1
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Merat R. The human antigen R as an actionable super-hub within the network of cancer cell persistency and plasticity. Transl Oncol 2023; 35:101722. [PMID: 37352624 DOI: 10.1016/j.tranon.2023.101722] [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: 04/07/2023] [Revised: 05/30/2023] [Accepted: 06/12/2023] [Indexed: 06/25/2023] Open
Abstract
In this perspective article, a clinically inspired phenotype-driven experimental approach is put forward to address the challenge of the adaptive response of solid cancers to small-molecule targeted therapies. A list of conditions is derived, including an experimental quantitative assessment of cell plasticity and an information theory-based detection of in vivo dependencies, for the discovery of post-transcriptional druggable mechanisms capable of preventing at multiple levels the emergence of plastic dedifferentiated slow-proliferating cells. The approach is illustrated by the author's own work in the example case of the adaptive response of BRAFV600-melanoma to BRAF inhibition. A bench-to-bedside and back to bench effort leads to a therapeutic strategy in which the inhibition of the baseline activity of the interferon-γ-activated inhibitor of translation (GAIT) complex, incriminated in the expression insufficiency of the RNA-binding protein HuR in a minority of cells, results in the suppression of the plastic, intermittently slow-proliferating cells involved in the adaptive response. A similar approach is recommended for the validation of other classes of mechanisms that we seek to modulate to overcome this complex challenge of modern cancer therapy.
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Affiliation(s)
- Rastine Merat
- Dermato-Oncology Unit, Division of Dermatology, Geneva University Hospitals, Switzerland; Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Switzerland.
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2
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Xue B, Chaddha M, Elasbali AM, Zhu Z, Jairajpuri DS, Alhumaydhi FA, Mohammad T, Abdulmonem WA, Sharaf SE, Hassan MI. Death-Associated Protein Kinase 3 Inhibitors Identified by Virtual Screening for Drug Discovery in Cancer and Hypertension. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:404-413. [PMID: 35759452 DOI: 10.1089/omi.2022.0044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Death-associated protein kinase 3 (DAPK3) is a serine/threonine protein kinase that regulates apoptosis, autophagy, transcription, and actin cytoskeleton reorganization. DAPK3 induces morphological alterations in apoptosis when overexpressed, and it is considered a potential drug target in antihypertensive and anticancer drug development. In this article, we report new findings from a structure-guided virtual screening for discovery of phytochemicals that could modulate the elevated expression of DAPK3, and with an eye to anticancer drug discovery. We used the Indian Medicinal Plants, Phytochemistry and Therapeutics (IMPPAT), a curated database, as part of the methodology. The potential initial hits were identified based on their physicochemical properties and binding affinity toward DAPK3. Subsequently, various filters for drug likeness followed by interaction analysis and molecular dynamics (MD) simulations for 100 nsec were performed to explore the conformational sampling and stability of DAPK3 with the candidate molecules. Notably, the data from all-atom MD simulations and principal component analysis suggested that DAPK3 forms stable complexes with ketanserin and rotenone. In conclusion, this study supports the idea that ketanserin and rotenone bind to DAPK3, and show stability, which can be further explored as promising scaffolds in drug development and therapeutics innovation in clinical contexts such as hypertension and various types of cancer.
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Affiliation(s)
- Bin Xue
- School of Engineering, Guangzhou College of Technology and Business, Guangzhou, China
| | - Muskan Chaddha
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Abdelbaset Mohamed Elasbali
- Department of Clinical Laboratory Science, College of Applied Sciences-Qurayyat, Jouf University, Sakakah, Saudi Arabia
| | - Zhixin Zhu
- School of Engineering, Guangzhou College of Technology and Business, Guangzhou, China
| | - Deeba Shamim Jairajpuri
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Waleed Al Abdulmonem
- Department of Pathology, College of Medicine, Qassim University, Buraidah, Saudia Arabia
| | - Sharaf E Sharaf
- Pharmaceutical Chemistry Department, College of Pharmacy Umm Al-Qura University, Makkah, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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3
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Bender A, Schneider N, Segler M, Patrick Walters W, Engkvist O, Rodrigues T. Evaluation guidelines for machine learning tools in the chemical sciences. Nat Rev Chem 2022; 6:428-442. [PMID: 37117429 DOI: 10.1038/s41570-022-00391-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2022] [Indexed: 02/07/2023]
Abstract
Machine learning (ML) promises to tackle the grand challenges in chemistry and speed up the generation, improvement and/or ordering of research hypotheses. Despite the overarching applicability of ML workflows, one usually finds diverse evaluation study designs. The current heterogeneity in evaluation techniques and metrics leads to difficulty in (or the impossibility of) comparing and assessing the relevance of new algorithms. Ultimately, this may delay the digitalization of chemistry at scale and confuse method developers, experimentalists, reviewers and journal editors. In this Perspective, we critically discuss a set of method development and evaluation guidelines for different types of ML-based publications, emphasizing supervised learning. We provide a diverse collection of examples from various authors and disciplines in chemistry. While taking into account varying accessibility across research groups, our recommendations focus on reporting completeness and standardizing comparisons between tools. We aim to further contribute to improved ML transparency and credibility by suggesting a checklist of retro-/prospective tests and dissecting their importance. We envisage that the wide adoption and continuous update of best practices will encourage an informed use of ML on real-world problems related to the chemical sciences.
