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Orsi M, Reymond JL. One chiral fingerprint to find them all. J Cheminform 2024; 16:53. [PMID: 38741153 DOI: 10.1186/s13321-024-00849-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/28/2024] [Indexed: 05/16/2024] Open
Abstract
Molecular fingerprints are indispensable tools in cheminformatics. However, stereochemistry is generally not considered, which is problematic for large molecules which are almost all chiral. Herein we report MAP4C, a chiral version of our previously reported fingerprint MAP4, which lists MinHashes computed from character strings containing the SMILES of all pairs of circular substructures up to a diameter of four bonds and the shortest topological distance between their central atoms. MAP4C includes the Cahn-Ingold-Prelog (CIP) annotation (R, S, r or s) whenever the chiral atom is the center of a circular substructure, a question mark for undefined stereocenters, and double bond cis-trans information if specified. MAP4C performs slightly better than the achiral MAP4, ECFP and AP fingerprints in non-stereoselective virtual screening benchmarks. Furthermore, MAP4C distinguishes between stereoisomers in chiral molecules from small molecule drugs to large natural products and peptides comprising thousands of diastereomers, with a degree of distinction smaller than between structural isomers and proportional to the number of chirality changes. Due to its excellent performance across diverse molecular classes and its ability to handle stereochemistry, MAP4C is recommended as a generally applicable chiral molecular fingerprint. SCIENTIFIC CONTRIBUTION: The ability of our chiral fingerprint MAP4C to handle stereoisomers from small molecules to large natural products and peptides is unprecedented and opens the way for cheminformatics to include stereochemistry as an important molecular parameter across all fields of molecular design.
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Affiliation(s)
- Markus Orsi
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland.
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2
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Qian W, Wang X, Kang Y, Pan P, Hou T, Hsieh CY. A general model for predicting enzyme functions based on enzymatic reactions. J Cheminform 2024; 16:38. [PMID: 38556873 PMCID: PMC10983695 DOI: 10.1186/s13321-024-00827-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/16/2024] [Indexed: 04/02/2024] Open
Abstract
Accurate prediction of the enzyme comission (EC) numbers for chemical reactions is essential for the understanding and manipulation of enzyme functions, biocatalytic processes and biosynthetic planning. A number of machine leanring (ML)-based models have been developed to classify enzymatic reactions, showing great advantages over costly and long-winded experimental verifications. However, the prediction accuracy for most available models trained on the records of chemical reactions without specifying the enzymatic catalysts is rather limited. In this study, we introduced BEC-Pred, a BERT-based multiclassification model, for predicting EC numbers associated with reactions. Leveraging transfer learning, our approach achieves precise forecasting across a wide variety of Enzyme Commission (EC) numbers solely through analysis of the SMILES sequences of substrates and products. BEC-Pred model outperformed other sequence and graph-based ML methods, attaining a higher accuracy of 91.6%, surpassing them by 5.5%, and exhibiting superior F1 scores with improvements of 6.6% and 6.0%, respectively. The enhanced performance highlights the potential of BEC-Pred to serve as a reliable foundational tool to accelerate the cutting-edge research in synthetic biology and drug metabolism. Moreover, we discussed a few examples on how BEC-Pred could accurately predict the enzymatic classification for the Novozym 435-induced hydrolysis and lipase efficient catalytic synthesis. We anticipate that BEC-Pred will have a positive impact on the progression of enzymatic research.
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Affiliation(s)
- Wenjia Qian
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Xiaorui Wang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao, 999078, China
- CarbonSilicon AI Technology Co., Ltd, Hangzhou, 310018, Zhejiang, China
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Peichen Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
| | - Chang-Yu Hsieh
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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3
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Zhang Y, Sui X, Pan F, Yu K, Li K, Tian S, Erdengasileng A, Han Q, Wang W, Wang J, Wang J, Sun D, Chung H, Zhou J, Zhou E, Lee B, Zhang P, Qiu X, Zhao T, Zhang J. BioKG: a comprehensive, large-scale biomedical knowledge graph for AI-powered, data-driven biomedical research. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562216. [PMID: 38168218 PMCID: PMC10760044 DOI: 10.1101/2023.10.13.562216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
To cope with the rapid growth of scientific publications and data in biomedical research, knowledge graphs (KGs) have emerged as a powerful data structure for integrating large volumes of heterogeneous data to facilitate accurate and efficient information retrieval and automated knowledge discovery (AKD). However, transforming unstructured content from scientific literature into KGs has remained a significant challenge, with previous methods unable to achieve human-level accuracy. In this study, we utilized an information extraction pipeline that won first place in the LitCoin NLP Challenge to construct a largescale KG using all PubMed abstracts. The quality of the large-scale information extraction rivals that of human expert annotations, signaling a new era of automatic, high-quality database construction from literature. Our extracted information markedly surpasses the amount of content in manually curated public databases. To enhance the KG's comprehensiveness, we integrated relation data from 40 public databases and relation information inferred from high-throughput genomics data. The comprehensive KG enabled rigorous performance evaluation of AKD, which was infeasible in previous studies. We designed an interpretable, probabilistic-based inference method to identify indirect causal relations and achieved unprecedented results for drug target identification and drug repurposing. Taking lung cancer as an example, we found that 40% of drug targets reported in literature could have been predicted by our algorithm about 15 years ago in a retrospective study, demonstrating that substantial acceleration in scientific discovery could be achieved through automated hypotheses generation and timely dissemination. A cloud-based platform (https://www.biokde.com) was developed for academic users to freely access this rich structured data and associated tools.
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Affiliation(s)
- Yuan Zhang
- Department of Statistics, Florida State University, Tallahassee, FL 32306
| | - Xin Sui
- Insilicom LLC, Tallahassee, FL 32303
| | - Feng Pan
- Insilicom LLC, Tallahassee, FL 32303
| | | | - Keqiao Li
- Department of Statistics, Florida State University, Tallahassee, FL 32306
| | - Shubo Tian
- Department of Statistics, Florida State University, Tallahassee, FL 32306
| | | | - Qing Han
- Department of Statistics, Florida State University, Tallahassee, FL 32306
| | - Wanjing Wang
- Department of Statistics, Florida State University, Tallahassee, FL 32306
| | | | - Jian Wang
- 977 Wisteria Ter., Sunnyvale, CA 94086
| | | | | | - Jun Zhou
- Insilicom LLC, Tallahassee, FL 32303
| | - Eric Zhou
- Insilicom LLC, Tallahassee, FL 32303
| | - Ben Lee
- Insilicom LLC, Tallahassee, FL 32303
| | - Peili Zhang
- Forward Informatics, Winchester, Massachusetts, 01890
| | - Xing Qiu
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY 14642
| | - Tingting Zhao
- Department of Geography, Florida State University, Tallahassee, FL 32306
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, FL 32306
- Insilicom LLC, Tallahassee, FL 32303
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4
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Han R, Yoon H, Kim G, Lee H, Lee Y. Revolutionizing Medicinal Chemistry: The Application of Artificial Intelligence (AI) in Early Drug Discovery. Pharmaceuticals (Basel) 2023; 16:1259. [PMID: 37765069 PMCID: PMC10537003 DOI: 10.3390/ph16091259] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/24/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Artificial intelligence (AI) has permeated various sectors, including the pharmaceutical industry and research, where it has been utilized to efficiently identify new chemical entities with desirable properties. The application of AI algorithms to drug discovery presents both remarkable opportunities and challenges. This review article focuses on the transformative role of AI in medicinal chemistry. We delve into the applications of machine learning and deep learning techniques in drug screening and design, discussing their potential to expedite the early drug discovery process. In particular, we provide a comprehensive overview of the use of AI algorithms in predicting protein structures, drug-target interactions, and molecular properties such as drug toxicity. While AI has accelerated the drug discovery process, data quality issues and technological constraints remain challenges. Nonetheless, new relationships and methods have been unveiled, demonstrating AI's expanding potential in predicting and understanding drug interactions and properties. For its full potential to be realized, interdisciplinary collaboration is essential. This review underscores AI's growing influence on the future trajectory of medicinal chemistry and stresses the importance of ongoing synergies between computational and domain experts.
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Affiliation(s)
| | | | | | | | - Yoonji Lee
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
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5
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Comparison of the individual and combined actions of charged amino acids and glycine on the lysis of Escherichia coli cells by human and chicken lysozyme. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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6
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Artificial intelligence and machine-learning approaches in structure and ligand-based discovery of drugs affecting central nervous system. Mol Divers 2022; 27:959-985. [PMID: 35819579 DOI: 10.1007/s11030-022-10489-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/21/2022] [Indexed: 12/11/2022]
Abstract
CNS disorders are indications with a very high unmet medical needs, relatively smaller number of available drugs, and a subpar satisfaction level among patients and caregiver. Discovery of CNS drugs is extremely expensive affair with its own unique challenges leading to extremely high attrition rates and low efficiency. With explosion of data in information age, there is hardly any aspect of life that has not been touched by data driven technologies such as artificial intelligence (AI) and machine learning (ML). Drug discovery is no exception, emergence of big data via genomic, proteomic, biological, and chemical technologies has driven pharmaceutical giants to collaborate with AI oriented companies to revolutionise drug discovery, with the goal of increasing the efficiency of the process. In recent years many examples of innovative applications of AI and ML techniques in CNS drug discovery has been reported. Research on therapeutics for diseases such as schizophrenia, Alzheimer's and Parkinsonism has been provided with a new direction and thrust from these developments. AI and ML has been applied to both ligand-based and structure-based drug discovery and design of CNS therapeutics. In this review, we have summarised the general aspects of AI and ML from the perspective of drug discovery followed by a comprehensive coverage of the recent developments in the applications of AI/ML techniques in CNS drug discovery.
