1
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McGibbon M, Shave S, Dong J, Gao Y, Houston DR, Xie J, Yang Y, Schwaller P, Blay V. From intuition to AI: evolution of small molecule representations in drug discovery. Brief Bioinform 2023; 25:bbad422. [PMID: 38033290 PMCID: PMC10689004 DOI: 10.1093/bib/bbad422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023] Open
Abstract
Within drug discovery, the goal of AI scientists and cheminformaticians is to help identify molecular starting points that will develop into safe and efficacious drugs while reducing costs, time and failure rates. To achieve this goal, it is crucial to represent molecules in a digital format that makes them machine-readable and facilitates the accurate prediction of properties that drive decision-making. Over the years, molecular representations have evolved from intuitive and human-readable formats to bespoke numerical descriptors and fingerprints, and now to learned representations that capture patterns and salient features across vast chemical spaces. Among these, sequence-based and graph-based representations of small molecules have become highly popular. However, each approach has strengths and weaknesses across dimensions such as generality, computational cost, inversibility for generative applications and interpretability, which can be critical in informing practitioners' decisions. As the drug discovery landscape evolves, opportunities for innovation continue to emerge. These include the creation of molecular representations for high-value, low-data regimes, the distillation of broader biological and chemical knowledge into novel learned representations and the modeling of up-and-coming therapeutic modalities.
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Affiliation(s)
- Miles McGibbon
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, Scotland EH9 3BF, United Kingdom
| | - Steven Shave
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, Scotland EH9 3BF, United Kingdom
| | - Jie Dong
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, China
| | - Yumiao Gao
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, Scotland EH9 3BF, United Kingdom
| | - Douglas R Houston
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, Scotland EH9 3BF, United Kingdom
| | - Jiancong Xie
- Key Laboratory of Machine Intelligence and Advanced Computing, Sun Yat-Sen University, Guangzhou, 510000, China
| | - Yuedong Yang
- Key Laboratory of Machine Intelligence and Advanced Computing, Sun Yat-Sen University, Guangzhou, 510000, China
| | - Philippe Schwaller
- Laboratory of Artificial Chemical Intelligence (LIAC), Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Vincent Blay
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, Scotland EH9 3BF, United Kingdom
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2
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Niazi SK, Mariam Z. Recent Advances in Machine-Learning-Based Chemoinformatics: A Comprehensive Review. Int J Mol Sci 2023; 24:11488. [PMID: 37511247 PMCID: PMC10380192 DOI: 10.3390/ijms241411488] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/30/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
In modern drug discovery, the combination of chemoinformatics and quantitative structure-activity relationship (QSAR) modeling has emerged as a formidable alliance, enabling researchers to harness the vast potential of machine learning (ML) techniques for predictive molecular design and analysis. This review delves into the fundamental aspects of chemoinformatics, elucidating the intricate nature of chemical data and the crucial role of molecular descriptors in unveiling the underlying molecular properties. Molecular descriptors, including 2D fingerprints and topological indices, in conjunction with the structure-activity relationships (SARs), are pivotal in unlocking the pathway to small-molecule drug discovery. Technical intricacies of developing robust ML-QSAR models, including feature selection, model validation, and performance evaluation, are discussed herewith. Various ML algorithms, such as regression analysis and support vector machines, are showcased in the text for their ability to predict and comprehend the relationships between molecular structures and biological activities. This review serves as a comprehensive guide for researchers, providing an understanding of the synergy between chemoinformatics, QSAR, and ML. Due to embracing these cutting-edge technologies, predictive molecular analysis holds promise for expediting the discovery of novel therapeutic agents in the pharmaceutical sciences.
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Affiliation(s)
- Sarfaraz K Niazi
- College of Pharmacy, University of Illinois, Chicago, IL 61820, USA
| | - Zamara Mariam
- Zamara Mariam, School of Interdisciplinary Engineering & Sciences (SINES), National University of Sciences & Technology (NUST), Islamabad 24090, Pakistan
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3
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Lin YT, Li Y, Hsu HC, Tsai JY, Lee JH, Tai CJ, Wu MJ, Wu CC. Discovery of 7, 4'-dimethoxy-3-hydroxyflavone as a protease-activated receptor 4 antagonist with antithrombotic activity and less bleeding tendency in mice. Biochem Pharmacol 2022; 202:115152. [PMID: 35752281 DOI: 10.1016/j.bcp.2022.115152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/31/2022] [Accepted: 06/17/2022] [Indexed: 11/29/2022]
Abstract
There is growing evidence of the importance of protease-activated receptor 4 (PAR4), one of thrombin receptors, as a therapeutic target in thrombotic cardiovascular diseases. In the present study, we utilized ligand-based virtual screening, bioassay, and structure-activity relationship study to discover PAR4 antagonists with new chemical scaffolds from natural origin, and examined their application as antiplatelet agents. By using these approaches, we have identified a flavonoid, 7, 4'-dimethoxy-3-hydroxyflavone, that exhibits anti-PAR4 activity. 7, 4'-Dimethoxy-3-hydroxyflavone inhibited PAR4-mediated human platelet aggregation, GPIIb/IIIa activation, and P-selectin secretion. Also, it inhibited PAR4 downstream signaling pathways, including Ca2+/protein kinase C, Akt, and MAP kinases ERK and p38, in human platelets, and suppressed PAR4-mediated β-arrestin recruitment in CHO-K1 cells exogenously expressed human PAR4. In a microfluidic system, 7, 4'-dimethoxy-3-hydroxyflavone reduced thrombus formation on collagen-coated chambers at an arterial shear rate in recalcified whole blood. Furthermore, mice treated with 7, 4'-dimethoxy-3-hydroxyflavone were significantly protected from FeCl3-induced carotid arterial occlusions, without significantly affecting tail bleeding time. In conclusion, 7, 4'-dimethoxy-3-hydroxyflavone represents a new class of nature-based PAR4 antagonist, it shows effective in vivo antithrombotic properties with less bleeding tendency, and could be a potential candidate for developing new antiplatelet agents.