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4
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Almeida AF, Ataíde FAP, Loureiro RMS, Moreira R, Rodrigues T. Augmenting Adaptive Machine Learning with Kinetic Modeling for Reaction Optimization. J Org Chem 2021; 86:14192-14198. [PMID: 34235919 DOI: 10.1021/acs.joc.1c01038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We combine random sampling and active machine learning (ML) to optimize the synthesis of isomacroin, executing only 3% of all possible Friedländer reactions. Employing kinetic modeling, we augment machine intuition by extracting mechanistic knowledge and verify that a global optimum was obtained with ML. Our study contributes evidence on the potential of multiscale approaches to expedite the access to chemical matter, further democratizing organic chemistry in a data-motivated fashion.
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Affiliation(s)
- A Filipa Almeida
- R&D, Process Chemistry Development, Hovione FarmaCiência S.A, Campus do Lumiar, Building S 1649-038 Lisboa, Portugal.,Research Institute for Medicines (iMed.Ulisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Filipe A P Ataíde
- R&D, Process Chemistry Development, Hovione FarmaCiência S.A, Campus do Lumiar, Building S 1649-038 Lisboa, Portugal
| | - Rui M S Loureiro
- R&D, Process Chemistry Development, Hovione FarmaCiência S.A, Campus do Lumiar, Building S 1649-038 Lisboa, Portugal
| | - Rui Moreira
- Research Institute for Medicines (iMed.Ulisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Tiago Rodrigues
- Research Institute for Medicines (iMed.Ulisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
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5
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Highly efficient azido-Ugi multicomponent reactions for the synthesis of bioactive tetrazoles bearing sulfonamide scaffolds. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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6
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Jin H, Xia J, Liu Z, Wang XS, Zhang L. A unique ligand-steered strategy for CC chemokine receptor 2 homology modeling to facilitate structure-based virtual screening. Chem Biol Drug Des 2021; 97:944-961. [PMID: 33386704 PMCID: PMC8048943 DOI: 10.1111/cbdd.13820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/12/2020] [Accepted: 12/13/2020] [Indexed: 12/29/2022]
Abstract
CC chemokine receptor 2 (CCR2) antagonists that disrupt CCR2/MCP-1 interaction are expected to treat a variety of inflammatory and autoimmune diseases. The lack of CCR2 crystal structure limits the application of structure-based drug design (SBDD) to this target. Although a few three-dimensional theoretical models have been reported, their accuracy remains to be improved in terms of templates and modeling approaches. In this study, we developed a unique ligand-steered strategy for CCR2 homology modeling. It starts with an initial model based on the X-ray structure of the closest homolog so far, that is, CXCR4. Then, it uses Elastic Network Normal Mode Analysis (EN-NMA) and flexible docking (FD) by AutoDock Vina software to generate ligand-induced fit models. It selects optimal model(s) as well as scoring function(s) via extensive evaluation of model performance based on a unique benchmarking set constructed by our in-house tool, that is, MUBD-DecoyMaker. The model of 81_04 presents the optimal enrichment when combined with the scoring function of PMF04, and the proposed binding mode between CCR2 and Teijin lead by this model complies with the reported mutagenesis data. To highlight the advantage of our strategy, we compared it with the only reported ligand-steered strategy for CCR2 homology modeling, that is, Discovery Studio/Ligand Minimization. Lastly, we performed prospective virtual screening based on 81_04 and CCR2 antagonist bioassay. The identification of two hit compounds, that is, E859-1281 and MolPort-007-767-945, validated the efficacy of our model and the ligand-steered strategy.