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7
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Huang Z, Chen MS, Woroch CP, Markland TE, Kanan MW. A framework for automated structure elucidation from routine NMR spectra. Chem Sci 2021; 12:15329-15338. [PMID: 34976353 PMCID: PMC8635205 DOI: 10.1039/d1sc04105c] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/08/2021] [Indexed: 12/25/2022] Open
Abstract
Methods to automate structure elucidation that can be applied broadly across chemical structure space have the potential to greatly accelerate chemical discovery. NMR spectroscopy is the most widely used and arguably the most powerful method for elucidating structures of organic molecules. Here we introduce a machine learning (ML) framework that provides a quantitative probabilistic ranking of the most likely structural connectivity of an unknown compound when given routine, experimental one dimensional 1H and/or 13C NMR spectra. In particular, our ML-based algorithm takes input NMR spectra and (i) predicts the presence of specific substructures out of hundreds of substructures it has learned to identify; (ii) annotates the spectrum to label peaks with predicted substructures; and (iii) uses the substructures to construct candidate constitutional isomers and assign to them a probabilistic ranking. Using experimental spectra and molecular formulae for molecules containing up to 10 non-hydrogen atoms, the correct constitutional isomer was the highest-ranking prediction made by our model in 67.4% of the cases and one of the top-ten predictions in 95.8% of the cases. This advance will aid in solving the structure of unknown compounds, and thus further the development of automated structure elucidation tools that could enable the creation of fully autonomous reaction discovery platforms. A machine learning model and graph generator were able to accurately predict for the presence of nearly 1000 substructures and the connectivity of small organic molecules from experimental 1D NMR data.![]()
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Affiliation(s)
- Zhaorui Huang
- Department of Chemistry, Stanford University Stanford CA 94305 USA
| | - Michael S Chen
- Department of Chemistry, Stanford University Stanford CA 94305 USA
| | | | | | - Matthew W Kanan
- Department of Chemistry, Stanford University Stanford CA 94305 USA
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8
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Ekaney LYE, Eni DB, Ntie-Kang F. Chemical similarity methods for analyzing secondary metabolite structures. PHYSICAL SCIENCES REVIEWS 2021. [DOI: 10.1515/psr-2018-0129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The relation that exists between the structure of a compound and its function is an integral part of chemoinformatics. The similarity principle states that “structurally similar molecules tend to have similar properties and similar molecules exert similar biological activities”. The similarity of the molecules can either be studied at the structure level or at the descriptor level (properties level). Generally, the objective of chemical similarity measures is to enhance prediction of the biological activities of molecules. In this article, an overview of various methods used to compare the similarity between metabolite structures has been provided, including two-dimensional (2D) and three-dimensional (3D) approaches. The focus has been on methods description; e.g. fingerprint-based similarity in which the molecules under study are first fragmented and their fingerprints are computed, 2D structural similarity by comparing the Tanimoto coefficients and Euclidean distances, as well as the use of physiochemical properties descriptor-based similarity methods. The similarity between molecules could also be measured by using data mining (clustering) techniques, e.g. by using virtual screening (VS)-based similarity methods. In this approach, the molecules with the desired descriptors or /and structures are screened from large databases. Lastly, SMILES-based chemical similarity search is an important method for studying the exact structure search, substructure search and also descriptor similarity. The use of a particular method depends upon the requirements of the researcher.
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Affiliation(s)
- Lena Y. E. Ekaney
- Faculty of Science, Department of Chemistry , University of Buea , P.O. Box 63 , Buea , Cameroon
| | - Donatus B. Eni
- Faculty of Science, Department of Chemistry , University of Buea , P.O. Box 63 , Buea , Cameroon
- Department of Inorganic Chemistry, Faculty of Science , University of Yaoundé I , Yaoundé , Cameroon
| | - Fidele Ntie-Kang
- Faculty of Science, Department of Chemistry , University of Buea , P.O. Box 63 , Buea , Cameroon
- Department of Pharmaceutical Chemistry , Martin-Luther University Halle-Wittenberg , Kurt-Mothes-Str. 3 , Halle (Saale) , 06120 Germany
- Department of Informatics and Chemistry , University of Chemistry and Technology Prague , Technická 5 Prague 6 , Dejvice , 166 28 Czech Republic
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9
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Zarnecka J, Lukac I, Messham SJ, Hussin A, Coppola F, Enoch SJ, Dossetter AG, Griffen EJ, Leach AG. Mapping Ligand-Shape Space for Protein-Ligand Systems: Distinguishing Key-in-Lock and Hand-in-Glove Proteins. J Chem Inf Model 2021; 61:1859-1874. [PMID: 33755448 DOI: 10.1021/acs.jcim.1c00089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many of the recently developed methods to study the shape of molecules permit one conformation of one molecule to be compared to another conformation of the same or a different molecule: a relative shape. Other methods provide an absolute description of the shape of a conformation that does not rely on comparisons or overlays. Any absolute description of shape can be used to generate a self-organizing map (shape map) that places all molecular shapes relative to one another; in the studies reported here, the shape fingerprint and ultrafast shape recognition methods are employed to create such maps. In the shape maps, molecules that are near one another have similar shapes, and the maps for the 102 targets in the DUD-E set have been generated. By examining the distribution of actives in comparison with their physical-property-matched decoys, we show that the proteins of key-in-lock type (relatively rigid receptor and ligand) can be distinguished from those that are more of a hand-in-glove type (more flexible receptor and ligand). These are linked to known differences in protein flexibility and binding-site size.
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Affiliation(s)
- Joanna Zarnecka
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, U.K
| | - Iva Lukac
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, U.K
| | - Stephen J Messham
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, U.K
| | - Alhusein Hussin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, U.K
| | - Francesco Coppola
- Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, U.K
| | - Steven J Enoch
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, U.K
| | | | - Edward J Griffen
- MedChemica Limited, Biohub, Mereside, Alderley Park, Macclesfield SK10 4TG, U.K
| | - Andrew G Leach
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, U.K.,MedChemica Limited, Biohub, Mereside, Alderley Park, Macclesfield SK10 4TG, U.K.,Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, U.K
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10
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Huang TT, Wang X, Qiang SJ, Zhao ZN, Wu ZX, Ashby CR, Li JZ, Chen ZS. The Discovery of Novel BCR-ABL Tyrosine Kinase Inhibitors Using a Pharmacophore Modeling and Virtual Screening Approach. Front Cell Dev Biol 2021; 9:649434. [PMID: 33748144 PMCID: PMC7969810 DOI: 10.3389/fcell.2021.649434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/10/2021] [Indexed: 11/23/2022] Open
Abstract
Chronic myelogenous leukemia (CML) typically results from a reciprocal translocation between chromosomes 9 and 22 to produce the bcr-abl oncogene that when translated, yields the p210 BCR-ABL protein in more than 90% of all CML patients. This protein has constitutive tyrosine kinase activity that activates numerous downstream pathways that ultimately produces uncontrolled myeloid proliferation. Although the use of the BCR-ABL tyrosine kinase inhibitors (TKIs), such as imatinib, nilotinib, dasatinib, bosutinib, and ponatinib have increased the overall survival of CML patients, their use is limited by drug resistance and severe adverse effects. Therefore, there is the need to develop novel compounds that can overcome these problems that limit the use of these drugs. Therefore, in this study, we sought to find novel compounds using Hypogen and Hiphip pharmacophore models based on the structures of clinically approved BCR-ABL TKIs. We also used optimal pharmacophore models such as three-dimensional queries to screen the ZINC database to search for potential BCR-ABL inhibitors. The hit compounds were further screened using Lipinski’s rule of five, ADMET and molecular docking, and the efficacy of the hit compounds was evaluated. Our in vitro results indicated that compound ZINC21710815 significantly inhibited the proliferation of K562, BaF3/WT, and BaF3/T315I leukemia cells by inducing cell cycle arrest. The compound ZINC21710815 decreased the expression of p-BCR-ABL, STAT5, and Crkl and produced apoptosis and autophagy. Our results suggest that ZINC21710815 may be a potential BCR-ABL inhibitor that should undergo in vivo evaluation.
