for model decisions.
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Affiliation(s)
- Alec Lamens
- Department of Life Science Informatics, B-IT, LIMES Program, Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 5/6, D-53115 Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program, Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 5/6, D-53115 Bonn, Germany
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28
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Primavera E, Palazzotti D, Barreca ML, Astolfi A. Computer-Aided Identification of Kinase-Targeted Small Molecules for Cancer: A Review on AKT Protein. Pharmaceuticals (Basel) 2023; 16:993. [PMID: 37513905 PMCID: PMC10384952 DOI: 10.3390/ph16070993] [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: 06/13/2023] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
AKT (also known as PKB) is a serine/threonine kinase that plays a pivotal regulatory role in the PI3K/AKT/mTOR signaling pathway. Dysregulation of AKT activity, especially its hyperactivation, is closely associated with the development of various human cancers and resistance to chemotherapy. Over the years, a wide array of AKT inhibitors has been discovered through experimental and computational approaches. In this regard, herein we present a comprehensive overview of AKT inhibitors identified using computer-assisted drug design methodologies (including docking-based and pharmacophore-based virtual screening, machine learning, and quantitative structure-activity relationships) and successfully validated small molecules endowed with anticancer activity. Thus, this review provides valuable insights to support scientists focused on AKT inhibition for cancer treatment and suggests untapped directions for future computer-aided drug discovery efforts.
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Affiliation(s)
- Erika Primavera
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, 06123 Perugia, Italy
| | - Deborah Palazzotti
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, 06123 Perugia, Italy
| | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, 06123 Perugia, Italy
| | - Andrea Astolfi
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, 06123 Perugia, Italy
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29
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Greenberg ZF, Graim KS, He M. Towards artificial intelligence-enabled extracellular vesicle precision drug delivery. Adv Drug Deliv Rev 2023:114974. [PMID: 37356623 DOI: 10.1016/j.addr.2023.114974] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
Extracellular Vesicles (EVs), particularly exosomes, recently exploded into nanomedicine as an emerging drug delivery approach due to their superior biocompatibility, circulating stability, and bioavailability in vivo. However, EV heterogeneity makes molecular targeting precision a critical challenge. Deciphering key molecular drivers for controlling EV tissue targeting specificity is in great need. Artificial intelligence (AI) brings powerful prediction ability for guiding the rational design of engineered EVs in precision control for drug delivery. This review focuses on cutting-edge nano-delivery via integrating large-scale EV data with AI to develop AI-directed EV therapies and illuminate the clinical translation potential. We briefly review the current status of EVs in drug delivery, including the current frontier, limitations, and considerations to advance the field. Subsequently, we detail the future of AI in drug delivery and its impact on precision EV delivery. Our review discusses the current universal challenge of standardization and critical considerations when using AI combined with EVs for precision drug delivery. Finally, we will conclude this review with a perspective on future clinical translation led by a combined effort of AI and EV research.
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Affiliation(s)
- Zachary F Greenberg
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida, 32610, USA
| | - Kiley S Graim
- Department of Computer & Information Science & Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, Florida, 32610, USA
| | - Mei He
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida, 32610, USA.
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30
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Singh I, Li F, Fink EA, Chau I, Li A, Rodriguez-Hernández A, Glenn I, Zapatero-Belinchón FJ, Rodriguez ML, Devkota K, Deng Z, White K, Wan X, Tolmachova NA, Moroz YS, Kaniskan HÜ, Ott M, García-Sastre A, Jin J, Fujimori DG, Irwin JJ, Vedadi M, Shoichet BK. Structure-Based Discovery of Inhibitors of the SARS-CoV-2 Nsp14 N7-Methyltransferase. J Med Chem 2023; 66:7785-7803. [PMID: 37294077 PMCID: PMC10374283 DOI: 10.1021/acs.jmedchem.2c02120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
An under-explored target for SARS-CoV-2 is the S-adenosyl methionine (SAM)-dependent methyltransferase Nsp14, which methylates the N7-guanosine of viral RNA at the 5'-end, allowing the virus to evade host immune response. We sought new Nsp14 inhibitors with three large library docking strategies. First, up to 1.1 billion lead-like molecules were docked against the enzyme's SAM site, leading to three inhibitors with IC50 values from 6 to 50 μM. Second, docking a library of 16 million fragments revealed 9 new inhibitors with IC50 values from 12 to 341 μM. Third, docking a library of 25 million electrophiles to covalently modify Cys387 revealed 7 inhibitors with IC50 values from 3.5 to 39 μM. Overall, 32 inhibitors encompassing 11 chemotypes had IC50 values < 50 μM and 5 inhibitors in 4 chemotypes had IC50 values < 10 μM. These molecules are among the first non-SAM-like inhibitors of Nsp14, providing starting points for future optimization.