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Affiliation(s)
- Ying-Ting Lin
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yu Li
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Hui-Ching Hsu
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Ju-Ying Tsai
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Jia-Hau Lee
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chi-Jung Tai
- Department of Family Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Ming-Jung Wu
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Chin-Chung Wu
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung 807, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan; Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
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4
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Abstract
Molecular descriptors encode a variety of molecular representations for computer-assisted drug discovery. Here, we focus on the Weighted Holistic Atom Localization and Entity Shape (WHALES) descriptors, which were originally designed for scaffold hopping from natural products to synthetic molecules. WHALES descriptors capture molecular shape and partial charges simultaneously. We introduce the key aspects of the WHALES concept and provide a step-by-step guide on how to use these descriptors for virtual compound screening and scaffold hopping. The results presented can be reproduced by using the code freely available from URL: github.com/ETHmodlab/scaffold_hopping_whales .
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Affiliation(s)
- Francesca Grisoni
- Department of Chemistry and Applied Biosciences, RETHINK, ETH Zurich, Zurich, Switzerland.
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, RETHINK, ETH Zurich, Zurich, Switzerland
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5
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Lovrics A, Pape VFS, Szisz D, Kalászi A, Heffeter P, Magyar C, Szakács G. Identifying new topoisomerase II poison scaffolds by combining publicly available toxicity data and 2D/3D-based virtual screening. J Cheminform 2019; 11:67. [PMID: 33430961 PMCID: PMC6842385 DOI: 10.1186/s13321-019-0390-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/23/2019] [Indexed: 01/17/2023] Open
Abstract
Molecular descriptor (2D) and three dimensional (3D) shape based similarity methods are widely used in ligand based virtual drug design. In the present study pairwise structure comparisons among a set of 4858 DTP compounds tested in the NCI60 tumor cell line anticancer drug screen were computed using chemical hashed fingerprints and 3D molecule shapes to calculate 2D and 3D similarities, respectively. Additionally, pairwise biological activity similarities were calculated by correlating the 60 element vectors of pGI50 values corresponding to the cytotoxicity of the compounds across the NCI60 panel. Subsequently, we compared the power of 2D and 3D structural similarity metrics to predict the toxicity pattern of compounds. We found that while the positive predictive value and sensitivity of 3D and molecular descriptor based approaches to predict biological activity are similar, a subset of molecule pairs yielded contradictory results. By simultaneously requiring similarity of biological activities and 3D shapes, and dissimilarity of molecular descriptor based comparisons, we identify pairs of scaffold hopping candidates displaying characteristic core structural changes such as heteroatom/heterocycle change and ring closure. Attempts to discover scaffold hopping candidates of mitoxantrone recovered known Topoisomerase II (Top2) inhibitors, and also predicted new, previously unknown chemotypes possessing in vitro Top2 inhibitory activity.![]()
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Affiliation(s)
- Anna Lovrics
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, 1117, Hungary
| | - Veronika F S Pape
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, 1117, Hungary.,Department of Physiology, Semmelweis University, Faculty of Medicine, Budapest, 1094, Hungary
| | - Dániel Szisz
- ChemAxon Ltd., Graphisoft park, Záhony u. 7, Budapest, 1031, Hungary
| | - Adrián Kalászi
- ChemAxon Ltd., Graphisoft park, Záhony u. 7, Budapest, 1031, Hungary
| | - Petra Heffeter
- Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria
| | - Csaba Magyar
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, 1117, Hungary
| | - Gergely Szakács
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, 1117, Hungary. .,Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria.