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Affiliation(s)
| | - Xin Wang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | | | - Zhen-Nan Zhao
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Zhuo-Xun Wu
- College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
| | - Charles R Ashby
- College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
| | - Jia-Zhong Li
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Zhe-Sheng Chen
- College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
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11
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de Jonge HR, Ardelean MC, Bijvelds MJC, Vergani P. Strategies for cystic fibrosis transmembrane conductance regulator inhibition: from molecular mechanisms to treatment for secretory diarrhoeas. FEBS Lett 2020; 594:4085-4108. [PMID: 33113586 PMCID: PMC7756540 DOI: 10.1002/1873-3468.13971] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/22/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023]
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) is an unusual ABC transporter. It acts as an anion‐selective channel that drives osmotic fluid transport across many epithelia. In the gut, CFTR is crucial for maintaining fluid and acid‐base homeostasis, and its activity is tightly controlled by multiple neuro‐endocrine factors. However, microbial toxins can disrupt this intricate control mechanism and trigger protracted activation of CFTR. This results in the massive faecal water loss, metabolic acidosis and dehydration that characterize secretory diarrhoeas, a major cause of malnutrition and death of children under 5 years of age. Compounds that inhibit CFTR could improve emergency treatment of diarrhoeal disease. Drawing on recent structural and functional insight, we discuss how existing CFTR inhibitors function at the molecular and cellular level. We compare their mechanisms of action to those of inhibitors of related ABC transporters, revealing some unexpected features of drug action on CFTR. Although challenges remain, especially relating to the practical effectiveness of currently available CFTR inhibitors, we discuss how recent technological advances might help develop therapies to better address this important global health need.
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Affiliation(s)
- Hugo R. de Jonge
- Department of Gastroenterology & HepatologyErasmus University Medical CenterRotterdamThe Netherlands
| | - Maria C. Ardelean
- Department of Neuroscience, Physiology and PharmacologyUniversity College LondonUK
- Department of Natural SciencesUniversity College LondonUK
| | - Marcel J. C. Bijvelds
- Department of Gastroenterology & HepatologyErasmus University Medical CenterRotterdamThe Netherlands
| | - Paola Vergani
- Department of Neuroscience, Physiology and PharmacologyUniversity College LondonUK
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12
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One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome. J Cheminform 2020; 12:43. [PMID: 33431010 PMCID: PMC7291580 DOI: 10.1186/s13321-020-00445-4] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/04/2020] [Indexed: 02/08/2023] Open
Abstract
Background Molecular fingerprints are essential cheminformatics tools for virtual screening and mapping chemical space. Among the different types of fingerprints, substructure fingerprints perform best for small molecules such as drugs, while atom-pair fingerprints are preferable for large molecules such as peptides. However, no available fingerprint achieves good performance on both classes of molecules. Results Here we set out to design a new fingerprint suitable for both small and large molecules by combining substructure and atom-pair concepts. Our quest resulted in a new fingerprint called MinHashed atom-pair fingerprint up to a diameter of four bonds (MAP4). In this fingerprint the circular substructures with radii of r = 1 and r = 2 bonds around each atom in an atom-pair are written as two pairs of SMILES, each pair being combined with the topological distance separating the two central atoms. These so-called atom-pair molecular shingles are hashed, and the resulting set of hashes is MinHashed to form the MAP4 fingerprint. MAP4 significantly outperforms all other fingerprints on an extended benchmark that combines the Riniker and Landrum small molecule benchmark with a peptide benchmark recovering BLAST analogs from either scrambled or point mutation analogs. MAP4 furthermore produces well-organized chemical space tree-maps (TMAPs) for databases as diverse as DrugBank, ChEMBL, SwissProt and the Human Metabolome Database (HMBD), and differentiates between all metabolites in HMBD, over 70% of which are indistinguishable from their nearest neighbor using substructure fingerprints. Conclusion MAP4 is a new molecular fingerprint suitable for drugs, biomolecules, and the metabolome and can be adopted as a universal fingerprint to describe and search chemical space. The source code is available at https://github.com/reymond-group/map4 and interactive MAP4 similarity search tools and TMAPs for various databases are accessible at http://map-search.gdb.tools/ and http://tm.gdb.tools/map4/.![]()
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13
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Capecchi A, Zhang A, Reymond JL. Populating Chemical Space with Peptides Using a Genetic Algorithm. J Chem Inf Model 2020; 60:121-132. [PMID: 31868369 DOI: 10.1021/acs.jcim.9b01014] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In drug discovery, one uses chemical space as a concept to organize molecules according to their structures and properties. One often would like to generate new possible molecules at a specific location in the chemical space marked by a molecule of interest. Herein, we report the peptide design genetic algorithm (PDGA, code available at https://github.com/reymond-group/PeptideDesignGA ), a computational tool capable of producing peptide sequences of various topologies (linear, cyclic/polycyclic, or dendritic) in proximity of any molecule of interest in a chemical space defined by macromolecule extended atom-pair fingerprint (MXFP), an atom-pair fingerprint describing molecular shape and pharmacophores. We show that the PDGA generates high-similarity analogues of bioactive peptides with diverse peptide chain topologies and of nonpeptide target molecules. We illustrate the chemical space accessible by the PDGA with an interactive 3D map of the MXFP property space available at http://faerun.gdb.tools/ . The PDGA should be generally useful to generate peptides at any location in the chemical space.
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Affiliation(s)
- Alice Capecchi
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland
| | - Alain Zhang
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland
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14
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Taylor R, Wood PA. A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts. Chem Rev 2019; 119:9427-9477. [PMID: 31244003 DOI: 10.1021/acs.chemrev.9b00155] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.
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Affiliation(s)
- Robin Taylor
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| | - Peter A Wood
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
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15
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Abstract
Introduction: The development of drug candidates with a defined selectivity profile and a unique molecular structure is of fundamental interest for drug discovery. In contrast to the costly screening of large substance libraries, the targeted de novo design of a drug by using structural information of either the biological target and/or structure-activity relationship data of active modulators offers an efficient and intellectually appealing alternative. Areas covered: This review provides an overview on the different techniques of de novo drug design (ligand-based drug design, structure-based drug design, and fragment-based drug design) and highlights successful examples of this targeted approach toward selective modulators of therapeutically relevant targets. Expert opinion: De novo drug design has established itself as a very efficient method for the development of potent and selective modulators for a variety of different biological target classes. The ever-growing wealth of structural data on therapeutic targets will certainly further enhance the importance of de novo design for the drug discovery process in the future. However, a consistent use of the terminology of de novo drug design in the scientific literature should be sought.
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Affiliation(s)
- Thomas Fischer
- a Center of Organic and Medicinal Chemistry, Institute of Chemistry and Biotechnology , Zurich University of Applied Sciences ZHAW , Wädenswil , Switzerland
| | - Silvia Gazzola
- b Dipartimento di Scienza e Alta Tecnologia , Università degli Studi dell'Insubria , Como , Italy
| | - Rainer Riedl
- a Center of Organic and Medicinal Chemistry, Institute of Chemistry and Biotechnology , Zurich University of Applied Sciences ZHAW , Wädenswil , Switzerland
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16
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Morstein J, Awale M, Reymond JL, Trauner D. Mapping the Azolog Space Enables the Optical Control of New Biological Targets. ACS CENTRAL SCIENCE 2019; 5:607-618. [PMID: 31041380 PMCID: PMC6487453 DOI: 10.1021/acscentsci.8b00881] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 06/01/2023]
Abstract
Photopharmacology relies on molecules that change their biological activity upon irradiation. Many of these are derived from known drugs by replacing their core with an isosteric azobenzene photoswitch (azologization). The question is how many of the known bioactive ligands could be addressed in such a way. Here, we systematically assess the space of molecules amenable to azologization from databases of bioactive molecules (DrugBank, PDB, CHEMBL) and the Cambridge Structural Database. Shape similarity scoring functions (3DAPfp) and analyses of dihedral angles are employed to quantify the structural homology between a bioactive molecule and the cis or trans isomer of its corresponding azolog ("azoster") and assess which isomer is likely to be active. Our analysis suggests that a very large number of bioactive ligands (>40 000) is amenable to azologization and that many new biological targets could be addressed with photopharmacology. N-Aryl benzamides, 1,2-diarylethanes, and benzyl phenyl ethers are particularly suited for this approach, while benzylanilines and sulfonamides appear to be less well-matched. On the basis of our analysis, the majority of azosters are expected to be active in their trans form. The broad applicability of our approach is demonstrated with photoswitches that target a nuclear hormone receptor (RAR) and a lipid processing enzyme (LTA4 hydrolase).
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Affiliation(s)
- Johannes Morstein
- Department
of Chemistry, New York University, 100 Washington Square East, New York, New York 10003-6699, United States
| | - Mahendra Awale
- Department
of Chemistry and Biochemistry, National Center for Competence in Research
NCCR TransCure, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Jean-Louis Reymond
- Department
of Chemistry and Biochemistry, National Center for Competence in Research
NCCR TransCure, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Dirk Trauner
- Department
of Chemistry, New York University, 100 Washington Square East, New York, New York 10003-6699, United States
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17
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Raschka S. Automated discovery of GPCR bioactive ligands. Curr Opin Struct Biol 2019; 55:17-24. [PMID: 30909105 DOI: 10.1016/j.sbi.2019.02.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 02/19/2019] [Indexed: 12/22/2022]
Abstract
While G-protein-coupled receptors (GPCRs) constitute the largest class of membrane proteins, structures and endogenous ligands of a large portion of GPCRs remain unknown. Because of the involvement of GPCRs in various signaling pathways and physiological roles, the identification of endogenous ligands as well as designing novel drugs is of high interest to the research and medical communities. Along with highlighting the recent advances in structure-based ligand discovery, including docking and molecular dynamics, this article focuses on the latest advances for automating the discovery of bioactive ligands using machine learning. Machine learning is centered around the development and applications of algorithms that can learn from data automatically. Such an approach offers immense opportunities for bioactivity prediction as well as quantitative structure-activity relationship studies. This review describes the most recent and successful applications of machine learning for bioactive ligand discovery, concluding with an outlook on deep learning methods that are capable of automatically extracting salient information from structural data as a promising future direction for rapid and efficient bioactive ligand discovery.