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Affiliation(s)
- Hongwei Jin
- State Key Laboratory of Natural and Biomimetic DrugsSchool of Pharmaceutical SciencesPeking UniversityBeijingChina
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural MedicinesDepartment of New Drug Research and DevelopmentInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic DrugsSchool of Pharmaceutical SciencesPeking UniversityBeijingChina
| | - Xiang Simon Wang
- Molecular Modeling and Drug Discovery Core for District of Columbia Center for AIDS Research (DC CFAR)Laboratory of Cheminformatics and Drug DesignDepartment of Pharmaceutical SciencesCollege of PharmacyHoward UniversityWashingtonDCUSA
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic DrugsSchool of Pharmaceutical SciencesPeking UniversityBeijingChina
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Saikia S, Bordoloi M. Molecular Docking: Challenges, Advances and its Use in Drug Discovery Perspective. Curr Drug Targets 2020; 20:501-521. [PMID: 30360733 DOI: 10.2174/1389450119666181022153016] [Citation(s) in RCA: 203] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/08/2018] [Accepted: 08/28/2018] [Indexed: 01/21/2023]
Abstract
Molecular docking is a process through which small molecules are docked into the macromolecular structures for scoring its complementary values at the binding sites. It is a vibrant research area with dynamic utility in structure-based drug-designing, lead optimization, biochemical pathway and for drug designing being the most attractive tools. Two pillars for a successful docking experiment are correct pose and affinity prediction. Each program has its own advantages and drawbacks with respect to their docking accuracy, ranking accuracy and time consumption so a general conclusion cannot be drawn. Moreover, users don't always consider sufficient diversity in their test sets which results in certain programs to outperform others. In this review, the prime focus has been laid on the challenges of docking and troubleshooters in existing programs, underlying algorithmic background of docking, preferences regarding the use of docking programs for best results illustrated with examples, comparison of performance for existing tools and algorithms, state of art in docking, recent trends of diseases and current drug industries, evidence from clinical trials and post-marketing surveillance are discussed. These aspects of the molecular drug designing paradigm are quite controversial and challenging and this review would be an asset to the bioinformatics and drug designing communities.
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Affiliation(s)
- Surovi Saikia
- Natural Products Chemistry Group, CSIR North East Institute of Science & Technology, Jorhat-785006, Assam, India
| | - Manobjyoti Bordoloi
- Natural Products Chemistry Group, CSIR North East Institute of Science & Technology, Jorhat-785006, Assam, India
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8
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9
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Rodrigues T. The good, the bad, and the ugly in chemical and biological data for machine learning. DRUG DISCOVERY TODAY. TECHNOLOGIES 2019; 32-33:3-8. [PMID: 33386092 PMCID: PMC7382642 DOI: 10.1016/j.ddtec.2020.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 02/05/2023]
Abstract
Machine learning and artificial intelligence (ML/AI) have become important research tools in molecular medicine and chemistry. Their rise and recent success in drug discovery promises a rapid progression of development pipelines while reshaping how fundamental and clinical research is conducted. By taking advantage of the ever-growing wealth of publicly available and proprietary data, learning algorithms now provide an attractive means to generate statistically motivated research hypotheses. Hitherto unknown data patterns may guide and prioritize experiments, and augment expert intuition. Therefore, data is a key component in the model building workflow. Herein, I aim to discuss types of chemical and biological data according to their quality and reemphasize general recommendations for their use in ML/AI.
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Affiliation(s)
- Tiago Rodrigues
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av Prof Egaz Moniz, 1649-028 Lisboa, Portugal; Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto 1649-003, Lisboa, Portugal.
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10
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Machine learning for target discovery in drug development. Curr Opin Chem Biol 2019; 56:16-22. [PMID: 31734566 DOI: 10.1016/j.cbpa.2019.10.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 10/01/2019] [Accepted: 10/03/2019] [Indexed: 12/15/2022]
Abstract
The discovery of macromolecular targets for bioactive agents is currently a bottleneck for the informed design of chemical probes and drug leads. Typically, activity profiling against genetically manipulated cell lines or chemical proteomics is pursued to shed light on their biology and deconvolute drug-target networks. By taking advantage of the ever-growing wealth of publicly available bioactivity data, learning algorithms now provide an attractive means to generate statistically motivated research hypotheses and thereby prioritize biochemical screens. Here, we highlight recent successes in machine intelligence for target identification and discuss challenges and opportunities for drug discovery.