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6
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Beshnova D, Carolan C, Grigorenko V, Rubtsova M, Gbekor E, Lewis J, Lamzin V, Egorov A. Scaffold hopping computational approach for searching novel β-lactamase inhibitors. ACTA ACUST UNITED AC 2019; 65:468-476. [DOI: 10.18097/pbmc20196506468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We present a novel computational ligand-based virtual screening approach with scaffold hopping capabilities for the identification of novel inhibitors of β-lactamases which confer bacterial resistance to β-lactam antibiotics. The structures of known β-lactamase inhibitors were used as query ligands, and a virtual in silico screening a database of 8 million drug-like compounds was performed in order to select the ligands with similar shape and charge distribution. A set of numerical descriptors was used such as chirality, eigen spectrum of matrices of interatomic distances and connectivity together with higher order moment invariants that showed their efficiency in the field of pattern recognition but have not yet been employed in drug discovery. The developed scaffold-hopping approach was applied for the discovery of analogues of four allosteric inhibitors of serine β-lactamases. After a virtual in silico screening, the effect of two selected ligands on the activity of TEM type β-lactamase was studied experimentally. New non-β-lactam inhibitors were found that showed more effective inhibition of β-lactamases compared to query ligands.
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Affiliation(s)
- D.A. Beshnova
- European Molecular Biology Laboratory, c/o DESY, Hamburg, Germany; UT Southwestern Medical Center, Dallas, TX, United States
| | - C. Carolan
- European Molecular Biology Laboratory, c/o DESY, Hamburg, Germany; International Civil Aviation Organization (ICAO), Montreal, Quebec, Canada
| | - V.G. Grigorenko
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - M.Yu. Rubtsova
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - E. Gbekor
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - J. Lewis
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - V.S. Lamzin
- European Molecular Biology Laboratory, c/o DESY, Hamburg, Germany
| | - A.M. Egorov
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
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7
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Lee PS, Lapointe G, Madera AM, Simmons RL, Xu W, Yifru A, Tjandra M, Karur S, Rico A, Thompson K, Bojkovic J, Xie L, Uehara K, Liu A, Shu W, Bellamacina C, McKenney D, Morris L, Tonn GR, Osborne C, Benton BM, McDowell L, Fu J, Sweeney ZK. Application of Virtual Screening to the Identification of New LpxC Inhibitor Chemotypes, Oxazolidinone and Isoxazoline. J Med Chem 2018; 61:9360-9370. [PMID: 30226381 DOI: 10.1021/acs.jmedchem.8b01287] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
This report summarizes the identification and synthesis of novel LpxC inhibitors aided by computational methods that leveraged numerous crystal structures. This effort led to the identification of oxazolidinone and isoxazoline inhibitors with potent in vitro activity against P. aeruginosa and other Gram-negative bacteria. Representative compound 13f demonstrated efficacy against P. aeruginosa in a mouse neutropenic thigh infection model. The antibacterial activity against K. pneumoniae could be potentiated by Gram-positive antibiotics rifampicin (RIF) and vancomycin (VAN) in both in vitro and in vivo models.
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Affiliation(s)
- Patrick S Lee
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Guillaume Lapointe
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Ann Marie Madera
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Robert L Simmons
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Wenjian Xu
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Aregahegn Yifru
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Meiliana Tjandra
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Subramanian Karur
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Alice Rico
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Katherine Thompson
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Jade Bojkovic
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Lili Xie
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Kyoko Uehara
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Amy Liu
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Wei Shu
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Cornelia Bellamacina
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - David McKenney
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Laura Morris
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - George R Tonn
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Colin Osborne
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Bret M Benton
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Laura McDowell
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Jiping Fu
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
| | - Zachary K Sweeney
- Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States
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8
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Kumar SP. Receptor pharmacophore ensemble (REPHARMBLE): a probabilistic pharmacophore modeling approach using multiple protein-ligand complexes. J Mol Model 2018; 24:282. [PMID: 30220049 DOI: 10.1007/s00894-018-3820-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/03/2018] [Indexed: 10/28/2022]
Abstract
Ensemble methods are gaining more importance in structure-based approaches as single protein-ligand complexes strongly influence the outcomes of virtual screening. Structure-based pharmacophore modeling based on a single protein-ligand complex with complex feature combinations is often limited to certain chemical classes. The REPHARMBLE (receptor pharmacophore ensemble) approach presented here examines the ability of an ensemble of selected protein-ligand complexes to populate pharmacophore space in the ligand binding site, rigorously assesses the importance of pharmacophore features using Poisson statistic and information theory-based entropy calculations, and generates pharmacophore models with high probabilities. In addition, an ensemble scoring function that combines all the resultant high-scoring pharmacophore models to score molecules is derived. The REPHARMBLE approach was evaluated on ten DUD-E benchmark datasets and afforded good screening performance, as measured by receiver operating characteristic, enrichment factor and Güner-Henry score. Although one of the high-scoring models achieved superior statistical results in each dataset, the ensemble scoring function balanced the shortcomings of each model and passed with close performance measures. This approach offers a reliable way of choosing the best-scoring features to build four-feature pharmacophore queries and customize a target-biased 'pharmacophore ensemble' scoring function for subsequent virtual screening.