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Affiliation(s)
- Sebastian Raschka
- Department of Statistics, University of Wisconsin-Madison, 1300 Medical Sciences Center, Madison, WI 53706, USA.
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18
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Capecchi A, Awale M, Probst D, Reymond JL. PubChem and ChEMBL beyond Lipinski. Mol Inform 2019; 38:e1900016. [PMID: 30844149 DOI: 10.1002/minf.201900016] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 02/18/2019] [Indexed: 12/13/2022]
Abstract
Seven million of the currently 94 million entries in the PubChem database break at least one of the four Lipinski constraints for oral bioavailability, 183,185 of which are also found in the ChEMBL database. These non-Lipinski PubChem (NLP) and ChEMBL (NLC) subsets are interesting because they contain new modalities that can display biological properties not accessible to small molecule drugs. Unfortunately, the current search tools in PubChem and ChEMBL are designed for small molecules and are not well suited to explore these subsets, which therefore remain poorly appreciated. Herein we report MXFP (macromolecule extended atom-pair fingerprint), a 217-D fingerprint tailored to analyze large molecules in terms of molecular shape and pharmacophores. We implement MXFP in two web-based applications, the first one to visualize NLP and NLC interactively using Faerun (http://faerun.gdb.tools/), the second one to perform MXFP nearest neighbor searches in NLP and NLC (http://similaritysearch.gdb.tools/). We show that these tools provide a meaningful insight into the diversity of large molecules in NLP and NLC. The interactive tools presented here are publicly available at http://gdb.unibe.ch and can be used freely to explore and better understand the diversity of non-Lipinski molecules in PubChem and ChEMBL.
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Affiliation(s)
- Alice Capecchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Daniel Probst
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
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19
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Siriwardena TN, Capecchi A, Gan B, Jin X, He R, Wei D, Ma L, Köhler T, van Delden C, Javor S, Reymond J. Optimizing Antimicrobial Peptide Dendrimers in Chemical Space. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Thissa N. Siriwardena
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Alice Capecchi
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Bee‐Ha Gan
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Xian Jin
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Runze He
- Shanghai Space Peptides Pharmaceutical Co., Ltd. Shanghai 201210 China
| | - Dengwen Wei
- Department of General Surgery Lanzhou General Hospital of Lanzhou Military Region, PLA 333 South Binhe Road, Qilihe District Lanzhou Gansu Province 730046 China
| | - Lan Ma
- Lanzhou Ruibei Pharmaceutical R&D Co., Ltd. Lanzhou Gansu Province 730000 China
| | - Thilo Köhler
- Department of Microbiology and Molecular Medicine University of Geneva
- Service of Infectious Diseases University Hospital of Geneva Geneva Switzerland
| | - Christian van Delden
- Department of Microbiology and Molecular Medicine University of Geneva
- Service of Infectious Diseases University Hospital of Geneva Geneva Switzerland
| | - Sacha Javor
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Jean‐Louis Reymond
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
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20
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Siriwardena TN, Capecchi A, Gan BH, Jin X, He R, Wei D, Ma L, Köhler T, van Delden C, Javor S, Reymond JL. Optimizing Antimicrobial Peptide Dendrimers in Chemical Space. Angew Chem Int Ed Engl 2018; 57:8483-8487. [PMID: 29767453 DOI: 10.1002/anie.201802837] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/08/2018] [Indexed: 12/13/2022]
Abstract
We used nearest-neighbor searches in chemical space to improve the activity of the antimicrobial peptide dendrimer (AMPD) G3KL and identified dendrimer T7, which has an expanded activity range against Gram-negative pathogenic bacteria including Klebsiellae pneumoniae, increased serum stability, and promising activity in an in vivo infection model against a multidrug-resistant strain of Acinetobacter baumannii. Imaging, spectroscopic studies, and a structural model from molecular dynamics simulations suggest that T7 acts through membrane disruption. These experiments provide the first example of using virtual screening in the field of dendrimers and show that dendrimer size does not limit the activity of AMPDs.
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Affiliation(s)
- Thissa N Siriwardena
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Alice Capecchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Bee-Ha Gan
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Xian Jin
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Runze He
- Shanghai Space Peptides Pharmaceutical Co., Ltd., Shanghai, 201210, China
| | - Dengwen Wei
- Department of General Surgery, Lanzhou General Hospital of Lanzhou Military Region, PLA, 333 South Binhe Road, Qilihe District, Lanzhou, Gansu Province, 730046, China
| | - Lan Ma
- Lanzhou Ruibei Pharmaceutical R&D Co., Ltd., Lanzhou, Gansu Province, 730000, China
| | - Thilo Köhler
- Department of Microbiology and Molecular Medicine, University of Geneva.,Service of Infectious Diseases, University Hospital of Geneva, Geneva, Switzerland
| | - Christian van Delden
- Department of Microbiology and Molecular Medicine, University of Geneva.,Service of Infectious Diseases, University Hospital of Geneva, Geneva, Switzerland
| | - Sacha Javor
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
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21
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Di Bonaventura I, Baeriswyl S, Capecchi A, Gan BH, Jin X, Siriwardena TN, He R, Köhler T, Pompilio A, Di Bonaventura G, van Delden C, Javor S, Reymond JL. An antimicrobial bicyclic peptide from chemical space against multidrug resistant Gram-negative bacteria. Chem Commun (Camb) 2018; 54:5130-5133. [PMID: 29717727 DOI: 10.1039/c8cc02412j] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We used the concept of chemical space to explore a virtual library of bicyclic peptides formed by double thioether cyclization of a precursor linear peptide, and identified an antimicrobial bicyclic peptide (AMBP) with remarkable activity against several MDR strains of Acinetobacter baumannii and Pseudomonas aeruginosa.
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Affiliation(s)
- Ivan Di Bonaventura
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
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22
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Nesbitt NM, Zheng X, Li Z, Manso JA, Yen WY, Malone LE, Ripoll-Rozada J, Pereira PJB, Mantle TJ, Wang J, Bahou WF. In silico and crystallographic studies identify key structural features of biliverdin IXβ reductase inhibitors having nanomolar potency. J Biol Chem 2018; 293:5431-5446. [PMID: 29487133 DOI: 10.1074/jbc.ra118.001803] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/23/2018] [Indexed: 12/20/2022] Open
Abstract
Heme cytotoxicity is minimized by a two-step catabolic reaction that generates biliverdin (BV) and bilirubin (BR) tetrapyrroles. The second step is regulated by two non-redundant biliverdin reductases (IXα (BLVRA) and IXβ (BLVRB)), which retain isomeric specificity and NAD(P)H-dependent redox coupling linked to BR's antioxidant function. Defective BLVRB enzymatic activity with antioxidant mishandling has been implicated in metabolic consequences of hematopoietic lineage fate and enhanced platelet counts in humans. We now outline an integrated platform of in silico and crystallographic studies for the identification of an initial class of compounds inhibiting BLVRB with potencies in the nanomolar range. We found that the most potent BLVRB inhibitors contain a tricyclic hydrocarbon core structure similar to the isoalloxazine ring of flavin mononucleotide and that both xanthene- and acridine-based compounds inhibit BLVRB's flavin and dichlorophenolindophenol (DCPIP) reductase functions. Crystallographic studies of ternary complexes with BLVRB-NADP+-xanthene-based compounds confirmed inhibitor binding adjacent to the cofactor nicotinamide and interactions with the Ser-111 side chain. This residue previously has been identified as critical for maintaining the enzymatic active site and cellular reductase functions in hematopoietic cells. Both acridine- and xanthene-based compounds caused selective and concentration-dependent loss of redox coupling in BLVRB-overexpressing promyelocytic HL-60 cells. These results provide promising chemical scaffolds for the development of enhanced BLVRB inhibitors and identify chemical probes to better dissect the role of biliverdins, alternative substrates, and BLVRB function in physiologically relevant cellular contexts.
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Affiliation(s)
| | - Xiliang Zheng
- the State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, ChangChun, Jilin 130022, China
| | | | - José A Manso
- the IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.,the i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal, and
| | | | | | - Jorge Ripoll-Rozada
- the IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.,the i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal, and
| | - Pedro José Barbosa Pereira
- the IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.,the i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal, and
| | - Timothy J Mantle
- the Department of Biochemistry, Trinity College, Dublin 2, Ireland
| | - Jin Wang
- Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, New York 11794-8151,
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23
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Visini R, Arús-Pous J, Awale M, Reymond JL. Virtual Exploration of the Ring Systems Chemical Universe. J Chem Inf Model 2017; 57:2707-2718. [PMID: 29019686 DOI: 10.1021/acs.jcim.7b00457] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Here, we explore the chemical space of all virtually possible organic molecules focusing on ring systems, which represent the cyclic cores of organic molecules obtained by removing all acyclic bonds and converting all remaining atoms to carbon. This approach circumvents the combinatorial explosion encountered when enumerating the molecules themselves. We report the chemical universe database GDB4c containing 916 130 ring systems up to four saturated or aromatic rings and maximum ring size of 14 atoms and GDB4c3D containing the corresponding 6 555 929 stereoisomers. Almost all (98.6%) of these ring systems are unknown and represent chiral 3D-shaped macrocycles containing small rings and quaternary centers reminiscent of polycyclic natural products. We envision that GDB4c can serve to select new ring systems from which to design analogs of such natural products. The database is available for download at www.gdb.unibe.ch together with interactive visualization and search tools as a resource for molecular design.