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Affiliation(s)
- Isha Singh
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Elissa A Fink
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Graduate Program in Biophysics, University of California San Francisco, San Francisco, California 94143, United States
| | - Irene Chau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Alice Li
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Annía Rodriguez-Hernández
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Isabella Glenn
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
| | | | - M Luis Rodriguez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Kanchan Devkota
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Zhijie Deng
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Kris White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Xiaobo Wan
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
| | - Nataliya A Tolmachova
- Enamine Ltd, Kyïv 02094, Ukraine
- Institute of Bioorganic Chemistry and Petrochemistry, National Ukrainian Academy of Science, Kyïv 02660, Ukraine
| | - Yurii S Moroz
- National Taras Shevchenko University of Kyïv, Kyïv 01601, Ukraine
- Chemspace, Riga LV-1082, Latvia
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Melanie Ott
- Gladstone Institutes, San Francisco, California 94158, United States
- QBI COVID-19 Research Group (QCRG), San Francisco, California 94158, United States
- Department of Medicine, University of California, San Francisco, San Francisco, California 94158, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- QBI COVID-19 Research Group (QCRG), San Francisco, California 94158, United States
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- QBI COVID-19 Research Group (QCRG), San Francisco, California 94158, United States
| | - Danica Galonić Fujimori
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
- QBI COVID-19 Research Group (QCRG), San Francisco, California 94158, United States
| | - John J Irwin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- QBI COVID-19 Research Group (QCRG), San Francisco, California 94158, United States
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- QBI COVID-19 Research Group (QCRG), San Francisco, California 94158, United States
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- QBI COVID-19 Research Group (QCRG), San Francisco, California 94158, United States
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31
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Lyu J, Irwin JJ, Shoichet BK. Modeling the expansion of virtual screening libraries. Nat Chem Biol 2023; 19:712-718. [PMID: 36646956 PMCID: PMC10243288 DOI: 10.1038/s41589-022-01234-w] [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] [Received: 08/01/2022] [Accepted: 11/22/2022] [Indexed: 01/17/2023]
Abstract
Recently, 'tangible' virtual libraries have made billions of molecules readily available. Prioritizing these molecules for synthesis and testing demands computational approaches, such as docking. Their success may depend on library diversity, their similarity to bio-like molecules and how receptor fit and artifacts change with library size. We compared a library of 3 million 'in-stock' molecules with billion-plus tangible libraries. The bias toward bio-like molecules in the tangible library decreases 19,000-fold versus those 'in-stock'. Similarly, thousands of high-ranking molecules, including experimental actives, from five ultra-large-library docking campaigns are also dissimilar to bio-like molecules. Meanwhile, better-fitting molecules are found as the library grows, with the score improving log-linearly with library size. Finally, as library size increases, so too do rare molecules that rank artifactually well. Although the nature of these artifacts changes from target to target, the expectation of their occurrence does not, and simple strategies can minimize their impact.
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Affiliation(s)
- Jiankun Lyu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - John J Irwin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
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32
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Leong SW, Wang J, Okuda KS, Su Q, Zhang Y, Abas F, Chia SL, Yusoff K. Discovery of a novel dual functional phenylpyrazole-styryl hybrid that induces apoptotic and autophagic cell death in bladder cancer cells. Eur J Med Chem 2023; 254:115335. [PMID: 37098306 DOI: 10.1016/j.ejmech.2023.115335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/27/2023]
Abstract
Unpleasant side effects and resistance development remained the Achilles heel of chemotherapy. Since low tumor-selectivity and monotonous effect of chemotherapy are closely related to such bottleneck, targeting tumor-selective multi-functional anticancer agents may be an ideal strategy in the search of new safer drugs. Herein, we report the discovery of compound 21, a nitro-substituted 1,5-diphenyl-3-styryl-1H-pyrazole that possesses dual functional characteristics. The 2D- and 3D-culture-based studies revealed that 21 not only could induce ROS-independent apoptotic and EGFR/AKT/mTOR-mediated autophagic cell deaths in EJ28 cells simultaneously but also has the ability in inducing cell death at both proliferating and quiescent zones of EJ28 spheroids. The molecular modelling analysis showed that 21 possesses EGFR targeting capability as it forms stable interactions in the EGFR active site. Together with its good safety profile in the zebrafish-based model, the present study showed that 21 is promising and may lead to the discovery of tumor-selective multi-functional anti-cancer agents.
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Affiliation(s)
- Sze Wei Leong
- Department of Chemistry, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
| | - JingJing Wang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Kazuhide Shaun Okuda
- Organogenesis and Cancer Program, Peter MacCallum Cancer Centre, Melbourne, Australia; Department of Anatomy and Physiology and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Qi Su
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Yanmin Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Faridah Abas
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, UPM, Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM, Serdang, Selangor, Malaysia
| | - Suet Lin Chia
- Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM, Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM, Serdang, Selangor, Malaysia; Malaysia Genome and Vaccine Institute (MGVI), National Institute of Biotechnology Malaysia (NIBM), Jalan Bangi, 43000, Kajang, Selangor, Malaysia.
| | - Khatijah Yusoff
- Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM, Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM, Serdang, Selangor, Malaysia; Malaysia Genome and Vaccine Institute (MGVI), National Institute of Biotechnology Malaysia (NIBM), Jalan Bangi, 43000, Kajang, Selangor, Malaysia
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33
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Siemers FM, Bajorath J. Differences in learning characteristics between support vector machine and random forest models for compound classification revealed by Shapley value analysis. Sci Rep 2023; 13:5983. [PMID: 37045972 PMCID: PMC10097675 DOI: 10.1038/s41598-023-33215-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/09/2023] [Indexed: 04/14/2023] Open
Abstract
The random forest (RF) and support vector machine (SVM) methods are mainstays in molecular machine learning (ML) and compound property prediction. We have explored in detail how binary classification models derived using these algorithms arrive at their predictions. To these ends, approaches from explainable artificial intelligence (XAI) are applicable such as the Shapley value concept originating from game theory that we adapted and further extended for our analysis. In large-scale activity-based compound classification using models derived from training sets of increasing size, RF and SVM with the Tanimoto kernel produced very similar predictions that could hardly be distinguished. However, Shapley value analysis revealed that their learning characteristics systematically differed and that chemically intuitive explanations of accurate RF and SVM predictions had different origins.
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Affiliation(s)
- Friederike Maite Siemers
- B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Department of Life Science Informatics and Data Science, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 5/6, 53115, Bonn, Germany
| | - Jürgen Bajorath
- B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Department of Life Science Informatics and Data Science, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 5/6, 53115, Bonn, Germany.
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34
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Janela T, Bajorath J. Large-Scale Predictions of Compound Potency with Original and Modified Activity Classes Reveal General Prediction Characteristics and Intrinsic Limitations of Conventional Benchmarking Calculations. Pharmaceuticals (Basel) 2023; 16:ph16040530. [PMID: 37111287 PMCID: PMC10143224 DOI: 10.3390/ph16040530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 03/27/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
Predicting compound potency is a major task in computational medicinal chemistry, for which machine learning is often applied. This study systematically predicted compound potency values for 367 target-based compound activity classes from medicinal chemistry using a preferred machine learning approach and simple control methods. The predictions produced unexpectedly similar results for different classes and comparably high accuracy for machine learning and simple control models. Based on these findings, the influence of different data set modifications on relative prediction accuracies was explored, including potency range balancing, removal of nearest neighbors, and analog series-based compound partitioning. The predictions were surprisingly resistant to these modifications, leading to only small error margin increases. These findings also show that conventional benchmark settings are unsuitable for directly comparing potency prediction methods.