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9
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Design, synthesis and pharmacological evaluation of N4,N6-disubstituted pyrimidine-4,6-diamine derivatives as potent EGFR inhibitors in non-small cell lung cancer. Eur J Med Chem 2018; 157:1300-1325. [PMID: 30195240 DOI: 10.1016/j.ejmech.2018.08.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/11/2018] [Accepted: 08/11/2018] [Indexed: 02/06/2023]
Abstract
A novel series of 4, 6-disubstituted pyrimidines derivatives were designed, synthesized, and evaluated as epidermal growth factor receptor (EGFR) inhibitors for non-small cell lung cancer(NSCLC). 4, 6-disubstituted pyrimidines as core structure was utilized to substitute the lead structure AZD3759 of the quinazoline basic skeleton via an approach involving scaffold hopping. It was found that compound Yfq07 exhibited the best inhibitory effect compared with AZD3759 in vitro and in vivo: Yfq07 exhibited a competitive ATP inhibitory effect, multiple target effects, and further featured a stronger activity against H3255, A431, HCC827, PC-9 and H1975 compared to AZD3759. Moreover, a stronger pro-apoptotic effect, inhibition of cell G2/M phase on A431, H3255, HCC827 and H1975 could also be observed. In this study, the ultimate goal was changing the core structure to improve other epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) properties while retaining the overall potency. Yfq07 was further explored as an effective 4, 6-pyrimidine anticancer agent for the treatment of human NSCLC.
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10
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Korotcov A, Tkachenko V, Russo DP, Ekins S. Comparison of Deep Learning With Multiple Machine Learning Methods and Metrics Using Diverse Drug Discovery Data Sets. Mol Pharm 2017; 14:4462-4475. [PMID: 29096442 PMCID: PMC5741413 DOI: 10.1021/acs.molpharmaceut.7b00578] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Machine learning methods have been applied to many data sets in pharmaceutical research for several decades. The relative ease and availability of fingerprint type molecular descriptors paired with Bayesian methods resulted in the widespread use of this approach for a diverse array of end points relevant to drug discovery. Deep learning is the latest machine learning algorithm attracting attention for many of pharmaceutical applications from docking to virtual screening. Deep learning is based on an artificial neural network with multiple hidden layers and has found considerable traction for many artificial intelligence applications. We have previously suggested the need for a comparison of different machine learning methods with deep learning across an array of varying data sets that is applicable to pharmaceutical research. End points relevant to pharmaceutical research include absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) properties, as well as activity against pathogens and drug discovery data sets. In this study, we have used data sets for solubility, probe-likeness, hERG, KCNQ1, bubonic plague, Chagas, tuberculosis, and malaria to compare different machine learning methods using FCFP6 fingerprints. These data sets represent whole cell screens, individual proteins, physicochemical properties as well as a data set with a complex end point. Our aim was to assess whether deep learning offered any improvement in testing when assessed using an array of metrics including AUC, F1 score, Cohen's kappa, Matthews correlation coefficient and others. Based on ranked normalized scores for the metrics or data sets Deep Neural Networks (DNN) ranked higher than SVM, which in turn was ranked higher than all the other machine learning methods. Visualizing these properties for training and test sets using radar type plots indicates when models are inferior or perhaps over trained. These results also suggest the need for assessing deep learning further using multiple metrics with much larger scale comparisons, prospective testing as well as assessment of different fingerprints and DNN architectures beyond those used.
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Affiliation(s)
- Alexandru Korotcov
- Science Data Software, LLC, 14914 Bradwill Court, Rockville, MD 20850, USA
| | - Valery Tkachenko
- Science Data Software, LLC, 14914 Bradwill Court, Rockville, MD 20850, USA
| | - Daniel P Russo
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
- The Rutgers Center for Computational and Integrative Biology, Camden, NJ, 08102, USA
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
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11
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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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12
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Lavecchia A, Cerchia C. In silico methods to address polypharmacology: current status, applications and future perspectives. Drug Discov Today 2015; 21:288-98. [PMID: 26743596 DOI: 10.1016/j.drudis.2015.12.007] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/20/2015] [Accepted: 12/21/2015] [Indexed: 12/15/2022]
Abstract
Polypharmacology, a new paradigm in drug discovery that focuses on multi-target drugs (MTDs), has potential application for drug repurposing, the process of finding new uses for existing approved drugs, prediction of off-target toxicities and rational design of MTDs. In this scenario, computational strategies have demonstrated great potential in predicting polypharmacology and in facilitating drug repurposing. Here, we provide a comprehensive overview of various computational approaches that enable the prediction and analysis of in vitro and in vivo drug-response phenotypes and outline their potential for drug discovery. We give an outlook on the latest advances in rational design of MTDs and discuss possible future directions of algorithm development in this field.