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11
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de Almeida AF, Moreira R, Rodrigues T. Synthetic organic chemistry driven by artificial intelligence. Nat Rev Chem 2019. [DOI: 10.1038/s41570-019-0124-0] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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12
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Abstract
Introduction: The development of drug candidates with a defined selectivity profile and a unique molecular structure is of fundamental interest for drug discovery. In contrast to the costly screening of large substance libraries, the targeted de novo design of a drug by using structural information of either the biological target and/or structure-activity relationship data of active modulators offers an efficient and intellectually appealing alternative. Areas covered: This review provides an overview on the different techniques of de novo drug design (ligand-based drug design, structure-based drug design, and fragment-based drug design) and highlights successful examples of this targeted approach toward selective modulators of therapeutically relevant targets. Expert opinion: De novo drug design has established itself as a very efficient method for the development of potent and selective modulators for a variety of different biological target classes. The ever-growing wealth of structural data on therapeutic targets will certainly further enhance the importance of de novo design for the drug discovery process in the future. However, a consistent use of the terminology of de novo drug design in the scientific literature should be sought.
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Affiliation(s)
- Thomas Fischer
- a Center of Organic and Medicinal Chemistry, Institute of Chemistry and Biotechnology , Zurich University of Applied Sciences ZHAW , Wädenswil , Switzerland
| | - Silvia Gazzola
- b Dipartimento di Scienza e Alta Tecnologia , Università degli Studi dell'Insubria , Como , Italy
| | - Rainer Riedl
- a Center of Organic and Medicinal Chemistry, Institute of Chemistry and Biotechnology , Zurich University of Applied Sciences ZHAW , Wädenswil , Switzerland
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13
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Schneider G, Clark DE. Automated De Novo Drug Design: Are We Nearly There Yet? Angew Chem Int Ed Engl 2019; 58:10792-10803. [PMID: 30730601 DOI: 10.1002/anie.201814681] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Indexed: 11/09/2022]
Abstract
Medicinal chemistry and, in particular, drug design have often been perceived as more of an art than a science. The many unknowns of human disease and the sheer complexity of chemical space render decision making in medicinal chemistry exceptionally demanding. Computational models can assist the medicinal chemist in this endeavour. Provided here is an overview of recent examples of automated de novo molecular design, a discussion of the concepts and computational approaches involved, and the daring prediction of some of the possibilities and limitations of drug design using machine intelligence.
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Affiliation(s)
- Gisbert Schneider
- ETH Zurich, Department of Chemistry and Applied Biosciences, RETHINK, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - David E Clark
- Charles River, 6-9 Spire Green Centre, Harlow, Essex, CM19 5TR, UK
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14
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Schneider G, Clark DE. Automated De Novo Drug Design: Are We Nearly There Yet? Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814681] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Gisbert Schneider
- ETH ZurichDepartment of Chemistry and Applied Biosciences, RETHINK Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - David E. Clark
- Charles River 6–9 Spire Green Centre Harlow Essex CM19 5TR UK
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15
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Reker D, Bernardes GJL, Rodrigues T. Computational advances in combating colloidal aggregation in drug discovery. Nat Chem 2019; 11:402-418. [PMID: 30988417 DOI: 10.1038/s41557-019-0234-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 02/21/2019] [Indexed: 02/07/2023]
Abstract
Small molecule effectors are essential for drug discovery. Specific molecular recognition, reversible binding and dose-dependency are usually key requirements to ensure utility of a novel chemical entity. However, artefactual frequent-hitter and assay interference compounds may divert lead optimization and screening programmes towards attrition-prone chemical matter. Colloidal aggregates are the prime source of false positive readouts, either through protein sequestration or protein-scaffold mimicry. Nevertheless, assessment of colloidal aggregation remains somewhat overlooked and under-appreciated. In this Review, we discuss the impact of aggregation in drug discovery by analysing select examples from the literature and publicly-available datasets. We also examine and comment on technologies used to experimentally identify these potentially problematic entities. We focus on evidence-based computational filters and machine learning algorithms that may be swiftly deployed to flag chemical matter and mitigate the impact of aggregates in discovery programmes. We highlight the tools that can be used to scrutinize libraries, and identify and eliminate these problematic compounds.