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Affiliation(s)
- Ricardo Visini
- Department of Chemistry and Biochemistry, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Josep Arús-Pous
- Department of Chemistry and Biochemistry, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
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24
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Di Bonaventura I, Jin X, Visini R, Probst D, Javor S, Gan BH, Michaud G, Natalello A, Doglia SM, Köhler T, van Delden C, Stocker A, Darbre T, Reymond JL. Chemical space guided discovery of antimicrobial bridged bicyclic peptides against Pseudomonas aeruginosa and its biofilms. Chem Sci 2017; 8:6784-6798. [PMID: 29147502 PMCID: PMC5643981 DOI: 10.1039/c7sc01314k] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/12/2017] [Indexed: 12/15/2022] Open
Abstract
Herein we report the discovery of antimicrobial bridged bicyclic peptides (AMBPs) active against Pseudomonas aeruginosa, a highly problematic Gram negative bacterium in the hospital environment. Two of these AMBPs show strong biofilm inhibition and dispersal activity and enhance the activity of polymyxin, currently a last resort antibiotic against which resistance is emerging. To discover our AMBPs we used the concept of chemical space, which is well known in the area of small molecule drug discovery, to define a small number of test compounds for synthesis and experimental evaluation. Our chemical space was calculated using 2DP, a new topological shape and pharmacophore fingerprint for peptides. This method provides a general strategy to search for bioactive peptides with unusual topologies and expand the structural diversity of peptide-based drugs.
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Affiliation(s)
- Ivan Di Bonaventura
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Xian Jin
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Ricardo Visini
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Daniel Probst
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Sacha Javor
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Bee-Ha Gan
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Gaëlle Michaud
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Antonino Natalello
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 Milan , Italy
| | - Silvia Maria Doglia
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 Milan , Italy
| | - Thilo Köhler
- Department of Microbiology and Molecular Medicine , University of Geneva, and Service of Infectious Diseases , University Hospital of Geneva , Geneva , Switzerland
| | - Christian van Delden
- Department of Microbiology and Molecular Medicine , University of Geneva, and Service of Infectious Diseases , University Hospital of Geneva , Geneva , Switzerland
| | - Achim Stocker
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Tamis Darbre
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
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25
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Axen SD, Huang XP, Cáceres EL, Gendelev L, Roth BL, Keiser MJ. A Simple Representation of Three-Dimensional Molecular Structure. J Med Chem 2017; 60:7393-7409. [PMID: 28731335 DOI: 10.1021/acs.jmedchem.7b00696] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Statistical and machine learning approaches predict drug-to-target relationships from 2D small-molecule topology patterns. One might expect 3D information to improve these calculations. Here we apply the logic of the extended connectivity fingerprint (ECFP) to develop a rapid, alignment-invariant 3D representation of molecular conformers, the extended three-dimensional fingerprint (E3FP). By integrating E3FP with the similarity ensemble approach (SEA), we achieve higher precision-recall performance relative to SEA with ECFP on ChEMBL20 and equivalent receiver operating characteristic performance. We identify classes of molecules for which E3FP is a better predictor of similarity in bioactivity than is ECFP. Finally, we report novel drug-to-target binding predictions inaccessible by 2D fingerprints and confirm three of them experimentally with ligand efficiencies from 0.442-0.637 kcal/mol/heavy atom.
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Affiliation(s)
- Seth D Axen
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco , 675 Nelson Rising Lane NS 416A, San Francisco, California 94143, United States
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina School of Medicine , Chapel Hill, North Carolina 27599, United States.,National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Elena L Cáceres
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco , 675 Nelson Rising Lane NS 416A, San Francisco, California 94143, United States.,Department of Pharmaceutical Chemistry, Institute for Neurodegenerative Diseases, and Institute for Computational Health Sciences, University of California, San Francisco , 675 Nelson Rising Lane NS 416A, San Francisco, California 94143, United States
| | - Leo Gendelev
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco , 675 Nelson Rising Lane NS 416A, San Francisco, California 94143, United States.,Department of Pharmaceutical Chemistry, Institute for Neurodegenerative Diseases, and Institute for Computational Health Sciences, University of California, San Francisco , 675 Nelson Rising Lane NS 416A, San Francisco, California 94143, United States
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina School of Medicine , Chapel Hill, North Carolina 27599, United States.,National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), University of North Carolina , Chapel Hill, North Carolina 27599, United States.,Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Michael J Keiser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco , 675 Nelson Rising Lane NS 416A, San Francisco, California 94143, United States.,Department of Pharmaceutical Chemistry, Institute for Neurodegenerative Diseases, and Institute for Computational Health Sciences, University of California, San Francisco , 675 Nelson Rising Lane NS 416A, San Francisco, California 94143, United States
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26
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Langron E, Simone MI, Delalande CMS, Reymond JL, Selwood DL, Vergani P. Improved fluorescence assays to measure the defects associated with F508del-CFTR allow identification of new active compounds. Br J Pharmacol 2017; 174:525-539. [PMID: 28094839 DOI: 10.1111/bph.13715] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 01/06/2017] [Accepted: 01/10/2017] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND AND PURPOSE Cystic fibrosis (CF) is a debilitating disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which codes for a Cl-/HCO3 - channel. F508del, the most common CF-associated mutation, causes both gating and biogenesis defects in the CFTR protein. This paper describes the optimization of two fluorescence assays, capable of measuring CFTR function and cellular localization, and their use in a pilot drug screen. EXPERIMENTAL APPROACH HEK293 cells expressing YFP-F508del-CFTR, in which halide sensitive YFP is tagged to the N-terminal of CFTR, were used to screen a small library of compounds based on the VX-770 scaffold. Cells expressing F508del-CFTR-pHTomato, in which a pH sensor is tagged to the fourth extracellular loop of CFTR, were used to measure CFTR plasma membrane exposure following chronic treatment with the novel potentiators. KEY RESULTS Active compounds with efficacy ~50% of VX-770, micromolar potency, and structurally distinct from VX-770 were identified in the screen. The F508del-CFTR-pHTomato assay suggests that the hit compound MS131A, unlike VX-770, does not decrease membrane exposure of F508del-CFTR. CONCLUSIONS AND IMPLICATIONS Most known potentiators have a negative influence on F508del-CFTR biogenesis/stability, which means membrane exposure needs to be monitored early during the development of drugs targeting CFTR. The combined use of the two fluorescence assays described here provides a useful tool for the identification of improved potentiators and correctors. The assays could also prove useful for basic scientific investigations on F508del-CFTR, and other CF-causing mutations.
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Affiliation(s)
- Emily Langron
- Research Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Michela I Simone
- Discipline of Chemistry, School of Environmental and Life Sciences, Priority Research Centre for Chemical Biology and Clinical Pharmacology, The University of Newcastle, Callaghan, NSW, Australia
| | | | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - David L Selwood
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Paola Vergani
- Research Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
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Hybrid Receptor-Bound/MM-GBSA-Per-residue Energy-Based Pharmacophore Modelling: Enhanced Approach for Identification of Selective LTA4H Inhibitors as Potential Anti-inflammatory Drugs. Cell Biochem Biophys 2016; 75:35-48. [PMID: 27914004 DOI: 10.1007/s12013-016-0772-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/15/2016] [Indexed: 10/20/2022]
Abstract
Leukotriene A4 hydrolase has been identified as an enzyme with dual anti- and pro-inflammatory role, thus, the conversion of leukotriene to leukotriene B4 in the initiation stage of inflammation and the removal of the chemotactic Pro-Gly-Pro tripeptide. These findings make leukotriene A4 hydrolase an attractive drug target: suggesting an innovative approach towards the identification and design of novel class of compounds that can selectively inhibit leukotriene B4 synthesis while sparing the aminopeptidase activity. Previous inhibitors block the dual activity of the enzyme. Recently, a small lead molecule inhibitor denoted as ARM1 has been identified to block the hydrolase activity of leukotriene A4 hydrolase whilst sparing the aminopeptidase activity. In this study, a hybrid receptor-bound/MM-GBSA-per-residue energy based pharmacophore modeling approach was implemented to identify potential selective hydrolase inhibitors of leukotriene A4 hydrolase. In this approach, active site residues that favorably contributed to the binding of the bound conformation of ARM1 were derived from MD ensembles and MM/GBSA thermodynamic calculations. These residues were then mapped to key pharmacophore features of ARM1. The generated pharmacophore model was used to search the ZINC database for 3D structures that match the pharmacophore. Five new compounds have been identified and proposed as potential epoxide hydrolase selective inhibitors of leukotriene A4 hydrolase. Molecular docking and MM/GBSA analyses revealed that, these top five lead-like compounds ZINC00142747, ZINC94260794, ZINC01382396, ZINC02508448, and ZINC53994447 showed better binding affinities to the hydrolase active site pocket compared to ARM1. Per-residue energy decomposition analysis revealed that amino acid residues Phe314, Tyr378, Pro382, Trp311, Val367, and Ala377 are key residues critical in the selective inhibition of these hits. Information highlighted in this study may guide the the design the next generation of novel and potent epoxide hydrolase selective inhibitors of leukotriene A4 hydrolase.