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Affiliation(s)
- Tiago Janela
- Department of Life Science Informatics and Data Science, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 6, D-53115 Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics and Data Science, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 6, D-53115 Bonn, Germany
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35
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Pognan F, Beilmann M, Boonen HCM, Czich A, Dear G, Hewitt P, Mow T, Oinonen T, Roth A, Steger-Hartmann T, Valentin JP, Van Goethem F, Weaver RJ, Newham P. The evolving role of investigative toxicology in the pharmaceutical industry. Nat Rev Drug Discov 2023; 22:317-335. [PMID: 36781957 PMCID: PMC9924869 DOI: 10.1038/s41573-022-00633-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2022] [Indexed: 02/15/2023]
Abstract
For decades, preclinical toxicology was essentially a descriptive discipline in which treatment-related effects were carefully reported and used as a basis to calculate safety margins for drug candidates. In recent years, however, technological advances have increasingly enabled researchers to gain insights into toxicity mechanisms, supporting greater understanding of species relevance and translatability to humans, prediction of safety events, mitigation of side effects and development of safety biomarkers. Consequently, investigative (or mechanistic) toxicology has been gaining momentum and is now a key capability in the pharmaceutical industry. Here, we provide an overview of the current status of the field using case studies and discuss the potential impact of ongoing technological developments, based on a survey of investigative toxicologists from 14 European-based medium-sized to large pharmaceutical companies.
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Affiliation(s)
- Francois Pognan
- Discovery and Investigative Safety, Novartis Pharma AG, Basel, Switzerland.
| | - Mario Beilmann
- Nonclinical Drug Safety Germany, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Harrie C M Boonen
- Drug Safety, Dept of Exploratory Toxicology, Lundbeck A/S, Valby, Denmark
| | | | - Gordon Dear
- In Vitro In Vivo Translation, GlaxoSmithKline David Jack Centre for Research, Ware, UK
| | - Philip Hewitt
- Chemical and Preclinical Safety, Merck Healthcare KGaA, Darmstadt, Germany
| | - Tomas Mow
- Safety Pharmacology and Early Toxicology, Novo Nordisk A/S, Maaloev, Denmark
| | - Teija Oinonen
- Preclinical Safety, Orion Corporation, Espoo, Finland
| | - Adrian Roth
- Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | | | | | - Freddy Van Goethem
- Predictive, Investigative & Translational Toxicology, Nonclinical Safety, Janssen Research & Development, Beerse, Belgium
| | - Richard J Weaver
- Innovation Life Cycle Management, Institut de Recherches Internationales Servier, Suresnes, France
| | - Peter Newham
- Clinical Pharmacology and Safety Sciences, AstraZeneca R&D, Cambridge, UK.
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36
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Wang X, Hembre EJ, Goldsmith PJ, Beck JP, Svensson KA, Willard FS, Bruns RF. Mutual Cooperativity of Three Allosteric Sites on the Dopamine D1 Receptor. Mol Pharmacol 2023; 103:176-187. [PMID: 36804203 DOI: 10.1124/molpharm.122.000605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022] Open
Abstract
An amine-containing molecule called Compound A has been reported by a group from Bristol-Myers Squibb to act as a positive allosteric modulator (PAM) at the dopamine D1 receptor. We synthesized the more active enantiomer of Compound A (BMS-A1) and compared it with the D1 PAMs DETQ and MLS6585, which are known to bind to intracellular loop 2 and the extracellular portion of transmembrane helix 7, respectively. Results from D1/D5 chimeras indicated that PAM activity of BMS-A1 tracked with the presence of D1 sequence in the N-terminal/extracellular region of the D1 receptor, a unique location compared with either of the other PAMs. In pairwise combinations, BMS-A1 potentiated the small allo-agonist activity of each of the other PAMs, while the triple PAM combination (in the absence of dopamine) produced a cAMP response about 64% of the maximum produced by dopamine. Each of the pairwise PAM combinations produced a much larger leftward shift of the dopamine EC50 than either single PAM alone. All three PAMs in combination produced a 1000-fold leftward shift of the dopamine curve. These results demonstrate the presence of three non-overlapping allosteric sites that cooperatively stabilize the same activated state of the human D1 receptor. SIGNIFICANCE STATEMENT: Deficiencies in dopamine D1 receptor activation are seen in Parkinson disease and other neuropsychiatric disorders. In this study, three positive allosteric modulators of the dopamine D1 receptor were found to bind to distinct and separate sites, interacting synergistically with each other and dopamine, with the triple combination causing a 1000-fold leftward shift of the response to dopamine. These results showcase multiple opportunities to modulate D1 tone and highlight new pharmacological approaches for allosteric modulation of G-protein-coupled receptors.
