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Dong J, Zhu MF, Yun YH, Lu AP, Hou TJ, Cao DS. BioMedR: an R/CRAN package for integrated data analysis pipeline in biomedical study. Brief Bioinform 2019; 22:474-484. [PMID: 31885044 DOI: 10.1093/bib/bbz150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/22/2019] [Accepted: 10/30/2019] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND With the increasing development of biotechnology and information technology, publicly available data in chemistry and biology are undergoing explosive growth. Such wealthy information in these resources needs to be extracted and then transformed to useful knowledge by various data mining methods. However, a main computational challenge is how to effectively represent or encode molecular objects under investigation such as chemicals, proteins, DNAs and even complicated interactions when data mining methods are employed. To further explore these complicated data, an integrated toolkit to represent different types of molecular objects and support various data mining algorithms is urgently needed. RESULTS We developed a freely available R/CRAN package, called BioMedR, for molecular representations of chemicals, proteins, DNAs and pairwise samples of their interactions. The current version of BioMedR could calculate 293 molecular descriptors and 13 kinds of molecular fingerprints for small molecules, 9920 protein descriptors based on protein sequences and six types of generalized scale-based descriptors for proteochemometric modeling, more than 6000 DNA descriptors from nucleotide sequences and six types of interaction descriptors using three different combining strategies. Moreover, this package realized five similarity calculation methods and four powerful clustering algorithms as well as several useful auxiliary tools, which aims at building an integrated analysis pipeline for data acquisition, data checking, descriptor calculation and data modeling. CONCLUSION BioMedR provides a comprehensive and uniform R package to link up different representations of molecular objects with each other and will benefit cheminformatics/bioinformatics and other biomedical users. It is available at: https://CRAN.R-project.org/package=BioMedR and https://github.com/wind22zhu/BioMedR/.
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Affiliation(s)
- Jie Dong
- National Engineering Laboratory for Deep Processing of Rice and Byproducts, Hunan Key Laboratory of Processed Food for Special Medical Purpose, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha,410003 P. R. China.,Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410003 P. R. China
| | - Min-Feng Zhu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410003 P. R. China
| | - Yong-Huan Yun
- College of Food Science and Engineering, Hainan University, Haikou, 570228 PR China
| | - Ai-Ping Lu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, P. R. China
| | - Ting-Jun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, P. R. China
| | - Dong-Sheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410003 P. R. China.,Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, P. R. China
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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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54
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Liu M, Quinn RJ. Fragment-based screening with natural products for novel anti-parasitic disease drug discovery. Expert Opin Drug Discov 2019; 14:1283-1295. [PMID: 31512943 PMCID: PMC6816479 DOI: 10.1080/17460441.2019.1653849] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 08/06/2019] [Indexed: 12/30/2022]
Abstract
Introduction: Fragment-based drug discovery can identify relatively simple compounds with low binding affinity due to fewer binding interactions with protein targets. FBDD reduces the library size and provides simpler starting points for subsequent chemical optimization of initial hits. A much greater proportion of chemical space can be sampled in fragment-based screening compared to larger molecules with typical molecular weights (MWs) of 250-500 g mol-1 used in high-throughput screening (HTS) libraries. Areas covered: The authors cover the role of natural products in fragment-based drug discovery against parasitic disease targets. They review the approaches to develop fragment-based libraries either using natural products or natural product-like compounds. The authors present approaches to fragment-based drug discovery against parasitic diseases and compare these libraries with the 3D attributes of natural products. Expert opinion: To effectively use the three-dimensional properties and the chemical diversity of natural products in fragment-based drug discovery against parasitic diseases, there needs to be a mind-shift. Library design, in the medicinal chemistry area, has acknowledged that escaping flat-land is very important to increase the chances of clinical success. Attempts to increase sp3 richness in fragment libraries are acknowledged. Sufficient low molecular weight natural products are known to create true natural product fragment libraries.
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Affiliation(s)
- Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Ronald J. Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
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55
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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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56
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Cockroft NT, Cheng X, Fuchs JR. STarFish: A Stacked Ensemble Target Fishing Approach and its Application to Natural Products. J Chem Inf Model 2019; 59:4906-4920. [PMID: 31589422 DOI: 10.1021/acs.jcim.9b00489] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Target fishing is the process of identifying the protein target of a bioactive small molecule. To do so experimentally requires a significant investment of time and resources, which can be expedited with a reliable computational target fishing model. The development of computational target fishing models using machine learning has become very popular over the last several years because of the increased availability of large amounts of public bioactivity data. Unfortunately, the applicability and performance of such models for natural products has not yet been comprehensively assessed. This is, in part, due to the relative lack of bioactivity data available for natural products compared to synthetic compounds. Moreover, the databases commonly used to train such models do not annotate which compounds are natural products, which makes the collection of a benchmarking set difficult. To address this knowledge gap, a data set composed of natural product structures and their associated protein targets was generated by cross-referencing 20 publicly available natural product databases with the bioactivity database ChEMBL. This data set contains 5589 compound-target pairs for 1943 unique compounds and 1023 unique targets. A synthetic data set comprising 107 190 compound-target pairs for 88 728 unique compounds and 1907 unique targets was used to train k-nearest neighbors, random forest, and multilayer perceptron models. The predictive performance of each model was assessed by stratified 10-fold cross-validation and benchmarking on the newly collected natural product data set. Strong performance was observed for each model during cross-validation with area under the receiver operating characteristic (AUROC) scores ranging from 0.94 to 0.99 and Boltzmann-enhanced discrimination of receiver operating characteristic (BEDROC) scores from 0.89 to 0.94. When tested on the natural product data set, performance dramatically decreased with AUROC scores ranging from 0.70 to 0.85 and BEDROC scores from 0.43 to 0.59. However, the implementation of a model stacking approach, which uses logistic regression as a meta-classifier to combine model predictions, dramatically improved the ability to correctly predict the protein targets of natural products and increased the AUROC score to 0.94 and BEDROC score to 0.73. This stacked model was deployed as a web application, called STarFish, and has been made available for use to aid in target identification for natural products.
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Affiliation(s)
- Nicholas T Cockroft
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Xiaolin Cheng
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy , The Ohio State University , Columbus , Ohio 43210 , United States
| | - James R Fuchs
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy , The Ohio State University , Columbus , Ohio 43210 , United States
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Bruns D, Merk D, Santhana Kumar K, Baumgartner M, Schneider G. Synthetic Activators of Cell Migration Designed by Constructive Machine Learning. ChemistryOpen 2019; 8:1303-1308. [PMID: 31660283 PMCID: PMC6807213 DOI: 10.1002/open.201900222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/11/2019] [Indexed: 11/26/2022] Open
Abstract
Constructive machine learning aims to create examples from its learned domain which are likely to exhibit similar properties. Here, a recurrent neural network was trained with the chemical structures of known cell-migration modulators. This machine learning model was used to generate new molecules that mimic the training compounds. Two top-scoring designs were synthesized, and tested for functional activity in a phenotypic spheroid cell migration assay. These computationally generated small molecules significantly increased the migration of medulloblastoma cells. The results further corroborate the applicability of constructive machine learning to the de novo design of druglike molecules with desired properties.