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Kilchmann F, Marcaida MJ, Kotak S, Schick T, Boss SD, Awale M, Gönczy P, Reymond JL. Discovery of a Selective Aurora A Kinase Inhibitor by Virtual Screening. J Med Chem 2016; 59:7188-211. [PMID: 27391133 DOI: 10.1021/acs.jmedchem.6b00709] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Here we report the discovery of a selective inhibitor of Aurora A, a key regulator of cell division and potential anticancer target. We used the atom category extended ligand overlap score (xLOS), a 3D ligand-based virtual screening method recently developed in our group, to select 437 shape and pharmacophore analogs of reference kinase inhibitors. Biochemical screening uncovered two inhibitor series with scaffolds unprecedented among kinase inhibitors. One of them was successfully optimized by structure-based design to a potent Aurora A inhibitor (IC50 = 2 nM) with very high kinome selectivity for Aurora kinases. This inhibitor locks Aurora A in an inactive conformation and disrupts binding to its activator protein TPX2, which impairs Aurora A localization at the mitotic spindle and induces cell division defects. This phenotype can be rescued by inhibitor-resistant Aurora A mutants. The inhibitor furthermore does not induce Aurora B specific effects in cells.
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Affiliation(s)
- Falco Kilchmann
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR Chemical Biology and NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Maria J Marcaida
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR Chemical Biology and NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Sachin Kotak
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, National Center of Competence in Research NCCR Chemical Biology, Swiss Federal Institute of Technology (EPFL) , CH-1015 Lausanne, Switzerland
| | - Thomas Schick
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR Chemical Biology and NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Silvan D Boss
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR Chemical Biology and NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR Chemical Biology and NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, National Center of Competence in Research NCCR Chemical Biology, Swiss Federal Institute of Technology (EPFL) , CH-1015 Lausanne, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR Chemical Biology and NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
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Bravo À, Li TS, Su AI, Good BM, Furlong LI. Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw094. [PMID: 27307137 PMCID: PMC4908671 DOI: 10.1093/database/baw094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 05/10/2016] [Indexed: 01/13/2023]
Abstract
Drug toxicity is a major concern for both regulatory agencies and the pharmaceutical industry. In this context, text-mining methods for the identification of drug side effects from free text are key for the development of up-to-date knowledge sources on drug adverse reactions. We present a new system for identification of drug side effects from the literature that combines three approaches: machine learning, rule- and knowledge-based approaches. This system has been developed to address the Task 3.B of Biocreative V challenge (BC5) dealing with Chemical-induced Disease (CID) relations. The first two approaches focus on identifying relations at the sentence-level, while the knowledge-based approach is applied both at sentence and abstract levels. The machine learning method is based on the BeFree system using two corpora as training data: the annotated data provided by the CID task organizers and a new CID corpus developed by crowdsourcing. Different combinations of results from the three strategies were selected for each run of the challenge. In the final evaluation setting, the system achieved the highest Recall of the challenge (63%). By performing an error analysis, we identified the main causes of misclassifications and areas for improving of our system, and highlighted the need of consistent gold standard data sets for advancing the state of the art in text mining of drug side effects. Database URL: https://zenodo.org/record/29887?ln¼en#.VsL3yDLWR_V
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Affiliation(s)
- Àlex Bravo
- Research Programme on Biomedical Informatics (GRIB), IMIM, UPF, Barcelona, Spain and
| | - Tong Shu Li
- Department of Molecular and Experimental Medicine, the Scripps Research Institute, La Jolla, CA, USA
| | - Andrew I Su
- Department of Molecular and Experimental Medicine, the Scripps Research Institute, La Jolla, CA, USA
| | - Benjamin M Good
- Department of Molecular and Experimental Medicine, the Scripps Research Institute, La Jolla, CA, USA
| | - Laura I Furlong
- Research Programme on Biomedical Informatics (GRIB), IMIM, UPF, Barcelona, Spain and
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Akhondi SA, Pons E, Afzal Z, van Haagen H, Becker BFH, Hettne KM, van Mulligen EM, Kors JA. Chemical entity recognition in patents by combining dictionary-based and statistical approaches. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw061. [PMID: 27141091 PMCID: PMC4852402 DOI: 10.1093/database/baw061] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 04/03/2016] [Indexed: 11/13/2022]
Abstract
We describe the development of a chemical entity recognition system and its application in the CHEMDNER-patent track of BioCreative 2015. This community challenge includes a Chemical Entity Mention in Patents (CEMP) recognition task and a Chemical Passage Detection (CPD) classification task. We addressed both tasks by an ensemble system that combines a dictionary-based approach with a statistical one. For this purpose the performance of several lexical resources was assessed using Peregrine, our open-source indexing engine. We combined our dictionary-based results on the patent corpus with the results of tmChem, a chemical recognizer using a conditional random field classifier. To improve the performance of tmChem, we utilized three additional features, viz. part-of-speech tags, lemmas and word-vector clusters. When evaluated on the training data, our final system obtained an F-score of 85.21% for the CEMP task, and an accuracy of 91.53% for the CPD task. On the test set, the best system ranked sixth among 21 teams for CEMP with an F-score of 86.82%, and second among nine teams for CPD with an accuracy of 94.23%. The differences in performance between the best ensemble system and the statistical system separately were small. Database URL: http://biosemantics.org/chemdner-patents
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Affiliation(s)
- Saber A Akhondi
- Department of Medical Informatics, Erasmus University Medical Center, PO Box 2040, 3000 CA Rotterdam
| | - Ewoud Pons
- Department of Medical Informatics, Erasmus University Medical Center, PO Box 2040, 3000 CA Rotterdam
| | - Zubair Afzal
- Department of Medical Informatics, Erasmus University Medical Center, PO Box 2040, 3000 CA Rotterdam
| | - Herman van Haagen
- Department of Medical Informatics, Erasmus University Medical Center, PO Box 2040, 3000 CA Rotterdam
| | - Benedikt F H Becker
- Department of Medical Informatics, Erasmus University Medical Center, PO Box 2040, 3000 CA Rotterdam
| | - Kristina M Hettne
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Erik M van Mulligen
- Department of Medical Informatics, Erasmus University Medical Center, PO Box 2040, 3000 CA Rotterdam
| | - Jan A Kors
- Department of Medical Informatics, Erasmus University Medical Center, PO Box 2040, 3000 CA Rotterdam
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Li TS, Bravo À, Furlong LI, Good BM, Su AI. A crowdsourcing workflow for extracting chemical-induced disease relations from free text. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw051. [PMID: 27087308 PMCID: PMC4834205 DOI: 10.1093/database/baw051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 03/17/2016] [Indexed: 01/05/2023]
Abstract
Relations between chemicals and diseases are one of the most queried biomedical interactions. Although expert manual curation is the standard method for extracting these relations from the literature, it is expensive and impractical to apply to large numbers of documents, and therefore alternative methods are required. We describe here a crowdsourcing workflow for extracting chemical-induced disease relations from free text as part of the BioCreative V Chemical Disease Relation challenge. Five non-expert workers on the CrowdFlower platform were shown each potential chemical-induced disease relation highlighted in the original source text and asked to make binary judgments about whether the text supported the relation. Worker responses were aggregated through voting, and relations receiving four or more votes were predicted as true. On the official evaluation dataset of 500 PubMed abstracts, the crowd attained a 0.505 F-score (0.475 precision, 0.540 recall), with a maximum theoretical recall of 0.751 due to errors with named entity recognition. The total crowdsourcing cost was $1290.67 ($2.58 per abstract) and took a total of 7 h. A qualitative error analysis revealed that 46.66% of sampled errors were due to task limitations and gold standard errors, indicating that performance can still be improved. All code and results are publicly available at https://github.com/SuLab/crowd_cid_relex Database URL: https://github.com/SuLab/crowd_cid_relex
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Affiliation(s)
- Tong Shu Li
- Department of Molecular and Experimental Medicine, the Scripps Research Institute, La Jolla, CA 92037, USA
| | - Àlex Bravo
- Research Programme on Biomedical Informatics (GRIB), IMIM, UPF, Barcelona, Spain
| | - Laura I Furlong
- Research Programme on Biomedical Informatics (GRIB), IMIM, UPF, Barcelona, Spain
| | - Benjamin M Good
- Department of Molecular and Experimental Medicine, the Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew I Su
- Department of Molecular and Experimental Medicine, the Scripps Research Institute, La Jolla, CA 92037, USA
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Pons E, Becker BFH, Akhondi SA, Afzal Z, van Mulligen EM, Kors JA. Extraction of chemical-induced diseases using prior knowledge and textual information. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw046. [PMID: 27081155 PMCID: PMC4831722 DOI: 10.1093/database/baw046] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/11/2016] [Indexed: 01/24/2023]
Abstract
We describe our approach to the chemical–disease relation (CDR) task in the BioCreative V challenge. The CDR task consists of two subtasks: automatic disease-named entity recognition and normalization (DNER), and extraction of chemical-induced diseases (CIDs) from Medline abstracts. For the DNER subtask, we used our concept recognition tool Peregrine, in combination with several optimization steps. For the CID subtask, our system, which we named RELigator, was trained on a rich feature set, comprising features derived from a graph database containing prior knowledge about chemicals and diseases, and linguistic and statistical features derived from the abstracts in the CDR training corpus. We describe the systems that were developed and present evaluation results for both subtasks on the CDR test set. For DNER, our Peregrine system reached an F-score of 0.757. For CID, the system achieved an F-score of 0.526, which ranked second among 18 participating teams. Several post-challenge modifications of the systems resulted in substantially improved F-scores (0.828 for DNER and 0.602 for CID). RELigator is available as a web service at http://biosemantics.org/index.php/software/religator.