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Affiliation(s)
- Xushan Wang
- Lilly Research Laboratories, Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana
| | - Erik J Hembre
- Lilly Research Laboratories, Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana
| | - Paul J Goldsmith
- Lilly Research Laboratories, Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana
| | - James P Beck
- Lilly Research Laboratories, Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana
| | - Kjell A Svensson
- Lilly Research Laboratories, Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana
| | - Francis S Willard
- Lilly Research Laboratories, Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana
| | - Robert F Bruns
- Lilly Research Laboratories, Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana
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37
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Li J, Zhou Y, Eelen G, Zhou QT, Feng WB, Labroska V, Ma FF, Lu HP, Dewerchin M, Carmeliet P, Wang MW, Yang DH. A high-throughput screening campaign against PFKFB3 identified potential inhibitors with novel scaffolds. Acta Pharmacol Sin 2023; 44:680-692. [PMID: 36114272 PMCID: PMC9958033 DOI: 10.1038/s41401-022-00989-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 08/23/2022] [Indexed: 11/08/2022] Open
Abstract
The growth of solid tumors depends on tumor vascularization and the endothelial cells (ECs) that line the lumen of blood vessels. ECs generate a large fraction of ATP through glycolysis, and elevation of their glycolytic activity is associated with angiogenic behavior in solid tumors. 6-Phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3) positively regulates glycolysis via fructose-2/6-bisphosphate, the product of its kinase activity. Partial inhibition of glycolysis in tumor ECs by targeting PFKFB3 normalizes the otherwise abnormal tumor vessels, thereby reducing metastasis and improving the outcome of chemotherapy. Although a limited number of tool compounds exist, orally available PFKFB3 inhibitors are unavailable. In this study we conducted a high-throughput screening campaign against the kinase activity of PFKFB3, involving 250,240 chemical compounds. A total of 507 initial hits showing >50% inhibition at 20 µM were identified, 66 of them plus 1 analog from a similarity search consistently displayed low IC50 values (<10 µM). In vitro experiments yielded 22 nontoxic hits that suppressed the tube formation of primary human umbilical vein ECs at 10 µM. Of them, 15 exhibited binding affinity to PFKFB3 in surface plasmon resonance assays, including 3 (WNN0403-E003, WNN1352-H007 and WNN1542-F004) that passed the pan-assay interference compounds screening without warning flags. This study provides potential leads to the development of new PFKFB3 inhibitors.
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Affiliation(s)
- Jie Li
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yan Zhou
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Guy Eelen
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven and Center for Cancer Biology, VIB-KU Leuven, Leuven, 3000, Belgium
| | - Qing-Tong Zhou
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Wen-Bo Feng
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Viktorija Labroska
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fen-Fen Ma
- Department of Pharmacy, Pudong Hospital, Fudan University, Shanghai, 201300, China
| | - Hui-Ping Lu
- Department of Pharmacy, Pudong Hospital, Fudan University, Shanghai, 201300, China
| | - Mieke Dewerchin
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven and Center for Cancer Biology, VIB-KU Leuven, Leuven, 3000, Belgium
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven and Center for Cancer Biology, VIB-KU Leuven, Leuven, 3000, Belgium
| | - Ming-Wei Wang
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Research Center for Deepsea Bioresources, Sanya, 572025, China.
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - De-Hua Yang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Research Center for Deepsea Bioresources, Sanya, 572025, China.
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38
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Guhathakurta P, Rebbeck RT, Denha SA, Keller AR, Carter AL, Atang AE, Svensson B, Thomas DD, Hays TS, Avery AW. Early-phase drug discovery of β-III-spectrin actin-binding modulators for treatment of spinocerebellar ataxia type 5. J Biol Chem 2023; 299:102956. [PMID: 36731793 PMCID: PMC9978034 DOI: 10.1016/j.jbc.2023.102956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/01/2023] Open
Abstract
β-III-Spectrin is a key cytoskeletal protein that localizes to the soma and dendrites of cerebellar Purkinje cells and is required for dendritic arborization and signaling. A spinocerebellar ataxia type 5 L253P mutation in the cytoskeletal protein β-III-spectrin causes high-affinity actin binding. Previously we reported a cell-based fluorescence assay for identification of small-molecule actin-binding modulators of the L253P mutant β-III-spectrin. Here we describe a complementary, in vitro, fluorescence resonance energy transfer (FRET) assay that uses purified L253P β-III-spectrin actin-binding domain (ABD) and F-actin. To validate the assay for high-throughput compatibility, we first confirmed that our 50% FRET signal was responsive to swinholide A, an actin-severing compound, and that this yielded excellent assay quality with a Z' value > 0.77. Second, we screened a 2684-compound library of US Food and Drug Administration-approved drugs. Importantly, the screening identified numerous compounds that decreased FRET between fluorescently labeled L253P ABD and F-actin. The activity and target of multiple Hit compounds were confirmed in orthologous cosedimentation actin-binding assays. Through future medicinal chemistry, the Hit compounds can potentially be developed into a spinocerebellar ataxia type 5-specific therapeutic. Furthermore, our validated FRET-based in vitro high-throughput screening platform is poised for screening large compound libraries for β-III-spectrin ABD modulators.
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Affiliation(s)
- Piyali Guhathakurta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Robyn T Rebbeck
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Sarah A Denha
- Department of Chemistry, Oakland University, Rochester, Michigan, USA
| | - Amanda R Keller
- Department of Chemistry, Oakland University, Rochester, Michigan, USA
| | - Anna L Carter
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Alexandra E Atang
- Department of Chemistry, Oakland University, Rochester, Michigan, USA
| | - Bengt Svensson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - David D Thomas
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Thomas S Hays
- Department of Genetics, Cellular Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Adam W Avery
- Department of Chemistry, Oakland University, Rochester, Michigan, USA.
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39
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Sharma AK, Poddar SM, Chakraborty J, Nayak BS, Kalathil S, Mitra N, Gayathri P, Srinivasan R. A mechanism of salt bridge-mediated resistance to FtsZ inhibitor PC190723 revealed by a cell-based screen. Mol Biol Cell 2023; 34:ar16. [PMID: 36652338 PMCID: PMC10011733 DOI: 10.1091/mbc.e22-12-0538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Bacterial cell division proteins, especially the tubulin homologue FtsZ, have emerged as strong targets for developing new antibiotics. Here, we have utilized the fission yeast heterologous expression system to develop a cell-based assay to screen for small molecules that directly and specifically target the bacterial cell division protein FtsZ. The strategy also allows for simultaneous assessment of the toxicity of the drugs to eukaryotic yeast cells. As a proof-of-concept of the utility of this assay, we demonstrate the effect of the inhibitors sanguinarine, berberine, and PC190723 on FtsZ. Though sanguinarine and berberine affect FtsZ polymerization, they exert a toxic effect on the cells. Further, using this assay system, we show that PC190723 affects Helicobacter pylori FtsZ function and gain new insights into the molecular determinants of resistance to PC190723. On the basis of sequence and structural analysis and site-specific mutations, we demonstrate that the presence of salt bridge interactions between the central H7 helix and β-strands S9 and S10 mediates resistance to PC190723 in FtsZ. The single-step in vivo cell-based assay using fission yeast enabled us to dissect the contribution of sequence-specific features of FtsZ and cell permeability effects associated with bacterial cell envelopes. Thus, our assay serves as a potent tool to rapidly identify novel compounds targeting polymeric bacterial cytoskeletal proteins like FtsZ to understand how they alter polymerization dynamics and address resistance determinants in targets.