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Affiliation(s)
- Dominique Bruns
- ETH Zurich, Department ofChemistry and Applied BiosciencesVladimir-Prelog-Weg 4CH-8093ZurichSwitzerland
| | - Daniel Merk
- ETH Zurich, Department ofChemistry and Applied BiosciencesVladimir-Prelog-Weg 4CH-8093ZurichSwitzerland
| | - Karthiga Santhana Kumar
- Pediatric Neuro-OncologyResearch Group, Department of Oncology, Children's Research Center, University Children's Hospital ZurichLengghalde 5CH-8008ZurichSwitzerland
| | - Martin Baumgartner
- Pediatric Neuro-OncologyResearch Group, Department of Oncology, Children's Research Center, University Children's Hospital ZurichLengghalde 5CH-8008ZurichSwitzerland
| | - Gisbert Schneider
- ETH Zurich, Department ofChemistry and Applied BiosciencesVladimir-Prelog-Weg 4CH-8093ZurichSwitzerland
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58
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Cardoso-Silva J, Papageorgiou LG, Tsoka S. Network-based piecewise linear regression for QSAR modelling. J Comput Aided Mol Des 2019; 33:831-844. [PMID: 31628660 PMCID: PMC6825651 DOI: 10.1007/s10822-019-00228-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 09/28/2019] [Indexed: 02/07/2023]
Abstract
Quantitative Structure-Activity Relationship (QSAR) models are critical in various areas of drug discovery, for example in lead optimisation and virtual screening. Recently, the need for models that are not only predictive but also interpretable has been highlighted. In this paper, a new methodology is proposed to build interpretable QSAR models by combining elements of network analysis and piecewise linear regression. The algorithm presented, modSAR, splits data using a two-step procedure. First, compounds associated with a common target are represented as a network in terms of their structural similarity, revealing modules of similar chemical properties. Second, each module is subdivided into subsets (regions), each of which is modelled by an independent linear equation. Comparative analysis of QSAR models across five data sets of protein inhibitors obtained from ChEMBL is reported and it is shown that modSAR offers similar predictive accuracy to popular algorithms, such as Random Forest and Support Vector Machine. Moreover, we show that models built by modSAR are interpretatable, capable of evaluating the applicability domain of the compounds and serve well tasks such as virtual screening and the development of new drug leads.
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Affiliation(s)
- Jonathan Cardoso-Silva
- Department of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, Bush House, 30 Aldwych, London, WC2B 4BG, UK
| | - Lazaros G Papageorgiou
- Centre for Process Systems Engineering, Department of Chemical Engineering, University College London, Roberts Building, Torrington Place, London, WC1E 7JE, UK
| | - Sophia Tsoka
- Department of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, Bush House, 30 Aldwych, London, WC2B 4BG, UK.
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59
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Forouzesh A, Samadi Foroushani S, Forouzesh F, Zand E. Reliable Target Prediction of Bioactive Molecules Based on Chemical Similarity Without Employing Statistical Methods. Front Pharmacol 2019; 10:835. [PMID: 31404334 PMCID: PMC6676798 DOI: 10.3389/fphar.2019.00835] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 07/01/2019] [Indexed: 12/11/2022] Open
Abstract
The prediction of biological targets of bioactive molecules from machine-readable materials can be routinely performed by computational target prediction tools (CTPTs). However, the prediction of biological targets of bioactive molecules from non-digital materials (e.g., printed or handwritten documents) has not been possible due to the complex nature of bioactive molecules and impossibility of employing computations. Improving the target prediction accuracy is the most important challenge for computational target prediction. A minimum structure is identified for each group of neighbor molecules in the proposed method. Each group of neighbor molecules represents a distinct structural class of molecules with the same function in relation to the target. The minimum structure is employed as a query to search for molecules that perfectly satisfy the minimum structure of what is guessed crucial for the targeted activity. The proposed method is based on chemical similarity, but only molecules that perfectly satisfy the minimum structure are considered. Structurally related bioactive molecules found with the same minimum structure were considered as neighbor molecules of the query molecule. The known target of the neighbor molecule is used as a reference for predicting the target of the neighbor molecule with an unknown target. A lot of information is needed to identify the minimum structure, because it is necessary to know which part(s) of the bioactive molecule determines the precise target or targets responsible for the observed phenotype. Therefore, the predicted target based on the minimum structure without employing the statistical significance is considered as a reliable prediction. Since only molecules that perfectly (and not partly) satisfy the minimum structure are considered, the minimum structure can be used without similarity calculations in non-digital materials and with similarity calculations (perfect similarity) in machine-readable materials. Nine tools (PASS online, PPB, SEA, TargetHunter, PharmMapper, ChemProt, HitPick, SuperPred, and SPiDER), which can be used for computational target prediction, are compared with the proposed method for 550 target predictions. The proposed method, SEA, PPB, and PASS online, showed the best quality and quantity for the accurate predictions.
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Affiliation(s)
- Abed Forouzesh
- Iranian Research Institute of Plant Protection, Agricultural Research Education and Extension Organization (AREEO), Tehran, Iran
| | - Sadegh Samadi Foroushani
- Iranian Research Institute of Plant Protection, Agricultural Research Education and Extension Organization (AREEO), Tehran, Iran
| | - Fatemeh Forouzesh
- Department of Medicine, Tehran Medical Branch, Islamic Azad University, Tehran, Iran
| | - Eskandar Zand
- Iranian Research Institute of Plant Protection, Agricultural Research Education and Extension Organization (AREEO), Tehran, Iran
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60
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Yang X, Wang Y, Byrne R, Schneider G, Yang S. Concepts of Artificial Intelligence for Computer-Assisted Drug Discovery. Chem Rev 2019; 119:10520-10594. [PMID: 31294972 DOI: 10.1021/acs.chemrev.8b00728] [Citation(s) in RCA: 351] [Impact Index Per Article: 70.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Artificial intelligence (AI), and, in particular, deep learning as a subcategory of AI, provides opportunities for the discovery and development of innovative drugs. Various machine learning approaches have recently (re)emerged, some of which may be considered instances of domain-specific AI which have been successfully employed for drug discovery and design. This review provides a comprehensive portrayal of these machine learning techniques and of their applications in medicinal chemistry. After introducing the basic principles, alongside some application notes, of the various machine learning algorithms, the current state-of-the art of AI-assisted pharmaceutical discovery is discussed, including applications in structure- and ligand-based virtual screening, de novo drug design, physicochemical and pharmacokinetic property prediction, drug repurposing, and related aspects. Finally, several challenges and limitations of the current methods are summarized, with a view to potential future directions for AI-assisted drug discovery and design.
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Affiliation(s)
- Xin Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University , Chengdu , Sichuan 610041 , China
| | - Yifei Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University , Chengdu , Sichuan 610041 , China
| | - Ryan Byrne
- ETH Zurich , Department of Chemistry and Applied Biosciences , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland
| | - Gisbert Schneider
- ETH Zurich , Department of Chemistry and Applied Biosciences , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland
| | - Shengyong Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University , Chengdu , Sichuan 610041 , China
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61
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Button A, Merk D, Hiss JA, Schneider G. Automated de novo molecular design by hybrid machine intelligence and rule-driven chemical synthesis. NAT MACH INTELL 2019. [DOI: 10.1038/s42256-019-0067-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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62
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Rodrigues T, de Almeida BP, Barbosa-Morais NL, Bernardes GJL. Dissecting celastrol with machine learning to unveil dark pharmacology. Chem Commun (Camb) 2019; 55:6369-6372. [PMID: 31089616 DOI: 10.1039/c9cc03116b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
By coalescing bespoke machine learning and bioinformatics analyses with cell-based assays, we unveil the pharmacology of celastrol. Celastrol is a direct modulator of the progesterone and cannabinoid receptors, and its effects correlate with the antiproliferative activity. We demonstrate how in silico methods may drive systems biology studies for natural products.