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Affiliation(s)
- Daniel Reker
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. .,MIT-IBM Watson AI Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.,Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Tiago Rodrigues
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal.
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16
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Affiliation(s)
- Shuanglong Jia
- Laboratoire de Synthèse Organique (LSO), CNRS; Ecole Polytechnique, ENSTA ParisTech-UMR 7652; Université Paris-Saclay; 828 Bd des Maréchaux 91128 Palaiseau. France
| | - Laurent El Kaïm
- Laboratoire de Synthèse Organique (LSO), CNRS; Ecole Polytechnique, ENSTA ParisTech-UMR 7652; Université Paris-Saclay; 828 Bd des Maréchaux 91128 Palaiseau. France
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17
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Cooper P, Crisenza GEM, Feron LJ, Bower JF. Iridium-Catalyzed α-Selective Arylation of Styrenes by Dual C-H Functionalization. Angew Chem Int Ed Engl 2018; 57:14198-14202. [PMID: 30171652 PMCID: PMC6391973 DOI: 10.1002/anie.201808299] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/21/2018] [Indexed: 11/21/2022]
Abstract
An IrI -system modified with a ferrocene derived bisphosphine ligand promotes α-selective arylation of styrenes by dual C-H functionalization. These studies offer a regioisomeric alternative to the Pd-catalyzed Fujiwara-Moritani reaction.
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Affiliation(s)
| | | | - Lyman J. Feron
- Medicinal ChemistryOncology, IMED Biotech UnitAstraZenecaCambridgeUK
| | - John F. Bower
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
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18
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Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. J Cheminform 2017; 9:64. [PMID: 29260340 PMCID: PMC5736515 DOI: 10.1186/s13321-017-0252-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 12/08/2017] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Network generation tools coupled with chemical reaction rules have been mainly developed for synthesis planning and more recently for metabolic engineering. Using the same core algorithm, these tools apply a set of rules to a source set of compounds, stopping when a sink set of compounds has been produced. When using the appropriate sink, source and rules, this core algorithm can be used for a variety of applications beyond those it has been developed for. RESULTS Here, we showcase the use of the open source workflow RetroPath2.0. First, we mathematically prove that we can generate all structural isomers of a molecule using a reduced set of reaction rules. We then use this enumeration strategy to screen the chemical space around a set of monomers and predict their glass transition temperatures, as well as around aminoglycosides to search structures maximizing antibacterial activity. We also perform a screening around aminoglycosides with enzymatic reaction rules to ensure biosynthetic accessibility. We finally use our workflow on an E. coli model to complete E. coli metabolome, with novel molecules generated using promiscuous enzymatic reaction rules. These novel molecules are searched on the MS spectra of an E. coli cell lysate interfacing our workflow with OpenMS through the KNIME Analytics Platform. CONCLUSION We provide an easy to use and modify, modular, and open-source workflow. We demonstrate its versatility through a variety of use cases including molecular structure enumeration, virtual screening in the chemical space, and metabolome completion. Because it is open source and freely available on MyExperiment.org, workflow community contributions should likely expand further the features of the tool, even beyond the use cases presented in the paper.
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Affiliation(s)
- Mathilde Koch
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Thomas Duigou
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Pablo Carbonell
- SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Jean-Loup Faulon
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. .,SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK. .,CNRS-UMR8030/Laboratoire iSSB, Université Paris-Saclay, 91000, Évry, France.
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Abstract
Small-molecule drug discovery can be viewed as a challenging multidimensional problem in which various characteristics of compounds - including efficacy, pharmacokinetics and safety - need to be optimized in parallel to provide drug candidates. Recent advances in areas such as microfluidics-assisted chemical synthesis and biological testing, as well as artificial intelligence systems that improve a design hypothesis through feedback analysis, are now providing a basis for the introduction of greater automation into aspects of this process. This could potentially accelerate time frames for compound discovery and optimization and enable more effective searches of chemical space. However, such approaches also raise considerable conceptual, technical and organizational challenges, as well as scepticism about the current hype around them. This article aims to identify the approaches and technologies that could be implemented robustly by medicinal chemists in the near future and to critically analyse the opportunities and challenges for their more widespread application.