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Affiliation(s)
- Ajay Kumar Sharma
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Centre for Interdisciplinary Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Homi Bhabha National Institutes, Anushakti Nagar, Mumbai 400094, India
| | - Sakshi Mahesh Poddar
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Centre for Interdisciplinary Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Homi Bhabha National Institutes, Anushakti Nagar, Mumbai 400094, India
| | - Joyeeta Chakraborty
- Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Bhagyashri Soumya Nayak
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Centre for Interdisciplinary Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Homi Bhabha National Institutes, Anushakti Nagar, Mumbai 400094, India
| | - Srilakshmi Kalathil
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Centre for Interdisciplinary Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Homi Bhabha National Institutes, Anushakti Nagar, Mumbai 400094, India
| | - Nivedita Mitra
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Centre for Interdisciplinary Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Homi Bhabha National Institutes, Anushakti Nagar, Mumbai 400094, India
| | - Pananghat Gayathri
- Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Ramanujam Srinivasan
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Centre for Interdisciplinary Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Homi Bhabha National Institutes, Anushakti Nagar, Mumbai 400094, India
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Wang Q, Meng F, Xie Y, Wang W, Meng Y, Li L, Liu T, Qi J, Ni X, Zheng S, Huang J, Huang N. In Silico Discovery of Small Molecule Modulators Targeting the Achilles' Heel of SARS-CoV-2 Spike Protein. ACS CENTRAL SCIENCE 2023; 9:252-265. [PMID: 36844485 PMCID: PMC9924089 DOI: 10.1021/acscentsci.2c01190] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Indexed: 05/27/2023]
Abstract
The spike protein of SARS-CoV-2 has been a promising target for developing vaccines and therapeutics due to its crucial role in the viral entry process. Previously reported cryogenic electron microscopy (cryo-EM) structures have revealed that free fatty acids (FFA) bind with SARS-CoV-2 spike protein, stabilizing its closed conformation and reducing its interaction with the host cell target in vitro. Inspired by these, we utilized a structure-based virtual screening approach against the conserved FFA-binding pocket to identify small molecule modulators of SARS-CoV-2 spike protein, which helped us identify six hits with micromolar binding affinities. Further evaluation of their commercially available and synthesized analogs enabled us to discover a series of compounds with better binding affinities and solubilities. Notably, our identified compounds exhibited similar binding affinities against the spike proteins of the prototypic SARS-CoV-2 and a currently circulating Omicron BA.4 variant. Furthermore, the cryo-EM structure of the compound SPC-14 bound spike revealed that SPC-14 could shift the conformational equilibrium of the spike protein toward the closed conformation, which is human ACE2 (hACE2) inaccessible. Our identified small molecule modulators targeting the conserved FFA-binding pocket could serve as the starting point for the future development of broad-spectrum COVID-19 intervention treatments.
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Affiliation(s)
- Qing Wang
- School
of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- National
Institute of Biological Sciences, Beijing, Zhongguancun Life Science Park, No. 7 Science Park Road, Beijing 102206, China
| | - Fanhao Meng
- Shuimu
Biosciences, Zhongguancun Life Science Park, No. 7 Science Park Road, Beijing 102206, China
| | - Yuting Xie
- National
Institute of Biological Sciences, Beijing, Zhongguancun Life Science Park, No. 7 Science Park Road, Beijing 102206, China
| | - Wei Wang
- National
Institute of Biological Sciences, Beijing, Zhongguancun Life Science Park, No. 7 Science Park Road, Beijing 102206, China
| | - Yumin Meng
- CAS
Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Linjie Li
- CAS
Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tao Liu
- Tsinghua
Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Jianxun Qi
- CAS
Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaodan Ni
- Shuimu
Biosciences, Zhongguancun Life Science Park, No. 7 Science Park Road, Beijing 102206, China
| | - Sanduo Zheng
- National
Institute of Biological Sciences, Beijing, Zhongguancun Life Science Park, No. 7 Science Park Road, Beijing 102206, China
- Tsinghua
Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Jianhui Huang
- School
of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Niu Huang
- National
Institute of Biological Sciences, Beijing, Zhongguancun Life Science Park, No. 7 Science Park Road, Beijing 102206, China
- Tsinghua
Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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Transformation of a Metal Chelate into a "Catch and Anchor" Inhibitor of Botulinum A Protease. Int J Mol Sci 2023; 24:ijms24054303. [PMID: 36901734 PMCID: PMC10001950 DOI: 10.3390/ijms24054303] [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: 01/28/2023] [Revised: 02/14/2023] [Accepted: 02/18/2023] [Indexed: 02/24/2023] Open
Abstract
Targeting the botulinum neurotoxin light chain (LC) metalloprotease using small-molecule metal chelate inhibitors is a promising approach to counter the effects of the lethal toxin. However, to overcome the pitfalls associated with simple reversible metal chelate inhibitors, it is crucial to investigate alternative scaffolds/strategies. In conjunction with Atomwise Inc., in silico and in vitro screenings were conducted, yielding a number of leads, including a novel 9-hydroxy-4H-pyrido [1,2-a]pyrimidin-4-one (PPO) scaffold. From this structure, an additional series of 43 derivatives were synthesized and tested, resulting in a lead candidate with a Ki of 150 nM in a BoNT/A LC enzyme assay and 17 µM in a motor neuron cell-based assay. These data combined with structure-activity relationship (SAR) analysis and docking led to a bifunctional design strategy, which we termed "catch and anchor" for the covalent inhibition of BoNT/A LC. Kinetic evaluation was conducted on structures prepared from this catch and anchor campaign, providing kinact/Ki values, and rationale for inhibition seen. Covalent modification was validated through additional assays, including an FRET endpoint assay, mass spectrometry, and exhaustive enzyme dialysis. The data presented support the PPO scaffold as a novel candidate for targeted covalent inhibition of BoNT/A LC.