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Affiliation(s)
- Tiago Rodrigues
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal.
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63
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Predicting protein-ligand interactions based on bow-pharmacological space and Bayesian additive regression trees. Sci Rep 2019; 9:7703. [PMID: 31118426 PMCID: PMC6531441 DOI: 10.1038/s41598-019-43125-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 04/12/2019] [Indexed: 02/08/2023] Open
Abstract
Identifying potential protein-ligand interactions is central to the field of drug discovery as it facilitates the identification of potential novel drug leads, contributes to advancement from hits to leads, predicts potential off-target explanations for side effects of approved drugs or candidates, as well as de-orphans phenotypic hits. For the rapid identification of protein-ligand interactions, we here present a novel chemogenomics algorithm for the prediction of protein-ligand interactions using a new machine learning approach and novel class of descriptor. The algorithm applies Bayesian Additive Regression Trees (BART) on a newly proposed proteochemical space, termed the bow-pharmacological space. The space spans three distinctive sub-spaces that cover the protein space, the ligand space, and the interaction space. Thereby, the model extends the scope of classical target prediction or chemogenomic modelling that relies on one or two of these subspaces. Our model demonstrated excellent prediction power, reaching accuracies of up to 94.5–98.4% when evaluated on four human target datasets constituting enzymes, nuclear receptors, ion channels, and G-protein-coupled receptors . BART provided a reliable probabilistic description of the likelihood of interaction between proteins and ligands, which can be used in the prioritization of assays to be performed in both discovery and vigilance phases of small molecule development.
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64
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Grisoni F, Merk D, Friedrich L, Schneider G. Design of Natural-Product-Inspired Multitarget Ligands by Machine Learning. ChemMedChem 2019; 14:1129-1134. [PMID: 30973672 DOI: 10.1002/cmdc.201900097] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/02/2019] [Indexed: 11/08/2022]
Abstract
A virtual screening protocol based on machine learning models was used to identify mimetics of the natural product (-)-galantamine. This fully automated approach identified eight compounds with bioactivities on at least one of the macromolecular targets of (-)-galantamine, with different polypharmacological profiles. Two of the computer-generated hits possess an expanded spectrum of bioactivity on targets relevant to the treatment of Alzheimer's disease and are suitable for hit-to-lead expansion. These results advocate multitarget drug design by advanced virtual screening protocols based on chemically informed machine learning models.
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Affiliation(s)
- Francesca Grisoni
- Department of Chemistry and Applied Biosciences, RETHINK, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Daniel Merk
- Department of Chemistry and Applied Biosciences, RETHINK, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Lukas Friedrich
- Department of Chemistry and Applied Biosciences, RETHINK, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, RETHINK, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
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65
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Ekins S, Puhl AC, Zorn KM, Lane TR, Russo DP, Klein JJ, Hickey AJ, Clark AM. Exploiting machine learning for end-to-end drug discovery and development. NATURE MATERIALS 2019; 18:435-441. [PMID: 31000803 PMCID: PMC6594828 DOI: 10.1038/s41563-019-0338-z] [Citation(s) in RCA: 242] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/07/2019] [Indexed: 05/20/2023]
Abstract
A variety of machine learning methods such as naive Bayesian, support vector machines and more recently deep neural networks are demonstrating their utility for drug discovery and development. These leverage the generally bigger datasets created from high-throughput screening data and allow prediction of bioactivities for targets and molecular properties with increased levels of accuracy. We have only just begun to exploit the potential of these techniques but they may already be fundamentally changing the research process for identifying new molecules and/or repurposing old drugs. The integrated application of such machine learning models for end-to-end (E2E) application is broadly relevant and has considerable implications for developing future therapies and their targeting.
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Affiliation(s)
- Sean Ekins
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, USA.
| | - Ana C Puhl
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, USA
| | | | - Thomas R Lane
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, USA
| | - Daniel P Russo
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, USA
- The Rutgers Center for Computational and Integrative Biology, Camden, NJ, USA
| | | | - Anthony J Hickey
- RTI International, Research Triangle Park, NC, USA
- UNC Catalyst for Rare Diseases, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alex M Clark
- Molecular Materials Informatics, Inc., Montreal, Quebec, Canada
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66
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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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67
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Schneidewind T, Kapoor S, Garivet G, Karageorgis G, Narayan R, Vendrell-Navarro G, Antonchick AP, Ziegler S, Waldmann H. The Pseudo Natural Product Myokinasib Is a Myosin Light Chain Kinase 1 Inhibitor with Unprecedented Chemotype. Cell Chem Biol 2019; 26:512-523.e5. [DOI: 10.1016/j.chembiol.2018.11.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 09/14/2018] [Accepted: 11/26/2018] [Indexed: 12/20/2022]
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68
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Nogueira MS, Koch O. The Development of Target-Specific Machine Learning Models as Scoring Functions for Docking-Based Target Prediction. J Chem Inf Model 2019; 59:1238-1252. [DOI: 10.1021/acs.jcim.8b00773] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Mauro S. Nogueira
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Oliver Koch
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
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70
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Abstract
Drug promiscuity or polypharmacology is the ability of small molecules to interact with multiple protein targets simultaneously. In drug discovery, understanding the polypharmacology of potential drug molecules is crucial to improve their efficacy and safety, and to discover the new therapeutic potentials of existing drugs. Over the past decade, several computational methods have been developed to study the polypharmacology of small molecules, many of which are available as Web services. In this chapter, we review some of these Web tools focusing on ligand based approaches. We highlight in particular our recently developed polypharmacology browser (PPB) and its application for finding the side targets of a new inhibitor of the TRPV6 calcium channel.
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Affiliation(s)
- Mahendra Awale
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Berne, Berne, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Berne, Berne, Switzerland.
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71
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Abstract
Retinoid X receptors (RXRs) are promiscuous partners of heterodimeric associations with other members of the Nuclear Receptor (NR) superfamily. RXR ligands ("rexinoids") either transcriptionally activate the "permissive" subclass of heterodimers or synergize with partner ligands in the "nonpermissive" subclass of heterodimers. The rationale for rexinoid design with a wide structural diversity going from the structures of existing complexes with RXR determined by X-Ray, to natural products and other ligands discovered by high-throughput screening (HTS), mere serendipity, and rationally designed based on Molecular Modeling, will be described. Included is the new generation of ligands that modulate the structure of specific receptor surfaces that serve to communicate with other regulators. The panel of the known RXR agonists, partial (ant)agonists, and/or heterodimer-selective rexinoids require the exploration of their therapeutic potential in order to overcome some of the current limitations of rexinoids in therapy.