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Affiliation(s)
- Antonio Lavecchia
- Department of Pharmacy, Drug Discovery Laboratory, University of Napoli Federico II, via D. Montesano 49, I-80131 Napoli, Italy.
| | - Carmen Cerchia
- Department of Pharmacy, Drug Discovery Laboratory, University of Napoli Federico II, via D. Montesano 49, I-80131 Napoli, Italy
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13
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Ibrahim TM, Bauer MR, Dörr A, Veyisoglu E, Boeckler FM. pROC-Chemotype Plots Enhance the Interpretability of Benchmarking Results in Structure-Based Virtual Screening. J Chem Inf Model 2015; 55:2297-307. [DOI: 10.1021/acs.jcim.5b00475] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tamer M. Ibrahim
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical
Sciences, Eberhard Karls Universität Tübingen, Auf
der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias R. Bauer
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical
Sciences, Eberhard Karls Universität Tübingen, Auf
der Morgenstelle 8, 72076 Tübingen, Germany
| | - Alexander Dörr
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls University Tübingen, Sand 1, 72076 Tübingen, Germany
| | - Erdem Veyisoglu
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical
Sciences, Eberhard Karls Universität Tübingen, Auf
der Morgenstelle 8, 72076 Tübingen, Germany
| | - Frank M. Boeckler
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical
Sciences, Eberhard Karls Universität Tübingen, Auf
der Morgenstelle 8, 72076 Tübingen, Germany
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls University Tübingen, Sand 1, 72076 Tübingen, Germany
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Kim S, Han L, Yu B, Hähnke VD, Bolton EE, Bryant SH. PubChem structure-activity relationship (SAR) clusters. J Cheminform 2015; 7:33. [PMID: 26150895 PMCID: PMC4492103 DOI: 10.1186/s13321-015-0070-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 04/21/2015] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Developing structure-activity relationships (SARs) of molecules is an important approach in facilitating hit exploration in the early stage of drug discovery. Although information on millions of compounds and their bioactivities is freely available to the public, it is very challenging to infer a meaningful and novel SAR from that information. RESULTS Research discussed in the present paper employed a bioactivity-centered clustering approach to group 843,845 non-inactive compounds stored in PubChem according to both structural similarity and bioactivity similarity, with the aim of mining bioactivity data in PubChem for useful SAR information. The compounds were clustered in three bioactivity similarity contexts: (1) non-inactive in a given bioassay, (2) non-inactive against a given protein, and (3) non-inactive against proteins involved in a given pathway. In each context, these small molecules were clustered according to their two-dimensional (2-D) and three-dimensional (3-D) structural similarities. The resulting 18 million clusters, named "PubChem SAR clusters", were delivered in such a way that each cluster contains a group of small molecules similar to each other in both structure and bioactivity. CONCLUSIONS The PubChem SAR clusters, pre-computed using publicly available bioactivity information, make it possible to quickly navigate and narrow down the compounds of interest. Each SAR cluster can be a useful resource in developing a meaningful SAR or enable one to design or expand compound libraries from the cluster. It can also help to predict the potential therapeutic effects and pharmacological actions of less-known compounds from those of well-known compounds (i.e., drugs) in the same cluster.
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Affiliation(s)
- Sunghwan Kim
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Lianyi Han
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Bo Yu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Volker D Hähnke
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Evan E Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Stephen H Bryant
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894 USA
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15
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Vasudevan SR, Singh N, Churchill GC. Scaffold hopping with virtual screening from IP3 to a drug-like partial agonist of the inositol trisphosphate receptor. Chembiochem 2014; 15:2774-82. [PMID: 25399672 DOI: 10.1002/cbic.201402440] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Indexed: 11/06/2022]
Abstract
Inositol 1,4,5-trisphosphate (IP3 ) is a universal signalling molecule that releases calcium from stores within cells by activating the IP3 receptor. Although chemical tools that modulate the IP3 receptor exist, none is ideal due to trade offs between potency, selectivity and cell permeability, and their chemical properties make them challenging starting points for optimisation. Therefore, to find new leads, we used virtual screening to scaffold hop from IP3 by using the program ROCS to perform a 3D ligand-based screen of the ZINC database of purchasable compounds. We then used the program FRED to dock the top-ranking hits into the IP3 binding pocket of the receptor. We tested the 12 highest-scoring hits in a calcium-release bioassay and identified SI-9 as a partial agonist. SI-9 competed with [(3) H]IP3 binding, and reduced histamine-induced calcium signalling in HeLa cells. SI-9 has a novel 2D scaffold that represents a tractable lead for designing improved IP3 receptor modulators.
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Affiliation(s)
- Sridhar R Vasudevan
- Department of Pharmacology, University of Oxford, Mansfield Road, OX1 3QT (UK).
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16
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Kawai K, Nagata N, Takahashi Y. De novo design of drug-like molecules by a fragment-based molecular evolutionary approach. J Chem Inf Model 2014; 54:49-56. [PMID: 24372539 DOI: 10.1021/ci400418c] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
This paper describes a similarity-driven simple evolutionary approach to producing candidate molecules of new drugs. The aim of the method is to explore the candidates that are structurally similar to the reference molecule and yet somewhat different in not only peripheral chains but also their scaffolds. The method employs a known active molecule of our interest as a reference molecule which is used to navigate a huge chemical space. The reference molecule is also used to obtain seed fragments. An initial set of individual structures is prepared with the seed fragments and additional fragments using several connection rules. The fragment library is preferably prepared from a collection of known molecules related to the target of the reference molecule. Every fragment of the library can be used for fragment-based mutation. All the fragments are categorized into three classes; rings, linkers, and side chains. New individuals are produced by the crossover and the fragment-based mutation with the fragment library. Computer experiments with our own fragment library prepared from GPCR SARfari verified the feasibility of our approach to drug discovery.