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Predicting Potent Compounds Using a Conditional Variational Autoencoder Based upon a New Structure-Potency Fingerprint. Biomolecules 2023; 13:biom13020393. [PMID: 36830761 PMCID: PMC9953226 DOI: 10.3390/biom13020393] [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: 12/14/2022] [Revised: 02/07/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Prediction of the potency of bioactive compounds generally relies on linear or nonlinear quantitative structure-activity relationship (QSAR) models. Nonlinear models are generated using machine learning methods. We introduce a novel approach for potency prediction that depends on a newly designed molecular fingerprint (FP) representation. This structure-potency fingerprint (SPFP) combines different modules accounting for the structural features of active compounds and their potency values in a single bit string, hence unifying structure and potency representation. This encoding enables the derivation of a conditional variational autoencoder (CVAE) using SPFPs of training compounds and apply the model to predict the SPFP potency module of test compounds using only their structure module as input. The SPFP-CVAE approach correctly predicts the potency values of compounds belonging to different activity classes with an accuracy comparable to support vector regression (SVR), representing the state-of-the-art in the field. In addition, highly potent compounds are predicted with very similar accuracy as SVR and deep neural networks.
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43
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das Neves GM, Kagami LP, Battastini AMO, Figueiró F, Eifler-Lima VL. Targeting ecto-5'-nucleotidase: A comprehensive review into small molecule inhibitors and expression modulators. Eur J Med Chem 2023; 247:115052. [PMID: 36599229 DOI: 10.1016/j.ejmech.2022.115052] [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: 10/20/2022] [Revised: 12/11/2022] [Accepted: 12/22/2022] [Indexed: 01/01/2023]
Abstract
The purinergic signaling has drawn attention from academia and more recently from pharmaceutical industries as a potential therapeutic route for cancer treatment, since ATP may act as chemotactic agent and possess in vitro antineoplastic activity. On the other way, adenosine, produced in extracellular medium by ecto-5'-NT, acts as immunosuppressor and is related to neoangiogenesis, vasculogenesis and evasion to the immune system. Consequently, inhibitors of ecto-5'-NT may prevent tumor progression, reducing adenosine concentrations, preventing escape from the host's immune system and slowing cancer's growth. This review aims to highlight important biochemical and structural features of ecto-5'NT, highlight its expression profile in normal and cancer cell lines detailing compounds which may act as expression regulators and to review the several classes of ecto-5'NT inhibitors developed in the past 12 years, in order to build a general structure-activity relationship model to guide further compound design.
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Affiliation(s)
- Gustavo Machado das Neves
- Laboratório de Síntese Orgânica Medicinal (LaSOM), Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Luciano Porto Kagami
- Laboratório de Síntese Orgânica Medicinal (LaSOM), Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ana Maria Oliveira Battastini
- Laboratório de Imunobioquímica do Câncer (LIBC), Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Fabrício Figueiró
- Laboratório de Imunobioquímica do Câncer (LIBC), Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Vera Lucia Eifler-Lima
- Laboratório de Síntese Orgânica Medicinal (LaSOM), Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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44
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Deng F, Sjöstedt N, Santo M, Neuvonen M, Niemi M, Kidron H. Novel inhibitors of breast cancer resistance protein (BCRP, ABCG2) among marketed drugs. Eur J Pharm Sci 2023; 181:106362. [PMID: 36529162 DOI: 10.1016/j.ejps.2022.106362] [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: 07/20/2022] [Revised: 11/11/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Drug-drug interactions (DDIs) are a major concern for the safe use of medications. Breast cancer resistance protein (BCRP) is a clinically relevant ATP-binding cassette (ABC) transporter for drug disposition. Inhibition of BCRP increases the plasma concentrations of BCRP substrate drugs, which potentially could lead to adverse drug reactions. The aim of the present study was to identify BCRP inhibitors amongst a library of 232 commonly used drugs and anticancer drugs approved by the United States Food and Drug Administration (FDA). BCRP inhibition studies were carried out using the vesicular transport assay. We found 75 drugs that reduced the relative transport activity of BCRP to less than 25% of the vehicle control and were categorized as strong inhibitors. The concentration required for 50% inhibition (IC50) was determined for 13 strong inhibitors that were previously poorly characterized for BCRP inhibition. The IC50 ranged from 1.1 to 11 µM, with vemurafenib, dabigatran etexilate and everolimus being the strongest inhibitors. According to the drug interaction guidance documents from the FDA and the European Medicines Agency (EMA), in vivo DDI studies are warranted if the theoretical intestinal luminal concentration of a drug exceeds its IC50 by tenfold. Here, the IC50 values for eight of the drugs were 100-fold lower than their theoretical intestinal luminal concentration. Moreover, a mechanistic static model suggested that vemurafenib, bexarotene, dabigatran etexilate, rifapentine, aprepitant, and ivacaftor could almost fully inhibit intestinal BCRP, increasing the exposure of concomitantly administered rosuvastatin over 90%. Therefore, clinical studies are warranted to investigate whether these drugs cause BCRP-mediated DDIs in humans.
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Affiliation(s)
- Feng Deng
- Department of Clinical Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland. Tukholmankatu 8 C, P.O. Box 20, 00014, Finland; Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland. Haartmaninkatu 8, P.O. Box 63, 00014, Finland
| | - Noora Sjöstedt
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland. Viikinkaari 5 E, P.O. Box 56, 00014, Finland
| | - Mariangela Santo
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland. Viikinkaari 5 E, P.O. Box 56, 00014, Finland
| | - Mikko Neuvonen
- Department of Clinical Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland. Tukholmankatu 8 C, P.O. Box 20, 00014, Finland; Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland. Haartmaninkatu 8, P.O. Box 63, 00014, Finland
| | - Mikko Niemi
- Department of Clinical Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland. Tukholmankatu 8 C, P.O. Box 20, 00014, Finland; Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland. Haartmaninkatu 8, P.O. Box 63, 00014, Finland; Department of Clinical Pharmacology, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Heidi Kidron
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland. Viikinkaari 5 E, P.O. Box 56, 00014, Finland.