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Affiliation(s)
- Claudio Martínez
- Departamento de Química Orgánica, Facultade de Química, CINBIO and IBIV, Universidade de Vigo, Vigo, Spain
| | - José A Souto
- Departamento de Química Orgánica, Facultade de Química, CINBIO and IBIV, Universidade de Vigo, Vigo, Spain
| | - Angel R de Lera
- Departamento de Química Orgánica, Facultade de Química, CINBIO and IBIV, Universidade de Vigo, Vigo, Spain.
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72
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[Special Issue for Honor Award dedicating to Prof Kimito Funatsu](Mini-review)Meanings of the Honor Award for Prof Kimito Funatsu. JOURNAL OF COMPUTER AIDED CHEMISTRY 2019. [DOI: 10.2751/jcac.20.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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73
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Abstract
Pharmacological science is trying to establish the link between chemicals, targets, and disease-related phenotypes. A plethora of chemical proteomics and structural data have been generated, thanks to the target-based approach that has dominated drug discovery at the turn of the century. There is an invaluable source of information for in silico target profiling. Prediction is based on the principle of chemical similarity (similar drugs bind similar targets) or on first principles from the biophysics of molecular interactions. In the first case, compound comparison is made through ligand-based chemical similarity search or through classifier-based machine learning approach. The 3D techniques are based on 3D structural descriptors or energy-based scoring scheme to infer a binding affinity of a compound with its putative target. More recently, a new approach based on compound set metric has been proposed in which a query compound is compared with a whole of compounds associated with a target or a family of targets. This chapter reviews the different techniques of in silico target profiling and their main applications such as inference of unwanted targets, drug repurposing, or compound prioritization after phenotypic-based screening campaigns.
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74
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Abstract
Drugs modulate disease states through their actions on targets in the body. Determining these targets aids the focused development of new treatments, and helps to better characterize those already employed. One means of accomplishing this is through the deployment of in silico methodologies, harnessing computational analytical and predictive power to produce educated hypotheses for experimental verification. Here, we provide an overview of the current state of the art, describe some of the well-established methods in detail, and reflect on how they, and emerging technologies promoting the incorporation of complex and heterogeneous data-sets, can be employed to improve our understanding of (poly)pharmacology.
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Affiliation(s)
- Ryan Byrne
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland.
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75
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A Toolbox for the Identification of Modes of Action of Natural Products. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 110 2019; 110:73-97. [DOI: 10.1007/978-3-030-14632-0_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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76
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Awale M, Reymond JL. Polypharmacology Browser PPB2: Target Prediction Combining Nearest Neighbors with Machine Learning. J Chem Inf Model 2018; 59:10-17. [PMID: 30558418 DOI: 10.1021/acs.jcim.8b00524] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Here we report PPB2 as a target prediction tool assigning targets to a query molecule based on ChEMBL data. PPB2 computes ligand similarities using molecular fingerprints encoding composition (MQN), molecular shape and pharmacophores (Xfp), and substructures (ECfp4) and features an unprecedented combination of nearest neighbor (NN) searches and Naı̈ve Bayes (NB) machine learning, together with simple NN searches, NB and Deep Neural Network (DNN) machine learning models as further options. Although NN(ECfp4) gives the best results in terms of recall in a 10-fold cross-validation study, combining NN searches with NB machine learning provides superior precision statistics, as well as better results in a case study predicting off-targets of a recently reported TRPV6 calcium channel inhibitor, illustrating the value of this combined approach. PPB2 is available to assess possible off-targets of small molecule drug-like compounds by public access at http://gdb.unibe.ch .
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Affiliation(s)
- Mahendra Awale
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland
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77
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Abstract
Abstract
The biological pre-validation of natural products (NPs) and their underlying frameworks ensures an unrivaled source of inspiration for chemical probe and drug design. However, the poor knowledge of their drug target counterparts critically hinders the broader exploration of NPs in chemical biology and molecular medicine. Cutting-edge algorithms now provide powerful means for the target deconvolution of phenotypic screen hits and generate motivated research hypotheses. Herein, we present recent progress in artificial intelligence applied to target identification that may accelerate future NP-inspired molecular medicine.
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78
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Uddin R, Masood F, Azam SS, Wadood A. Identification of putative non-host essential genes and novel drug targets against Acinetobacter baumannii by in silico comparative genome analysis. Microb Pathog 2018; 128:28-35. [PMID: 30550846 DOI: 10.1016/j.micpath.2018.12.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 12/10/2018] [Accepted: 12/10/2018] [Indexed: 10/27/2022]
Abstract
Acinetobacter baumannii, the gram-negative bacteria emerged as an extremely critical pathogen causing nosocomial and different kinds of infections. A. baumannii exhibit resistivity towards various classes of antibiotics that shows that there is a dire need to search more drug targets by exploiting the full genome of the bacteria. In doing so, a strategy is made with the combination of computational biology, pathogen informatics and cheminformatics. Comparative genomics analysis, modeling and docking studies have been performed for the prediction of non-host essential genes and novel drug candidates against A. baumannii. Among 37 unique and 82 common metabolic pathways, 92 genes were predicted as non-host genes. Similarly, using homology search between A. baumannii genome and essential genes of different bacteria, 293 genes were predicted as essential genes of A. baumannii. Among these predicted non-host and essential genes, 86 genes were predicted as non-host essential genes which could serve as potential novel drug and vaccine targets. Additional drug-target like physicochemical properties were estimated such as the molecular weight, subcellular localization and druggability potential. On the structural part, the crystal structures of all the non-host essential genes of A. baumannii were found except the three genes. Out of these three, a homology model of Undecaprenyl-diphosphatase was built using a PDB template by MODELLER [version 9.18]. The quality of the model was assessed by the ProSA and RAMPAGE. The built model was subjected as a receptor for the molecular docking with Adenosine diphosphate (ADP) as a ligand. The molecular docking was performed by AutoDock4 and the best conformation with lowest binding energy (-4.39 kcal/mol) was obtained. The LigPlot was used to identify the close interactions between the ligand the receptor's residues. This study will further aid for the selection of putative inhibitors against a novel drug target identified against A. baumannii and hence could lead to the better therapeutics.
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Affiliation(s)
- Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan.
| | - Fareha Masood
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan
| | - Syed Sikander Azam
- National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
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79
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Poirier M, Awale M, Roelli MA, Giuffredi GT, Ruddigkeit L, Evensen L, Stooss A, Calarco S, Lorens JB, Charles RP, Reymond JL. Identifying Lysophosphatidic Acid Acyltransferase β (LPAAT-β) as the Target of a Nanomolar Angiogenesis Inhibitor from a Phenotypic Screen Using the Polypharmacology Browser PPB2. ChemMedChem 2018; 14:224-236. [PMID: 30520265 DOI: 10.1002/cmdc.201800554] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Indexed: 12/11/2022]
Abstract
By screening a focused library of kinase inhibitor analogues in a phenotypic co-culture assay for angiogenesis inhibition, we identified an aminotriazine that acts as a cytostatic nanomolar inhibitor. However, this aminotriazine was found to be completely inactive in a whole-kinome profiling assay. To decipher its mechanism of action, we used the online target prediction tool PPB2 (http://ppb2.gdb.tools), which suggested lysophosphatidic acid acyltransferase β (LPAAT-β) as a possible target for this aminotriazine as well as several analogues identified by structure-activity relationship profiling. LPAAT-β inhibition (IC50 ≈15 nm) was confirmed in a biochemical assay and by its effects on cell proliferation in comparison with a known LPAAT-β inhibitor. These experiments illustrate the value of target-prediction tools to guide target identification for phenotypic screening hits and significantly expand the rather limited pharmacology of LPAAT-β inhibitors.