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Affiliation(s)
- Kentaro Kawai
- Central Research Laboratories, Kaken Pharmaceutical Co. Ltd. , 14, Shinomiya Minamikawara-cho, Yamashina, Kyoto 607-8042, Japan
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17
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18
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'Fuzziness' in pharmacophore-based virtual screening and de novo design. DRUG DISCOVERY TODAY. TECHNOLOGIES 2013; 7:e203-70. [PMID: 24103799 DOI: 10.1016/j.ddtec.2010.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Zhou W, Liu X, Tu Z, Zhang L, Ku X, Bai F, Zhao Z, Xu Y, Ding K, Li H. Discovery of Pteridin-7(8H)-one-Based Irreversible Inhibitors Targeting the Epidermal Growth Factor Receptor (EGFR) Kinase T790M/L858R Mutant. J Med Chem 2013; 56:7821-37. [DOI: 10.1021/jm401045n] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Wei Zhou
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Xiaofeng Liu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Zhengchao Tu
- Key
Laboratory of Regenerative Biology and Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Lianwen Zhang
- Key
Laboratory of Regenerative Biology and Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xin Ku
- Lehrstuhl
für Proteomik und Bioanalytik, Technische Universität München, Freising 85354, Germany
| | | | - Zhenjiang Zhao
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Yufang Xu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Ke Ding
- Key
Laboratory of Regenerative Biology and Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
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20
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MacCuish JD, MacCuish NE. Chemoinformatics applications of cluster analysis. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1152] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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21
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Westermaier Y, Veurink M, Riis-Johannessen T, Guinchard S, Gurny R, Scapozza L. Identification of aggregation breakers for bevacizumab (Avastin®) self-association through similarity searching and interaction studies. Eur J Pharm Biopharm 2013; 85:773-80. [PMID: 23665445 DOI: 10.1016/j.ejpb.2013.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 04/16/2013] [Accepted: 04/19/2013] [Indexed: 10/26/2022]
Abstract
Aggregation is a common challenge in the optimization of therapeutic antibody formulations. Since initial self-association of two monomers is typically a reversible process, the aim of this study is to identify different excipients that are able to shift this equilibrium to the monomeric state. The hypothesis is that a specific interaction between excipient and antibody may hinder two monomers from approaching each other, based on previous work in which dexamethasone phosphate showed the ability to partially reverse formed aggregates of the monoclonal IgG1 antibody bevacizumab back into monomers. The current study focuses on the selection of therapeutically inactive compounds with similar properties. Adenosine monophosphate, adenosine triphosphate, sucrose-6-phosphate and guanosine monophosphate were selected in silico through similarity searching and docking. All four compounds were predicted to bind to a protein-protein interaction hotspot on the Fc region of bevacizumab and thereby breaking dimer formation. The predictions were supported in vitro: An interaction between AMP and bevacizumab with a dissociation constant of 9.59±0.15 mM was observed by microscale thermophoresis. The stability of the antibody at elevated temperature (40 °C) in a 51 mM phosphate buffer pH 7 was investigated in presence and absence of the excipients. Quantification of the different aggregation species by asymmetrical flow field-flow fractionation and size exclusion chromatography demonstrates that all four excipients are able to partially overcome the initial self-association of bevacizumab monomers.
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Affiliation(s)
- Y Westermaier
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva 4, Switzerland
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22
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Papp A, Szommer T, Barna L, Gyimesi G, Ferdinandy P, Spadoni C, Darvas F, Fujita T, Urge L, Dormán G. Enhanced hit-to-lead process using bioanalogous lead evolution and chemogenomics: application in designing selective matrix metalloprotease inhibitors. Expert Opin Drug Discov 2013; 2:707-23. [PMID: 23488960 DOI: 10.1517/17460441.2.5.707] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The authors describe an innovative approach for designing novel inhibitors. This approach effectively integrates the emerging chemogenomics concept of target-family-based drug discovery with bioanalogous design strategies, including privileged structures, molecular frameworks as well as bioisosteric and bioanalogous/isofunctional modifications. The authors applied this method in the design of selective inhibitors of matrix metalloproteases (MMPs), also referred to as matrixins, on the basis of a unique analysis of the ligand-target knowledge base, the 'matrixinome'. For this analysis, the authors created an annotated MMP database containing ∼ 300 inhibitors with their published activity profile. The ligand space was then arranged into a lead evolution tree, where the substructural transformations in each virtual step led to marked changes in the activity pattern. This allowed subtype-specific privileged fragments to be extracted as well as modifications, which improve activity and/or selectivity. Furthermore, the compounds with the preferred activity profile were correlated with sequence homology as well as binding site similarity within the target family, thereby leading to the identification of substructural modifications that turn non-selective, biohomologous structures into selective inhibitors. The matrixinomic application of the authors' approach, therefore, provides an example of how the combination of ligand space knowledge with sequence-related data can radically improve the outcome of the lead optimisation process to achieve higher selectivity within a given target family.