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45
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In silico studies, X-ray diffraction analysis and biological investigation of fluorinated pyrrolylated-chalcones in zebrafish epilepsy models. Heliyon 2023; 9:e13685. [PMID: 36852036 PMCID: PMC9958447 DOI: 10.1016/j.heliyon.2023.e13685] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023] Open
Abstract
Epilepsy is the third most common known brain disease worldwide. Several antiepileptic drugs (AEDs) are available to improve seizure control. However, the associated side effects limit their practical use and highlight the ongoing search for safer and effective AEDs. Eighteen newly designed fluorine-containing pyrrolylated chalcones were extensively studied in silico, synthesized, structurally analyzed by X-ray diffraction (XRD), and biologically and toxicologically tested as potential new AEDs in zebrafish epilepsy in vivo models. The results predicted that 3-(3,5-difluorophenyl)-1-(1H-pyrrol-2-yl)prop-2-en-1-one (compound 8) had a good drug-like profile with binding affinity to γ-aminobutyric acid receptor type-A (GABAA, -8.0 kcal/mol). This predicted active compound 8 was effective in reducing convulsive behaviour in pentylenetetrazol (PTZ)-induced larvae and hyperactive movements in zc4h2 knockout (KO) zebrafish, experimentally. Moreover, no cardiotoxic effect of compound 8 was observed in zebrafish. Overall, pyrrolylated chalcones could serve as alternative AEDs and warrant further in-depth pharmacological studies to uncover their mechanism of action.
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Khamto N, Utama K, Tateing S, Sangthong P, Rithchumpon P, Cheechana N, Saiai A, Semakul N, Punyodom W, Meepowpan P. Discovery of Natural Bisbenzylisoquinoline Analogs from the Library of Thai Traditional Plants as SARS-CoV-2 3CL Pro Inhibitors: In Silico Molecular Docking, Molecular Dynamics, and In Vitro Enzymatic Activity. J Chem Inf Model 2023; 63:2104-2121. [PMID: 36647612 DOI: 10.1021/acs.jcim.2c01309] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The emergence of SARS-CoV-2 in December 2019 has become a global issue due to the continuous upsurge in patients and the lack of drug efficacy for treatment. SARS-CoV-2 3CLPro is one of the most intriguing biomolecular targets among scientists worldwide for developing antiviral drugs due to its relevance in viral replication and transcription. Herein, we utilized computer-assisted drug screening to investigate 326 natural products from Thai traditional plants using structure-based virtual screening against SARS-CoV-2 3CLPro. Following the virtual screening, the top 15 compounds based on binding energy and their interactions with key amino acid Cys145 were obtained. Subsequently, they were further evaluated for protein-ligand complex stability via molecular dynamics simulation and binding free energy calculation using molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approaches. Following drug-likeness and ADME/Tox assessments, seven bisbenzylisoquinolines were obtained, including neferine (3), liensinine (4), isoliensinine (5), dinklacorine (8), tiliacorinine (13), 2'-nortiliacorinine (14), and yanangcorinine (15). These compounds computationally showed a higher binding affinity than native N3 and GC-373 inhibitors and attained stable interactions on the active site of 3CLpro during 100 ns in molecular dynamics (MD) simulation. Moreover, the in vitro enzymatic assay showed that most bisbenzylisoquinolines could experimentally inhibit SARS-CoV-2 3CLPro. To our delight, isoliensinine (5) isolated from Nelumbo nucifera demonstrated the highest inhibition of protease activity with the IC50 value of 29.93 μM with low toxicity on Vero cells. Our findings suggested that bisbenzylisoquinoline scaffolds could be potentially used as an in vivo model for the development of effective anti-SARS-CoV-2 drugs.
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Affiliation(s)
- Nopawit Khamto
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand.,Graduate School, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand
| | - Kraikrit Utama
- Interdisciplinary Program in Biotechnology, Graduate School, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand.,Research Center on Chemistry for Development of Health Promoting Products from Northern Resources, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand
| | - Suriya Tateing
- Department of Plant and Soil Sciences, Faculty of Agriculture, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand
| | - Padchanee Sangthong
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand.,Research Center on Chemistry for Development of Health Promoting Products from Northern Resources, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand
| | - Puracheth Rithchumpon
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand
| | - Nathaporn Cheechana
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand.,Graduate School, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand
| | - Aroonchai Saiai
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand
| | - Natthawat Semakul
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand.,Research Center on Chemistry for Development of Health Promoting Products from Northern Resources, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand.,Center of Excellence in Materials Science and Technology, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand
| | - Winita Punyodom
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand.,Center of Excellence in Materials Science and Technology, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand.,Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand
| | - Puttinan Meepowpan
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand.,Center of Excellence in Materials Science and Technology, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand.,Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai50200, Thailand
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47
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Lamens A, Bajorath J. Explaining Accurate Predictions of Multitarget Compounds with Machine Learning Models Derived for Individual Targets. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020825. [PMID: 36677879 PMCID: PMC9860926 DOI: 10.3390/molecules28020825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023]
Abstract
In drug discovery, compounds with well-defined activity against multiple targets (multitarget compounds, MT-CPDs) provide the basis for polypharmacology and are thus of high interest. Typically, MT-CPDs for polypharmacology have been discovered serendipitously. Therefore, over the past decade, computational approaches have also been adapted for the design of MT-CPDs or their identification via computational screening. Such approaches continue to be under development and are far from being routine. Recently, different machine learning (ML) models have been derived to distinguish between MT-CPDs and corresponding compounds with activity against the individual targets (single-target compounds, ST-CPDs). When evaluating alternative models for predicting MT-CPDs, we discovered that MT-CPDs could also be accurately predicted with models derived for corresponding ST-CPDs; this was an unexpected finding that we further investigated using explainable ML. The analysis revealed that accurate predictions of ST-CPDs were determined by subsets of structural features of MT-CPDs required for their prediction. These findings provided a chemically intuitive rationale for the successful prediction of MT-CPDs using different ML models and uncovered general-feature subset relationships between MT- and ST-CPDs with activities against different targets.