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Affiliation(s)
- Marion Poirier
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Matthias A Roelli
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3000, Bern 9, Switzerland
| | - Guy T Giuffredi
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Lars Ruddigkeit
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Lasse Evensen
- Department of Biomedicine, Centre for Cancer Biomarkers (CCBIO), University of Bergen, Jonas Lies vei 91, 5009, Bergen, Norway
| | - Amandine Stooss
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3000, Bern 9, Switzerland
| | - Serafina Calarco
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3000, Bern 9, Switzerland
| | - James B Lorens
- Department of Biomedicine, Centre for Cancer Biomarkers (CCBIO), University of Bergen, Jonas Lies vei 91, 5009, Bergen, Norway
| | - Roch-Philippe Charles
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3000, Bern 9, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
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80
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Grisoni F, Merk D, Byrne R, Schneider G. Scaffold-Hopping from Synthetic Drugs by Holistic Molecular Representation. Sci Rep 2018; 8:16469. [PMID: 30405170 PMCID: PMC6220272 DOI: 10.1038/s41598-018-34677-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/16/2018] [Indexed: 12/31/2022] Open
Abstract
The discovery of novel ligand chemotypes allows to explore uncharted regions in chemical space, thereby potentially improving synthetic accessibility, potency, and the drug-likeness of molecules. Here, we demonstrate the scaffold-hopping ability of the new Weighted Holistic Atom Localization and Entity Shape (WHALES) molecular descriptors compared to seven state-of-the-art molecular representations on 30,000 compounds and 182 biological targets. In a prospective application, we apply WHALES to the discovery of novel retinoid X receptor (RXR) modulators. WHALES descriptors identified four agonists with innovative molecular scaffolds, populating uncharted regions of the chemical space. One of the agonists, possessing a rare non-acidic chemotype, revealed high selectivity on 12 nuclear receptors and comparable efficacy as bexarotene on induction of ATP-binding cassette transporter A1, angiopoietin like protein 4 and apolipoprotein E. The outcome of this research supports WHALES as an innovative tool to explore novel regions of the chemical space and to detect novel bioactive chemotypes by straightforward similarity searching.
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Affiliation(s)
- Francesca Grisoni
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland. .,Milano Chemometrics & QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, IT-20126, Milano, Italy.
| | - Daniel Merk
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Ryan Byrne
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Gisbert Schneider
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland.
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81
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Merk D, Grisoni F, Friedrich L, Schneider G. Tuning artificial intelligence on the de novo design of natural-product-inspired retinoid X receptor modulators. Commun Chem 2018. [DOI: 10.1038/s42004-018-0068-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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82
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Merk D, Grisoni F, Friedrich L, Gelzinyte E, Schneider G. Scaffold hopping from synthetic RXR modulators by virtual screening and de novo design. MEDCHEMCOMM 2018; 9:1289-1292. [PMID: 30151082 PMCID: PMC6096356 DOI: 10.1039/c8md00134k] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 04/15/2018] [Indexed: 01/03/2023]
Abstract
The lack of potent subtype-selective modulators of retinoid X receptors (RXRs) has hindered their full exploitation as promising drug targets. Using computational similarity searching, target prediction and automated de novo design, we identified novel RXR ligands exhibiting innovative molecular frameworks, pronounced receptor-subtype preference and suitable properties for hit-to-lead expansion.
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Affiliation(s)
- Daniel Merk
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland .
| | - Francesca Grisoni
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland .
- Department of Earth and Environmental Sciences , University of Milano-Bicocca , P.za della Scienza, 1 , IT-20126 Milan , Italy
| | - Lukas Friedrich
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland .
| | - Elena Gelzinyte
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland .
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland .
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83
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Henson AB, Gromski PS, Cronin L. Designing Algorithms To Aid Discovery by Chemical Robots. ACS CENTRAL SCIENCE 2018; 4:793-804. [PMID: 30062108 PMCID: PMC6062836 DOI: 10.1021/acscentsci.8b00176] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Indexed: 05/25/2023]
Abstract
Recently, automated robotic systems have become very efficient, thanks to improved coupling between sensor systems and algorithms, of which the latter have been gaining significance thanks to the increase in computing power over the past few decades. However, intelligent automated chemistry platforms for discovery orientated tasks need to be able to cope with the unknown, which is a profoundly hard problem. In this Outlook, we describe how recent advances in the design and application of algorithms, coupled with the increased amount of chemical data available, and automation and control systems may allow more productive chemical research and the development of chemical robots able to target discovery. This is shown through examples of workflow and data processing with automation and control, and through the use of both well-used and cutting-edge algorithms illustrated using recent studies in chemistry. Finally, several algorithms are presented in relation to chemical robots and chemical intelligence for knowledge discovery.
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84
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Rodrigues T, Werner M, Roth J, da Cruz EHG, Marques MC, Akkapeddi P, Lobo SA, Koeberle A, Corzana F, da Silva Júnior EN, Werz O, Bernardes GJL. Machine intelligence decrypts β-lapachone as an allosteric 5-lipoxygenase inhibitor. Chem Sci 2018; 9:6899-6903. [PMID: 30310622 PMCID: PMC6138237 DOI: 10.1039/c8sc02634c] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 07/17/2018] [Indexed: 12/04/2022] Open
Abstract
Using machine learning, targets were identified for β-lapachone.
Using machine learning, targets were identified for β-lapachone. Resorting to biochemical assays, β-lapachone was validated as a potent, ligand efficient, allosteric and reversible modulator of 5-lipoxygenase (5-LO). Moreover, we provide a rationale for 5-LO modulation and show that inhibition of 5-LO is relevant for the anticancer activity of β-lapachone. This work demonstrates the power of machine intelligence to deconvolute complex phenotypes, as an alternative and/or complement to chemoproteomics and as a viable general approach for systems pharmacology studies.