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Affiliation(s)
- Akos Papp
- AMRI Hungary, Inc., Záhony utca 7, 1031 Budapest, Hungary +361 6666 129 ; +361 6666 110 ;
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23
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Kim S, Bolton EE, Bryant SH. Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis. J Cheminform 2012; 4:28. [PMID: 23134593 PMCID: PMC3537644 DOI: 10.1186/1758-2946-4-28] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 10/03/2012] [Indexed: 01/08/2023] Open
Abstract
Background To improve the utility of PubChem, a public repository containing biological activities of small molecules, the PubChem3D project adds computationally-derived three-dimensional (3-D) descriptions to the small-molecule records contained in the PubChem Compound database and provides various search and analysis tools that exploit 3-D molecular similarity. Therefore, the efficient use of PubChem3D resources requires an understanding of the statistical and biological meaning of computed 3-D molecular similarity scores between molecules. Results The present study investigated effects of employing multiple conformers per compound upon the 3-D similarity scores between ten thousand randomly selected biologically-tested compounds (10-K set) and between non-inactive compounds in a given biological assay (156-K set). When the “best-conformer-pair” approach, in which a 3-D similarity score between two compounds is represented by the greatest similarity score among all possible conformer pairs arising from a compound pair, was employed with ten diverse conformers per compound, the average 3-D similarity scores for the 10-K set increased by 0.11, 0.09, 0.15, 0.16, 0.07, and 0.18 for STST-opt, CTST-opt, ComboTST-opt, STCT-opt, CTCT-opt, and ComboTCT-opt, respectively, relative to the corresponding averages computed using a single conformer per compound. Interestingly, the best-conformer-pair approach also increased the average 3-D similarity scores for the non-inactive–non-inactive (NN) pairs for a given assay, by comparable amounts to those for the random compound pairs, although some assays showed a pronounced increase in the per-assay NN-pair 3-D similarity scores, compared to the average increase for the random compound pairs. Conclusion These results suggest that the use of ten diverse conformers per compound in PubChem bioassay data analysis using 3-D molecular similarity is not expected to increase the separation of non-inactive from random and inactive spaces “on average”, although some assays show a noticeable separation between the non-inactive and random spaces when multiple conformers are used for each compound. The present study is a critical next step to understand effects of conformational diversity of the molecules upon the 3-D molecular similarity and its application to biological activity data analysis in PubChem. The results of this study may be helpful to build search and analysis tools that exploit 3-D molecular similarity between compounds archived in PubChem and other molecular libraries in a more efficient way.
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Affiliation(s)
- Sunghwan Kim
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, 20894, MD, USA.
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24
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Schuffenhauer A. Computational methods for scaffold hopping. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1106] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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25
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Sun H, Tawa G, Wallqvist A. Classification of scaffold-hopping approaches. Drug Discov Today 2012; 17:310-24. [PMID: 22056715 PMCID: PMC3328312 DOI: 10.1016/j.drudis.2011.10.024] [Citation(s) in RCA: 247] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 10/17/2011] [Accepted: 10/19/2011] [Indexed: 10/15/2022]
Abstract
The general goal of drug discovery is to identify novel compounds that are active against a preselected biological target with acceptable pharmacological properties defined by marketed drugs. Scaffold hopping has been widely applied by medicinal chemists to discover equipotent compounds with novel backbones that have improved properties. In this article we classify scaffold hopping into four major categories, namely heterocycle replacements, ring opening or closure, peptidomimetics and topology-based hopping. We review the structural diversity of original and final scaffolds with respect to each category. We discuss the advantages and limitations of small, medium and large-step scaffold hopping. Finally, we summarize software that is frequently used to facilitate different kinds of scaffold-hopping methods.
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Affiliation(s)
- Hongmao Sun
- Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Frederick, MD 21702, USA.
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26
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Liu P, Agrafiotis DK, Rassokhin DN. Power Keys: A Novel Class of Topological Descriptors Based on Exhaustive Subgraph Enumeration and their Application in Substructure Searching. J Chem Inf Model 2011; 51:2843-51. [DOI: 10.1021/ci200282z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Pu Liu
- Johnson & Johnson Pharmaceutical Research & Development, L.L.C., Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Dimitris K. Agrafiotis
- Johnson & Johnson Pharmaceutical Research & Development, L.L.C., Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Dmitrii N. Rassokhin
- Johnson & Johnson Pharmaceutical Research & Development, L.L.C., Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
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27
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Xie L, Xie L, Kinnings SL, Bourne PE. Novel computational approaches to polypharmacology as a means to define responses to individual drugs. Annu Rev Pharmacol Toxicol 2011; 52:361-79. [PMID: 22017683 DOI: 10.1146/annurev-pharmtox-010611-134630] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polypharmacology, which focuses on designing therapeutics to target multiple receptors, has emerged as a new paradigm in drug discovery. Polypharmacological effects are an attribute of most, if not all, drug molecules. The efficacy and toxicity of drugs, whether designed as single- or multitarget therapeutics, result from complex interactions between pharmacodynamic, pharmacokinetic, genetic, epigenetic, and environmental factors. Ultimately, to predict a drug response phenotype, it is necessary to understand the change in information flow through cellular networks resulting from dynamic drug-target interactions and the impact that this has on the complete biological system. Although such is a future objective, we review recent progress and challenges in computational techniques that enable the prediction and analysis of in vitro and in vivo drug-response phenotypes.