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48
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Sidhom PA, El-Bastawissy E, Ibrahim MAA, Shawky AM, Salama A, El-Moselhy T. Mechanistic Insight of Synthesized 1,4-Dihydropyridines as an Antidiabetic Sword against Reactive Oxygen Species. J Med Chem 2023; 66:991-1010. [PMID: 36584305 DOI: 10.1021/acs.jmedchem.2c01818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The pharmacologically privileged DHP derivatives were synthesized using the pragmatic multicomponent Hantzsch synthesis to screen the antidiabetic activity. Initially, the candidates were screened using an in vivo blood glucose test, where compound 8b showed the most prominent antidiabetic effect (% potency = 218%) compared to glimepiride. Then, a propositioned structure-activity relationship study was executed to reveal that longer side chains decreased the DHP's antidiabetic action. Mechanistically, compound 8b diminished ROS in β-cells and muscle cells simultaneously, which was proved by enhanced serum biochemical markers. Also, compound 8b decreased blood glucose by α-glucosidase inhibition (IC50 = 4.48 ± 0.32 μM), compared to acarbose (7.40 ± 0.41 μM), based selectively on the plasma window of 8b. Acarbose demonstrated auspicious inhibitor activity according to the binding affinity (ΔGbinding), which was slightly lower than that of compound 8b (-54.7 and -46.8 kcal/mol, respectively). During the 100 ns molecular dynamics simulations, the structural and energetic assessments exposed the high consistency of compound 8b to bind to the α-glucosidase.
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Affiliation(s)
- Peter A Sidhom
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, 31527 Tanta, Egypt
| | - Eman El-Bastawissy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, 31527 Tanta, Egypt
| | - Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Abeer Salama
- Pharmacology Department, National Research Centre (NRC), 33 El-Bohouth St. (Former El-Tahrir St.), 12622 Dokki, Giza, Egypt
| | - Tarek El-Moselhy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, 31527 Tanta, Egypt
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49
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Collins SJ, Guo J, Rizzo RC, Miller WT. Inhibition of mutationally activated HER2. Chem Biol Drug Des 2023; 101:87-102. [PMID: 36029027 PMCID: PMC9879383 DOI: 10.1111/cbdd.14125] [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: 04/25/2022] [Revised: 06/24/2022] [Accepted: 07/30/2022] [Indexed: 01/28/2023]
Abstract
Human epidermal growth factor receptor 2 (HER2) is an oncogenic driver and key therapeutic target for human cancers. Current therapies targeting HER2 are primarily based on overexpression of the wild-type form of HER2. However, kinase domain mutations have been identified that can increase the activity of HER2 even when expressed at basal levels. Using purified enzymes, we confirmed the hyperactivity of two HER2 mutants (D769Y and P780insGSP). To identify small molecule inhibitors against these cancer-associated variants, we used a combined approach consisting of biochemical testing, similarity-based searching, and in silico modeling. These approaches resulted in the identification of a candidate molecule that inhibits mutant forms of HER2 in vitro and in cell-based assays. Our structural model predicts that the compound takes advantage of water-mediated interactions in the HER2 kinase binding pocket.
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Affiliation(s)
- Stephen J. Collins
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
| | - Jiaye Guo
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York, USA
| | - Robert C. Rizzo
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York, USA,Laufer Center for Physical & Quantitative Biology, Stony Brook University, Stony Brook, New York, USA,Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York, USA
| | - W. Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA,Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York, USA,Department of Veterans Affairs Medical Center, Northport, New York, USA
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50
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Kandagalla S, Novak J, Shekarappa SB, Grishina MA, Potemkin VA, Kumbar B. Exploring potential inhibitors against Kyasanur forest disease by utilizing molecular dynamics simulations and ensemble docking. J Biomol Struct Dyn 2022; 40:13547-13563. [PMID: 34662258 DOI: 10.1080/07391102.2021.1990131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Kyasanur forest disease (KFD) is a tick-borne, neglected tropical disease, caused by KFD virus (KFDV) which belongs to Flavivirus (Flaviviridae family). This emerging viral disease is a major threat to humans. Currently, vaccination is the only controlling method against the KFDV, and its effectiveness is very low. An effective control strategy is required to combat this emerging tropical disease using the existing resources. In this regard, in silico drug repurposing method offers an effective strategy to find suitable antiviral drugs against KFDV proteins. Drug repurposing is an effective strategy to identify new use for approved or investigational drugs that are outside the scope of their initial usage and the repurposed drugs have lower risk and higher safety compared to de novo developed drugs, because their toxicity and safety issues are profoundly investigated during the preclinical trials in human/other models. In the present work, we evaluated the effectiveness of the FDA approved and natural compounds against KFDV proteins using in silico molecular docking and molecular simulations. At present, no experimentally solved 3D structures for the KFD viral proteins are available in Protein Data Bank and hence their homology model was developed and used for the analysis. The present analysis successfully developed the reliable homology model of NS3 of KFDV, in terms of geometry and energy contour. Further, in silico molecular docking and molecular dynamics simulations successfully presented four FDA approved drugs and one natural compound against the NS3 homology model of KFDV. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shivananda Kandagalla
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Jurica Novak
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Sharath Belenahalli Shekarappa
- Department of PG Studies and Research in Biotechnology and Bioinformatics, Kuvempu University, Shivamogga, Karnataka, India
| | - Maria A Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Vladimir A Potemkin
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Bhimanagoud Kumbar
- Department of PG Studies and Research in Biotechnology and Bioinformatics, Kuvempu University, Shivamogga, Karnataka, India.,ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
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