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Affiliation(s)
- Tiago Rodrigues
- Instituto de Medicina Molecular , Faculdade de Medicina da Universidade de Lisboa , Av Prof Egaz Moniz , 1649-028 Lisboa , Portugal . ;
| | - Markus Werner
- Institute of Pharmacy , Friedrich-Schiller-University Jena , Philosophenweg 14 , D-07743 , Jena , Germany
| | - Jakob Roth
- Institute of Pharmacy , Friedrich-Schiller-University Jena , Philosophenweg 14 , D-07743 , Jena , Germany
| | - Eduardo H G da Cruz
- Institute of Exact Sciences , Department of Chemistry , Federal University of Minas Gerais , Belo Horizonte , Brazil
| | - Marta C Marques
- Instituto de Medicina Molecular , Faculdade de Medicina da Universidade de Lisboa , Av Prof Egaz Moniz , 1649-028 Lisboa , Portugal . ;
| | - Padma Akkapeddi
- Instituto de Medicina Molecular , Faculdade de Medicina da Universidade de Lisboa , Av Prof Egaz Moniz , 1649-028 Lisboa , Portugal . ;
| | - Susana A Lobo
- Instituto de Medicina Molecular , Faculdade de Medicina da Universidade de Lisboa , Av Prof Egaz Moniz , 1649-028 Lisboa , Portugal . ;
| | - Andreas Koeberle
- Institute of Pharmacy , Friedrich-Schiller-University Jena , Philosophenweg 14 , D-07743 , Jena , Germany
| | - Francisco Corzana
- Departamento de Química , Centro de Investigacíon en Síntesis Química , Universidad de la Rioja , 26006 Logroño , Spain
| | - Eufrânio N da Silva Júnior
- Institute of Exact Sciences , Department of Chemistry , Federal University of Minas Gerais , Belo Horizonte , Brazil
| | - Oliver Werz
- Institute of Pharmacy , Friedrich-Schiller-University Jena , Philosophenweg 14 , D-07743 , Jena , Germany
| | - Gonçalo J L Bernardes
- Instituto de Medicina Molecular , Faculdade de Medicina da Universidade de Lisboa , Av Prof Egaz Moniz , 1649-028 Lisboa , Portugal . ; .,Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW Cambridge , UK .
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85
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Pereira F, Aires-de-Sousa J. Computational Methodologies in the Exploration of Marine Natural Product Leads. Mar Drugs 2018; 16:md16070236. [PMID: 30011882 PMCID: PMC6070892 DOI: 10.3390/md16070236] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/02/2018] [Accepted: 07/06/2018] [Indexed: 12/18/2022] Open
Abstract
Computational methodologies are assisting the exploration of marine natural products (MNPs) to make the discovery of new leads more efficient, to repurpose known MNPs, to target new metabolites on the basis of genome analysis, to reveal mechanisms of action, and to optimize leads. In silico efforts in drug discovery of NPs have mainly focused on two tasks: dereplication and prediction of bioactivities. The exploration of new chemical spaces and the application of predicted spectral data must be included in new approaches to select species, extracts, and growth conditions with maximum probabilities of medicinal chemistry novelty. In this review, the most relevant current computational dereplication methodologies are highlighted. Structure-based (SB) and ligand-based (LB) chemoinformatics approaches have become essential tools for the virtual screening of NPs either in small datasets of isolated compounds or in large-scale databases. The most common LB techniques include Quantitative Structure–Activity Relationships (QSAR), estimation of drug likeness, prediction of adsorption, distribution, metabolism, excretion, and toxicity (ADMET) properties, similarity searching, and pharmacophore identification. Analogously, molecular dynamics, docking and binding cavity analysis have been used in SB approaches. Their significance and achievements are the main focus of this review.
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Affiliation(s)
- Florbela Pereira
- LAQV and REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
| | - Joao Aires-de-Sousa
- LAQV and REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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86
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Brand S, Roy S, Schröder P, Rathmer B, Roos J, Kapoor S, Patil S, Pommerenke C, Maier T, Janning P, Eberth S, Steinhilber D, Schade D, Schneider G, Kumar K, Ziegler S, Waldmann H. Combined Proteomic and In Silico Target Identification Reveal a Role for 5-Lipoxygenase in Developmental Signaling Pathways. Cell Chem Biol 2018; 25:1095-1106.e23. [PMID: 30251630 DOI: 10.1016/j.chembiol.2018.05.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 02/26/2018] [Accepted: 05/22/2018] [Indexed: 12/21/2022]
Abstract
Identification and validation of the targets of bioactive small molecules identified in cell-based screening is challenging and often meets with failure, calling for the development of new methodology. We demonstrate that a combination of chemical proteomics with in silico target prediction employing the SPiDER method may provide efficient guidance for target candidate selection and prioritization for experimental in-depth evaluation. We identify 5-lipoxygenase (5-LO) as the target of the Wnt pathway inhibitor Lipoxygenin. Lipoxygenin is a non-redox 5-LO inhibitor, modulates the β-catenin-5-LO complex and induces reduction of both β-catenin and 5-LO levels in the nucleus. Lipoxygenin and the structurally unrelated 5-LO inhibitor CJ-13,610 promote cardiac differentiation of human induced pluripotent stem cells and inhibit Hedgehog, TGF-β, BMP, and Activin A signaling, suggesting an unexpected and yet unknown role of 5-LO in these developmental pathways.
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Affiliation(s)
- Silke Brand
- Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund 44227, Germany; Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, Dortmund 44227, Germany
| | - Sayantani Roy
- Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Peter Schröder
- Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund 44227, Germany; Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, Dortmund 44227, Germany
| | - Bernd Rathmer
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, Dortmund 44227, Germany
| | - Jessica Roos
- Goethe Universität, Institut für Pharmazeutische Chemie, Max-von-Laue-Strasse 9, Frankfurt am Main 60438, Germany
| | - Shobhna Kapoor
- Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Sumersing Patil
- Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Claudia Pommerenke
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, Braunschweig 38124, Germany
| | - Thorsten Maier
- Department for Anesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Theodor-Stern-Kai 7, Frankfurt 60590, Germany; Aarhus University, Department of Biomedicine, Bartholins Allé 6, Aarhus C 8000, Denmark
| | - Petra Janning
- Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Sonja Eberth
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, Braunschweig 38124, Germany
| | - Dieter Steinhilber
- Goethe Universität, Institut für Pharmazeutische Chemie, Max-von-Laue-Strasse 9, Frankfurt am Main 60438, Germany
| | - Dennis Schade
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, Dortmund 44227, Germany
| | - Gisbert Schneider
- ETH Zürich, Institut für Pharmazeutische Wissenschaften, Vladimir-Prelog-Weg 1-5/10, Zürich CH-8093, Switzerland
| | - Kamal Kumar
- Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Slava Ziegler
- Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Herbert Waldmann
- Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund 44227, Germany; Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, Dortmund 44227, Germany.
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87
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Merk D, Grisoni F, Friedrich L, Gelzinyte E, Schneider G. Computer-Assisted Discovery of Retinoid X Receptor Modulating Natural Products and Isofunctional Mimetics. J Med Chem 2018; 61:5442-5447. [DOI: 10.1021/acs.jmedchem.8b00494] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Daniel Merk
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Francesca Grisoni
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza, 1, IT-20126 Milan, Italy
| | - Lukas Friedrich
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Elena Gelzinyte
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
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88
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Giordano A, Forte G, Massimo L, Riccio R, Bifulco G, Di Micco S. Discovery of new erbB4 inhibitors: Repositioning an orphan chemical library by inverse virtual screening. Eur J Med Chem 2018; 152:253-263. [PMID: 29730188 DOI: 10.1016/j.ejmech.2018.04.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/05/2018] [Accepted: 04/09/2018] [Indexed: 01/20/2023]
Abstract
Inverse Virtual Screening (IVS) is a docking based approach aimed to the evaluation of the virtual ability of a single compound to interact with a library of proteins. For the first time, we applied this methodology to a library of synthetic compounds, which proved to be inactive towards the target they were initially designed for. Trifluoromethyl-benzenesulfonamides 3-21 were repositioned by means of IVS identifying new lead compounds (14-16, 19 and 20) for the inhibition of erbB4 in the low micromolar range. Among these, compound 20 exhibited an interesting value of IC50 on MCF7 cell lines, thus validating IVS in lead repurposing.