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Affiliation(s)
- Ewoud Pons
- Department of Medical Informatics Department of Radiology, Erasmus University Medical Center, 3000 DR Rotterdam, PO Box 2040, The Netherlands
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Zhou H, Deng H, Chen L, Yang Y, Jia C, Huang D. Exploiting syntactic and semantics information for chemical-disease relation extraction. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw048. [PMID: 27081156 PMCID: PMC4831723 DOI: 10.1093/database/baw048] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/15/2016] [Indexed: 11/13/2022]
Abstract
Identifying chemical-disease relations (CDR) from biomedical literature could improve chemical safety and toxicity studies. This article proposes a novel syntactic and semantic information exploitation method for CDR extraction. The proposed method consists of a feature-based model, a tree kernel-based model and a neural network model. The feature-based model exploits lexical features, the tree kernel-based model captures syntactic structure features, and the neural network model generates semantic representations. The motivation of our method is to fully utilize the nice properties of the three models to explore diverse information for CDR extraction. Experiments on the BioCreative V CDR dataset show that the three models are all effective for CDR extraction, and their combination could further improve extraction performance.Database URL:http://www.biocreative.org/resources/corpora/biocreative-v-cdr-corpus/.
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Affiliation(s)
- Huiwei Zhou
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Huijie Deng
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Long Chen
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Yunlong Yang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Chen Jia
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Degen Huang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
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Balachandran P, Parthasarathy V, Ajay Kumar T. Isolation of Compounds from Sargassum wightii by GCMS and the Molecular Docking against Anti-Inflammatory Marker COX2. ACTA ACUST UNITED AC 2016. [DOI: 10.18052/www.scipress.com/ilcpa.63.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The study focused on the molecular docking of GC-MS isolated compounds from theSargassum wightiiagainst inflammatory marker Cycloxigenase-2 (COX2). Seven compounds isolated by GC-MS were tested for their anti-inflammatory action using insilico analysis. The crystal structure obtained from the protein data bank was docked against seven compounds and the glide score as well as glide energy were determined using Schrödinger Maestro software (version 2013.1). The results of molecular docking showed that out of the seven bioactive compounds tested, methyl salicylate, benzoic acid, 2-hydroxy-,ethyl ester, diethyl phthalate, hexadecanoic acid, ethyl ester and (E) -9-octadecenoic acid ethyl ester were effectively inhibited the COX2 protein. The ADME properties of the compounds analyzed using Qikprop version 3.6 software of Schrodinger suite and the results showed that all the compounds were biologically active and the scores were within the acceptable range. This study revealed that the possibility of using these compounds against COX2 to treat inflammation.
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35
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Muegge I, Mukherjee P. An overview of molecular fingerprint similarity search in virtual screening. Expert Opin Drug Discov 2015; 11:137-48. [PMID: 26558489 DOI: 10.1517/17460441.2016.1117070] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION A central premise of medicinal chemistry is that structurally similar molecules exhibit similar biological activities. Molecular fingerprints encode properties of small molecules and assess their similarities computationally through bit string comparisons. Based on the similarity to a biologically active template, molecular fingerprint methods allow for identifying additional compounds with a higher chance of displaying similar biological activities against the same target - a process commonly referred to as virtual screening (VS). AREAS COVERED This article focuses on fingerprint similarity searches in the context of compound selection for enhancing hit sets, comparing compound decks, and VS. In addition, the authors discuss the application of fingerprints in predictive modeling. EXPERT OPINION Fingerprint similarity search methods are especially useful in VS if only a few unrelated ligands are known for a given target and therefore more complex and information rich methods such as pharmacophore searches or structure-based design are not applicable. In addition, fingerprint methods are used in characterizing properties of compound collections such as chemical diversity, density in chemical space, and content of biologically active molecules (biodiversity). Such assessments are important for deciding what compounds to experimentally screen, to purchase, or to assemble in a virtual compound deck for in silico screening or de novo design.
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Affiliation(s)
- Ingo Muegge
- a Boehringer Ingelheim Pharmaceuticals , Department of Small Molecule Discovery Research , Ridgefield , CT , USA
| | - Prasenjit Mukherjee
- a Boehringer Ingelheim Pharmaceuticals , Department of Small Molecule Discovery Research , Ridgefield , CT , USA
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Simonin C, Awale M, Brand M, van Deursen R, Schwartz J, Fine M, Kovacs G, Häfliger P, Gyimesi G, Sithampari A, Charles R, Hediger MA, Reymond J. Optimization of TRPV6 Calcium Channel Inhibitors Using a 3D Ligand‐Based Virtual Screening Method. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Céline Simonin
- 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)
| | - Michael Brand
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Bern, Freiestrasse 3, 3012 Bern (Switzerland)
| | - Ruud van Deursen
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Bern, Freiestrasse 3, 3012 Bern (Switzerland)
| | - Julian Schwartz
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Bern, Freiestrasse 3, 3012 Bern (Switzerland)
| | - Michael Fine
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern (Switzerland)
| | - Gergely Kovacs
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern (Switzerland)
| | - Pascal Häfliger
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern (Switzerland)
| | - Gergely Gyimesi
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern (Switzerland)
| | - Abilashan Sithampari
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern (Switzerland)
| | - Roch‐Philippe Charles
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern (Switzerland)
| | - Matthias A. Hediger
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern (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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Jin X, Awale M, Zasso M, Kostro D, Patiny L, Reymond JL. PDB-Explorer: a web-based interactive map of the protein data bank in shape space. BMC Bioinformatics 2015; 16:339. [PMID: 26493835 PMCID: PMC4619230 DOI: 10.1186/s12859-015-0776-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/14/2015] [Indexed: 11/17/2022] Open
Abstract
Background The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited. Methods A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as virus particles. The principle component analysis was used to obtain the visualization of PDB in 3DP-space. Results The 3DP property space groups proteins and protein assemblies according to their 3D-shape similarity, yet shows exquisite ability to distinguish between closely related structures. An interactive website called PDB-Explorer is presented featuring a color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer website allows performing 3DP-nearest neighbor searches of any PDB-entry or of any structure uploaded as protein-type PDB file. All functionalities on the website are implemented in JavaScript in a platform-independent manner and draw data from a server that is updated daily with the latest PDB additions, ensuring complete and up-to-date coverage. The essentially instantaneous 3DP-similarity search with the PDB-Explorer provides results comparable to those of much slower 3D-alignment algorithms, and automatically clusters proteins from the same superfamilies in tight groups. Conclusion A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3D-fingerprint for proteins and implemented in a web-based database exploration tool comprising an interactive color-coded map of the PDB chemical space and a nearest neighbor search tool. The PDB-Explorer website is freely available at www.cheminfo.org/pdbexplorer and represents an unprecedented opportunity to interactively visualize and explore the structural diversity of the PDB. ᅟ ᅟMaps of PDB in 3DP-space color-coded by heavy atom count and shape. ![]()
Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0776-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xian Jin
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012, Berne, Switzerland.
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012, Berne, Switzerland.
| | - Michaël Zasso
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC), Lausanne, 1015, Switzerland.
| | - Daniel Kostro
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC), Lausanne, 1015, Switzerland.
| | - Luc Patiny
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC), Lausanne, 1015, Switzerland.
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012, Berne, Switzerland.
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Per-Residue Energy Footprints-Based Pharmacophore Modeling as an Enhanced In Silico Approach in Drug Discovery: A Case Study on the Identification of Novel β-Secretase1 (BACE1) Inhibitors as Anti-Alzheimer Agents. Cell Mol Bioeng 2015. [DOI: 10.1007/s12195-015-0421-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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39
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Simonin C, Awale M, Brand M, van Deursen R, Schwartz J, Fine M, Kovacs G, Häfliger P, Gyimesi G, Sithampari A, Charles RP, Hediger MA, Reymond JL. Optimization of TRPV6 Calcium Channel Inhibitors Using a 3D Ligand-Based Virtual Screening Method. Angew Chem Int Ed Engl 2015; 54:14748-52. [PMID: 26457814 DOI: 10.1002/anie.201507320] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/02/2015] [Indexed: 12/31/2022]
Abstract
Herein, we report the discovery of the first potent and selective inhibitor of TRPV6, a calcium channel overexpressed in breast and prostate cancer, and its use to test the effect of blocking TRPV6-mediated Ca(2+)-influx on cell growth. The inhibitor was discovered through a computational method, xLOS, a 3D-shape and pharmacophore similarity algorithm, a type of ligand-based virtual screening (LBVS) method described briefly here. Starting with a single weakly active seed molecule, two successive rounds of LBVS followed by optimization by chemical synthesis led to a selective molecule with 0.3 μM inhibition of TRPV6. The ability of xLOS to identify different scaffolds early in LBVS was essential to success. The xLOS method may be generally useful to develop tool compounds for poorly characterized targets.