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20
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Enriching biologically relevant chemical space around 2-aminothiazole template for anticancer drug development. Med Chem Res 2017. [DOI: 10.1007/s00044-017-2039-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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21
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22
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Grisoni F, Reker D, Schneider P, Friedrich L, Consonni V, Todeschini R, Koeberle A, Werz O, Schneider G. Matrix-based Molecular Descriptors for Prospective Virtual Compound Screening. Mol Inform 2016; 36. [DOI: 10.1002/minf.201600091] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/07/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Francesca Grisoni
- University of Milano-Bicocca; Dept. of Earth and Environmental Sciences; P.za della Scienza 1 20126 Milano Italy
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Daniel Reker
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Petra Schneider
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
- inSili.com LLC; Segantinisteig 3 8049 Zurich Switzerland
| | - Lukas Friedrich
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Viviana Consonni
- University of Milano-Bicocca; Dept. of Earth and Environmental Sciences; P.za della Scienza 1 20126 Milano Italy
| | - Roberto Todeschini
- University of Milano-Bicocca; Dept. of Earth and Environmental Sciences; P.za della Scienza 1 20126 Milano Italy
| | - Andreas Koeberle
- University of Jena; Institute of Pharmacy; Philosophenweg 14 07743 Jena Germany
| | - Oliver Werz
- University of Jena; Institute of Pharmacy; Philosophenweg 14 07743 Jena Germany
| | - Gisbert Schneider
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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23
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Reker D, Schneider P, Schneider G. Multi-objective active machine learning rapidly improves structure-activity models and reveals new protein-protein interaction inhibitors. Chem Sci 2016; 7:3919-3927. [PMID: 30155037 PMCID: PMC6013791 DOI: 10.1039/c5sc04272k] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/27/2016] [Indexed: 11/21/2022] Open
Abstract
Active machine learning puts artificial intelligence in charge of a sequential, feedback-driven discovery process. We present the application of a multi-objective active learning scheme for identifying small molecules that inhibit the protein-protein interaction between the anti-cancer target CXC chemokine receptor 4 (CXCR4) and its endogenous ligand CXCL-12 (SDF-1). Experimental design by active learning was used to retrieve informative active compounds that continuously improved the adaptive structure-activity model. The balanced character of the compound selection function rapidly delivered new molecular structures with the desired inhibitory activity and at the same time allowed us to focus on informative compounds for model adjustment. The results of our study validate active learning for prospective ligand finding by adaptive, focused screening of large compound repositories and virtual compound libraries.
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Affiliation(s)
- D Reker
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog Weg 4 , 8093 Zürich , Switzerland .
| | - P Schneider
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog Weg 4 , 8093 Zürich , Switzerland .
| | - G Schneider
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog Weg 4 , 8093 Zürich , Switzerland .
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Friedrich L, Rodrigues T, Neuhaus CS, Schneider P, Schneider G. From Complex Natural Products to Simple Synthetic Mimetics by Computational De Novo Design. Angew Chem Int Ed Engl 2016; 55:6789-92. [DOI: 10.1002/anie.201601941] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/03/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Lukas Friedrich
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology (ETH); Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Tiago Rodrigues
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology (ETH); Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Claudia S. Neuhaus
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology (ETH); Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Petra Schneider
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology (ETH); Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
- inSili.com GmbH; Segantinisteig 3 8049 Zurich Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology (ETH); Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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25
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Friedrich L, Rodrigues T, Neuhaus CS, Schneider P, Schneider G. Von komplexen Naturstoffen zu synthetisch leicht zugänglichen Mimetika mithilfe von computergestütztem De-novo-Design. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601941] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lukas Friedrich
- Department für Chemie und Angewandte Biowissenschaften; Eidgenössische Technische Hochschule; Vladimir-Prelog-Weg 4 8093 Zürich Schweiz
| | - Tiago Rodrigues
- Department für Chemie und Angewandte Biowissenschaften; Eidgenössische Technische Hochschule; Vladimir-Prelog-Weg 4 8093 Zürich Schweiz
| | - Claudia S. Neuhaus
- Department für Chemie und Angewandte Biowissenschaften; Eidgenössische Technische Hochschule; Vladimir-Prelog-Weg 4 8093 Zürich Schweiz
| | - Petra Schneider
- Department für Chemie und Angewandte Biowissenschaften; Eidgenössische Technische Hochschule; Vladimir-Prelog-Weg 4 8093 Zürich Schweiz
- inSili.com GmbH; Segantinisteig 3 8049 Zürich Schweiz
| | - Gisbert Schneider
- Department für Chemie und Angewandte Biowissenschaften; Eidgenössische Technische Hochschule; Vladimir-Prelog-Weg 4 8093 Zürich Schweiz
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