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Affiliation(s)
- Assunta Giordano
- Institute of Biomolecular Chemistry (ICB), Consiglio Nazionale delle Ricerche (CNR), Via Campi Flegrei 34, I-80078, Pozzuoli, Napoli, Italy; Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy
| | - Giovanni Forte
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy
| | - Luigia Massimo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy; PhD Program in Drug Discovery and Development, University of Salerno, Via Giovanni Paolo II 132, I-84084, Fisciano, SA, Italy
| | - Raffaele Riccio
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
| | - Simone Di Micco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
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89
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Thomford NE, Senthebane DA, Rowe A, Munro D, Seele P, Maroyi A, Dzobo K. Natural Products for Drug Discovery in the 21st Century: Innovations for Novel Drug Discovery. Int J Mol Sci 2018; 19:E1578. [PMID: 29799486 PMCID: PMC6032166 DOI: 10.3390/ijms19061578] [Citation(s) in RCA: 566] [Impact Index Per Article: 94.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/16/2018] [Accepted: 05/18/2018] [Indexed: 12/12/2022] Open
Abstract
The therapeutic properties of plants have been recognised since time immemorial. Many pathological conditions have been treated using plant-derived medicines. These medicines are used as concoctions or concentrated plant extracts without isolation of active compounds. Modern medicine however, requires the isolation and purification of one or two active compounds. There are however a lot of global health challenges with diseases such as cancer, degenerative diseases, HIV/AIDS and diabetes, of which modern medicine is struggling to provide cures. Many times the isolation of "active compound" has made the compound ineffective. Drug discovery is a multidimensional problem requiring several parameters of both natural and synthetic compounds such as safety, pharmacokinetics and efficacy to be evaluated during drug candidate selection. The advent of latest technologies that enhance drug design hypotheses such as Artificial Intelligence, the use of 'organ-on chip' and microfluidics technologies, means that automation has become part of drug discovery. This has resulted in increased speed in drug discovery and evaluation of the safety, pharmacokinetics and efficacy of candidate compounds whilst allowing novel ways of drug design and synthesis based on natural compounds. Recent advances in analytical and computational techniques have opened new avenues to process complex natural products and to use their structures to derive new and innovative drugs. Indeed, we are in the era of computational molecular design, as applied to natural products. Predictive computational softwares have contributed to the discovery of molecular targets of natural products and their derivatives. In future the use of quantum computing, computational softwares and databases in modelling molecular interactions and predicting features and parameters needed for drug development, such as pharmacokinetic and pharmacodynamics, will result in few false positive leads in drug development. This review discusses plant-based natural product drug discovery and how innovative technologies play a role in next-generation drug discovery.
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Affiliation(s)
- Nicholas Ekow Thomford
- Pharmacogenomics and Drug Metabolism Group, Division of Human Genetics, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa.
- School of Medical Sciences, University of Cape Coast, PMB, Cape Coast, Ghana.
| | - Dimakatso Alice Senthebane
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Wernher and Beit Building (South), University of Cape Town Medical Campus, Anzio Road, Observatory, Cape Town 7925, South Africa.
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa.
| | - Arielle Rowe
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Wernher and Beit Building (South), University of Cape Town Medical Campus, Anzio Road, Observatory, Cape Town 7925, South Africa.
| | - Daniella Munro
- Pharmacogenomics and Drug Metabolism Group, Division of Human Genetics, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa.
| | - Palesa Seele
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa.
| | - Alfred Maroyi
- Department of Botany, University of Fort Hare, Private Bag, Alice X1314, South Africa.
| | - Kevin Dzobo
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Wernher and Beit Building (South), University of Cape Town Medical Campus, Anzio Road, Observatory, Cape Town 7925, South Africa.
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa.
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90
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Schneider P, Schneider G. Polypharmacological Drug−target Inference for Chemogenomics. Mol Inform 2018; 37:e1800050. [DOI: 10.1002/minf.201800050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 04/24/2018] [Indexed: 01/10/2023]
Affiliation(s)
- Petra Schneider
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology (ETH); Vladimir-Prelog-Weg 4 CH-8093 Zurich Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology (ETH); Vladimir-Prelog-Weg 4 CH-8093 Zurich Switzerland
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91
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Comess KM, McLoughlin SM, Oyer JA, Richardson PL, Stöckmann H, Vasudevan A, Warder SE. Emerging Approaches for the Identification of Protein Targets of Small Molecules - A Practitioners’ Perspective. J Med Chem 2018; 61:8504-8535. [DOI: 10.1021/acs.jmedchem.7b01921] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Kenneth M. Comess
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Shaun M. McLoughlin
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Jon A. Oyer
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Paul L. Richardson
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Henning Stöckmann
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Anil Vasudevan
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Scott E. Warder
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
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92
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Rodrigues T. Harnessing the potential of natural products in drug discovery from a cheminformatics vantage point. Org Biomol Chem 2018; 15:9275-9282. [PMID: 29085945 DOI: 10.1039/c7ob02193c] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Natural products (NPs) present a privileged source of inspiration for chemical probe and drug design. Despite the biological pre-validation of the underlying molecular architectures and their relevance in drug discovery, the poor accessibility to NPs, complexity of the synthetic routes and scarce knowledge of their macromolecular counterparts in phenotypic screens still hinder their broader exploration. Cheminformatics algorithms now provide a powerful means of circumventing the abovementioned challenges and unlocking the full potential of NPs in a drug discovery context. Herein, I discuss recent advances in the computer-assisted design of NP mimics and how artificial intelligence may accelerate future NP-inspired molecular medicine.
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Affiliation(s)
- Tiago Rodrigues
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal.
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93
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94
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Cui J, Hollmén M, Li L, Chen Y, Proulx ST, Reker D, Schneider G, Detmar M. New use of an old drug: inhibition of breast cancer stem cells by benztropine mesylate. Oncotarget 2018; 8:1007-1022. [PMID: 27894093 PMCID: PMC5352030 DOI: 10.18632/oncotarget.13537] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 11/06/2016] [Indexed: 01/06/2023] Open
Abstract
Cancer stem cells (CSCs) play major roles in cancer initiation, metastasis, recurrence and therapeutic resistance. Targeting CSCs represents a promising strategy for cancer treatment. The purpose of this study was to identify selective inhibitors of breast CSCs (BCSCs). We carried out a cell-based phenotypic screening with cell viability as a primary endpoint, using a collection of 2,546 FDA-approved drugs and drug-like molecules in spheres formed by malignant human breast gland-derived cells (HMLER-shEcad cells, representing BCSCs) and control immortalized non-tumorigenic human mammary cells (HMLE cells, representing normal stem cells). 19 compounds were identified from screening. The chemically related molecules benztropine mesylate and deptropine citrate were selected for further validation and both potently inhibited sphere formation and self-renewal of BCSCs in vitro. Benztropine mesylate treatment decreased cell subpopulations with high ALDH activity and with a CD44+/CD24− phenotype. In vivo, benztropine mesylate inhibited tumor-initiating potential in a 4T1 mouse model. Functional studies indicated that benztropine mesylate inhibits functions of CSCs via the acetylcholine receptors, dopamine transporters/receptors, and/or histamine receptors. In summary, our findings identify benztropine mesylate as an inhibitor of BCSCs in vitro and in vivo. This study also provides a screening platform for identification of additional anti-CSC agents.