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Affiliation(s)
- Céline Simonin
- 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)
| | - Michael Brand
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Bern, Freiestrasse 3, 3012 Bern (Switzerland)
| | - Ruud van Deursen
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Bern, Freiestrasse 3, 3012 Bern (Switzerland)
| | - Julian Schwartz
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Bern, Freiestrasse 3, 3012 Bern (Switzerland)
| | - Michael Fine
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern (Switzerland)
| | - Gergely Kovacs
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern (Switzerland)
| | - Pascal Häfliger
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern (Switzerland)
| | - Gergely Gyimesi
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern (Switzerland)
| | - Abilashan Sithampari
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern (Switzerland)
| | - Roch-Philippe Charles
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern (Switzerland)
| | - Matthias A Hediger
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern (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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Awale M, Reymond JL. Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces. J Chem Inf Model 2015. [PMID: 26207526 DOI: 10.1021/acs.jcim.5b00182] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
An Internet portal accessible at www.gdb.unibe.ch has been set up to automatically generate color-coded similarity maps of the ChEMBL database in relation to up to two sets of active compounds taken from the enhanced Directory of Useful Decoys (eDUD), a random set of molecules, or up to two sets of user-defined reference molecules. These maps visualize the relationships between the selected compounds and ChEMBL in six different high dimensional chemical spaces, namely MQN (42-D molecular quantum numbers), SMIfp (34-D SMILES fingerprint), APfp (20-D shape fingerprint), Xfp (55-D pharmacophore fingerprint), Sfp (1024-bit substructure fingerprint), and ECfp4 (1024-bit extended connectivity fingerprint). The maps are supplied in form of Java based desktop applications called "similarity mapplets" allowing interactive content browsing and linked to a "Multifingerprint Browser for ChEMBL" (also accessible directly at www.gdb.unibe.ch ) to perform nearest neighbor searches. One can obtain six similarity mapplets of ChEMBL relative to random reference compounds, 606 similarity mapplets relative to single eDUD active sets, 30,300 similarity mapplets relative to pairs of eDUD active sets, and any number of similarity mapplets relative to user-defined reference sets to help visualize the structural diversity of compound series in drug optimization projects and their relationship to other known bioactive compounds.
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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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Montalbetti N, Simonin A, Simonin C, Awale M, Reymond JL, Hediger MA. Discovery and characterization of a novel non-competitive inhibitor of the divalent metal transporter DMT1/SLC11A2. Biochem Pharmacol 2015; 96:216-24. [PMID: 26047847 DOI: 10.1016/j.bcp.2015.05.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 05/05/2015] [Indexed: 10/23/2022]
Abstract
Divalent metal transporter-1 (SLC11A2/DMT1) uses the H(+) electrochemical gradient as the driving force to transport divalent metal ions such as Fe(2+), Mn(2+) and others metals into mammalian cells. DMT1 is ubiquitously expressed, most notably in proximal duodenum, immature erythroid cells, brain and kidney. This transporter mediates H(+)-coupled transport of ferrous iron across the apical membrane of enterocytes. In addition, in cells such as to erythroid precursors, following transferrin receptor (TfR) mediated endocytosis; it mediates H(+)-coupled exit of ferrous iron from endocytic vesicles into the cytosol. Dysfunction of human DMT1 is associated with several pathologies such as iron deficiency anemia hemochromatosis, Parkinson's disease and Alzheimer's disease, as well as colorectal cancer and esophageal adenocarcinoma, making DMT1 an attractive target for drug discovery. In the present study, we performed a ligand-based virtual screening of the Princeton database (700,000 commercially available compounds) to search for pharmacophore shape analogs of recently reported DMT1 inhibitors. We discovered a new compound, named pyrimidinone 8, which mediates a reversible linear non-competitive inhibition of human DMT1 (hDMT1) transport activity with a Ki of ∼20μM. This compound does not affect hDMT1 cell surface expression and shows no dependence on extracellular pH. To our knowledge, this is the first experimental evidence that hDMT1 can be allosterically modulated by pharmacological agents. Pyrimidinone 8 represents a novel versatile tool compound and it may serve as a lead structure for the development of therapeutic compounds for pre-clinical assessment.
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Affiliation(s)
- Nicolas Montalbetti
- Institute of Biochemistry and Molecular Medicine, University of Bern, Switzerland; Swiss National Center of Competence in Research, NCCR TransCure, University of Bern, Switzerland.
| | - Alexandre Simonin
- Institute of Biochemistry and Molecular Medicine, University of Bern, Switzerland; Swiss National Center of Competence in Research, NCCR TransCure, University of Bern, Switzerland.
| | - Céline Simonin
- Department of Chemistry and Biochemistry, University of Bern, Switzerland; Swiss National Center of Competence in Research, NCCR TransCure, University of Bern, Switzerland
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, University of Bern, Switzerland; Swiss National Center of Competence in Research, NCCR TransCure, University of Bern, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Bern, Switzerland; Swiss National Center of Competence in Research, NCCR TransCure, University of Bern, Switzerland.
| | - Matthias A Hediger
- Institute of Biochemistry and Molecular Medicine, University of Bern, Switzerland; Swiss National Center of Competence in Research, NCCR TransCure, University of Bern, Switzerland.
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Huang CC, Lu Z. Community challenges in biomedical text mining over 10 years: success, failure and the future. Brief Bioinform 2015; 17:132-44. [PMID: 25935162 DOI: 10.1093/bib/bbv024] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Indexed: 11/13/2022] Open
Abstract
One effective way to improve the state of the art is through competitions. Following the success of the Critical Assessment of protein Structure Prediction (CASP) in bioinformatics research, a number of challenge evaluations have been organized by the text-mining research community to assess and advance natural language processing (NLP) research for biomedicine. In this article, we review the different community challenge evaluations held from 2002 to 2014 and their respective tasks. Furthermore, we examine these challenge tasks through their targeted problems in NLP research and biomedical applications, respectively. Next, we describe the general workflow of organizing a Biomedical NLP (BioNLP) challenge and involved stakeholders (task organizers, task data producers, task participants and end users). Finally, we summarize the impact and contributions by taking into account different BioNLP challenges as a whole, followed by a discussion of their limitations and difficulties. We conclude with future trends in BioNLP challenge evaluations.
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Khare R, Good BM, Leaman R, Su AI, Lu Z. Crowdsourcing in biomedicine: challenges and opportunities. Brief Bioinform 2015; 17:23-32. [PMID: 25888696 DOI: 10.1093/bib/bbv021] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The use of crowdsourcing to solve important but complex problems in biomedical and clinical sciences is growing and encompasses a wide variety of approaches. The crowd is diverse and includes online marketplace workers, health information seekers, science enthusiasts and domain experts. In this article, we review and highlight recent studies that use crowdsourcing to advance biomedicine. We classify these studies into two broad categories: (i) mining big data generated from a crowd (e.g. search logs) and (ii) active crowdsourcing via specific technical platforms, e.g. labor markets, wikis, scientific games and community challenges. Through describing each study in detail, we demonstrate the applicability of different methods in a variety of domains in biomedical research, including genomics, biocuration and clinical research. Furthermore, we discuss and highlight the strengths and limitations of different crowdsourcing platforms. Finally, we identify important emerging trends, opportunities and remaining challenges for future crowdsourcing research in biomedicine.
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Li J, Zheng S, Chen B, Butte AJ, Swamidass SJ, Lu Z. A survey of current trends in computational drug repositioning. Brief Bioinform 2015; 17:2-12. [PMID: 25832646 DOI: 10.1093/bib/bbv020] [Citation(s) in RCA: 338] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Indexed: 12/26/2022] Open
Abstract
Computational drug repositioning or repurposing is a promising and efficient tool for discovering new uses from existing drugs and holds the great potential for precision medicine in the age of big data. The explosive growth of large-scale genomic and phenotypic data, as well as data of small molecular compounds with granted regulatory approval, is enabling new developments for computational repositioning. To achieve the shortest path toward new drug indications, advanced data processing and analysis strategies are critical for making sense of these heterogeneous molecular measurements. In this review, we show recent advancements in the critical areas of computational drug repositioning from multiple aspects. First, we summarize available data sources and the corresponding computational repositioning strategies. Second, we characterize the commonly used computational techniques. Third, we discuss validation strategies for repositioning studies, including both computational and experimental methods. Finally, we highlight potential opportunities and use-cases, including a few target areas such as cancers. We conclude with a brief discussion of the remaining challenges in computational drug repositioning.
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