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Affiliation(s)
- Jihong Cui
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | - Maija Hollmén
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | - Lina Li
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | - Yong Chen
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | - Steven T Proulx
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | - Daniel Reker
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | - Gisbert Schneider
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | - Michael Detmar
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
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95
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Rakers C, Najnin RA, Polash AH, Takeda S, Brown J. Chemogenomic Active Learning's Domain of Applicability on Small, Sparse qHTS Matrices: A Study Using Cytochrome P450 and Nuclear Hormone Receptor Families. ChemMedChem 2018; 13:511-521. [DOI: 10.1002/cmdc.201700677] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/04/2017] [Indexed: 01/21/2023]
Affiliation(s)
- Christin Rakers
- Institute of Transformative bio-Molecules, WPI-ITbM; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8602 Japan
| | - Rifat Ara Najnin
- Department of Radiation Genetics; Kyoto University Graduate School of Medicine; Sakyo, Yoshida-konoemachi Building D, 3F Kyoto 606-8501 Japan
| | - Ahsan Habib Polash
- Department of Radiation Genetics; Kyoto University Graduate School of Medicine; Sakyo, Yoshida-konoemachi Building D, 3F Kyoto 606-8501 Japan
| | - Shunichi Takeda
- Department of Radiation Genetics; Kyoto University Graduate School of Medicine; Sakyo, Yoshida-konoemachi Building D, 3F Kyoto 606-8501 Japan
| | - J.B. Brown
- Laboratory for Molecular Biosciences; Kyoto University Graduate School of Medicine; Yoshida-konoemachi Building E 606-8501 Kyoto Sakyo Japan
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96
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Rodrigues T, Sieglitz F, Bernardes GJL. Natural product modulators of transient receptor potential (TRP) channels as potential anti-cancer agents. Chem Soc Rev 2018; 45:6130-6137. [PMID: 26890476 DOI: 10.1039/c5cs00916b] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Treatment of cancer is a significant challenge in clinical medicine, and its research is a top priority in chemical biology and drug discovery. Consequently, there is an urgent need for identifying innovative chemotypes capable of modulating unexploited drug targets. The transient receptor potential (TRPs) channels persist scarcely explored as targets, despite intervening in a plethora of pathophysiological events in numerous diseases, including cancer. Both agonists and antagonists have proven capable of evoking phenotype changes leading to either cell death or reduced cell migration. Among these, natural products entail biologically pre-validated and privileged architectures for TRP recognition. Furthermore, several natural products have significantly contributed to our current knowledge on TRP biology. In this Tutorial Review we focus on selected natural products, e.g. capsaicinoids, cannabinoids and terpenes, by highlighting challenges and opportunities in their use as starting points for designing natural product-inspired TRP channel modulators. Importantly, the de-orphanization of natural products as TRP channel ligands may leverage their exploration as viable strategy for developing anticancer therapies. Finally, we foresee that TRP channels may be explored for the selective pharmacodelivery of cytotoxic payloads to diseased tissues, providing an innovative platform in chemical biology and molecular medicine.
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Affiliation(s)
- Tiago Rodrigues
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Florian Sieglitz
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Gonçalo J L Bernardes
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal and Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK.
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97
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Zheng M, Zhao J, Cui C, Fu Z, Li X, Liu X, Ding X, Tan X, Li F, Luo X, Chen K, Jiang H. Computational chemical biology and drug design: Facilitating protein structure, function, and modulation studies. Med Res Rev 2018; 38:914-950. [DOI: 10.1002/med.21483] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/13/2017] [Accepted: 12/15/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Mingyue Zheng
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Jihui Zhao
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Chen Cui
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Zunyun Fu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Xutong Li
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Xiaohong Liu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
- School of Life Science and Technology; ShanghaiTech University; Shanghai China
| | - Xiaoyu Ding
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Xiaoqin Tan
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Fei Li
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
- Department of Chemistry, College of Sciences; Shanghai University; Shanghai China
| | - Xiaomin Luo
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Kaixian Chen
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
- School of Life Science and Technology; ShanghaiTech University; Shanghai China
| | - Hualiang Jiang
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
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98
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Abstract
Following the elucidation of the human genome, chemogenomics emerged in the beginning of the twenty-first century as an interdisciplinary research field with the aim to accelerate target and drug discovery by making best usage of the genomic data and the data linkable to it. What started as a systematization approach within protein target families now encompasses all types of chemical compounds and gene products. A key objective of chemogenomics is the establishment, extension, analysis, and prediction of a comprehensive SAR matrix which by application will enable further systematization in drug discovery. Herein we outline future perspectives of chemogenomics including the extension to new molecular modalities, or the potential extension beyond the pharma to the agro and nutrition sectors, and the importance for environmental protection. The focus is on computational sciences with potential applications for compound library design, virtual screening, hit assessment, analysis of phenotypic screens, lead finding and optimization, and systems biology-based prediction of toxicology and translational research.
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Affiliation(s)
- Edgar Jacoby
- Janssen Research & Development, Beerse, Belgium.
| | - J B Brown
- Life Science Informatics Research Unit, Laboratory of Molecular Biosciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
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99
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Catto M, Trisciuzzi D, Alberga D, Mangiatordi GF, Nicolotti O. Multitarget Drug Design for Neurodegenerative Diseases. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2018. [DOI: 10.1007/7653_2018_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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100
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Merk D, Friedrich L, Grisoni F, Schneider G. De Novo Design of Bioactive Small Molecules by Artificial Intelligence. Mol Inform 2018; 37:1700153. [PMID: 29319225 PMCID: PMC5838524 DOI: 10.1002/minf.201700153] [Citation(s) in RCA: 201] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 12/20/2017] [Indexed: 11/12/2022]
Abstract
Generative artificial intelligence offers a fresh view on molecular design. We present the first-time prospective application of a deep learning model for designing new druglike compounds with desired activities. For this purpose, we trained a recurrent neural network to capture the constitution of a large set of known bioactive compounds represented as SMILES strings. By transfer learning, this general model was fine-tuned on recognizing retinoid X and peroxisome proliferator-activated receptor agonists. We synthesized five top-ranking compounds designed by the generative model. Four of the compounds revealed nanomolar to low-micromolar receptor modulatory activity in cell-based assays. Apparently, the computational model intrinsically captured relevant chemical and biological knowledge without the need for explicit rules. The results of this study advocate generative artificial intelligence for prospective de novo molecular design, and demonstrate the potential of these methods for future medicinal chemistry.
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Affiliation(s)
- Daniel Merk
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH)Vladimir-Prelog-Weg 4, CH-8093ZurichSwitzerland
| | - Lukas Friedrich
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH)Vladimir-Prelog-Weg 4, CH-8093ZurichSwitzerland
| | - Francesca Grisoni
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH)Vladimir-Prelog-Weg 4, CH-8093ZurichSwitzerland
- Department of Earth and Environmental SciencesUniversity of Milano-BicoccaP.za della Scienza, 1, IT-20126MilanItaly
| | - Gisbert Schneider
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH)Vladimir-Prelog-Weg 4, CH-8093ZurichSwitzerland
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