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Affiliation(s)
- Lei Xie
- Department of Computer Science, Hunter College, The City University of New York, New York, New York 10065, USA.
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28
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Krein MP, Sukumar N. Exploration of the Topology of Chemical Spaces with Network Measures. J Phys Chem A 2011; 115:12905-18. [DOI: 10.1021/jp204022u] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Michael P. Krein
- Rensselaer Exploratory Center for Cheminformatics Research, and Department of Chemistry & Chemical Biology, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - N. Sukumar
- Rensselaer Exploratory Center for Cheminformatics Research, and Department of Chemistry & Chemical Biology, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
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29
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Southan C, Boppana K, Jagarlapudi SA, Muresan S. Analysis of in vitro bioactivity data extracted from drug discovery literature and patents: Ranking 1654 human protein targets by assayed compounds and molecular scaffolds. J Cheminform 2011; 3:14. [PMID: 21569515 PMCID: PMC3118229 DOI: 10.1186/1758-2946-3-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 05/13/2011] [Indexed: 01/19/2023] Open
Abstract
Background Since the classic Hopkins and Groom druggable genome review in 2002, there have been a number of publications updating both the hypothetical and successful human drug target statistics. However, listings of research targets that define the area between these two extremes are sparse because of the challenges of collating published information at the necessary scale. We have addressed this by interrogating databases, populated by expert curation, of bioactivity data extracted from patents and journal papers over the last 30 years. Results From a subset of just over 27,000 documents we have extracted a set of compound-to-target relationships for biochemical in vitro binding-type assay data for 1,736 human proteins and 1,654 gene identifiers. These are linked to 1,671,951 compound records derived from 823,179 unique chemical structures. The distribution showed a compounds-per-target average of 964 with a maximum of 42,869 (Factor Xa). The list includes non-targets, failed targets and cross-screening targets. The top-278 most actively pursued targets cover 90% of the compounds. We further investigated target ranking by determining the number of molecular frameworks and scaffolds. These were compared to the compound counts as alternative measures of chemical diversity on a per-target basis. Conclusions The compounds-per-protein listing generated in this work (provided as a supplementary file) represents the major proportion of the human drug target landscape defined by published data. We supplemented the simple ranking by the number of compounds assayed with additional rankings by molecular topology. These showed significant differences and provide complementary assessments of chemical tractability.
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Affiliation(s)
- Christopher Southan
- DECS Global Compound Sciences, Computational Chemistry, AstraZeneca R&D Mölndal, S-431 83 Mölndal, Sweden.
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Abstract
This article reviews the use of informatics and computational chemistry methods in medicinal chemistry, with special consideration of how computational techniques can be adapted and extended to obtain more and higher-quality information. Special consideration is given to the computation of protein–ligand binding affinities, to the prediction of off-target bioactivities, bioactivity spectra and computational toxicology, and also to calculating absorption-, distribution-, metabolism- and excretion-relevant properties, such as solubility.
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Briansó F, Carrascosa MC, Oprea TI, Mestres J. Cross-pharmacology analysis of G protein-coupled receptors. Curr Top Med Chem 2011; 11:1956-63. [PMID: 21851335 PMCID: PMC3717414 DOI: 10.2174/156802611796391285] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 06/24/2011] [Indexed: 11/22/2022]
Abstract
The degree of applicability of chemogenomic approaches to protein families depends on the accuracy and completeness of pharmacological data and the corresponding level of pharmacological similarity observed among their protein members. The recent public domain availability of pharmacological data for thousands of small molecules on 204 G protein-coupled receptors (GPCRs) provides a firm basis for an in-depth cross-pharmacology analysis of this superfamily. The number of protein targets included in the cross-pharmacology profile of the different GPCRs changes significantly upon varying the ligand similarity and binding affinity criteria. However, with the exception of muscarinic receptors, aminergic GPCRs distinguish themselves from the rest of the members in the family by their remarkably high levels of pharmacological similarity among them. Clusters of non-GPCR targets related by cross-pharmacology with particular GPCRs are identified and the implications for unwanted side-effects, as well as for repurposing opportunities, discussed.
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Affiliation(s)
- Ferran Briansó
- Chemogenomics Laboratory, Research Unit on Biomedical Informatics, Institut Municipal d'Investigació Mèdica and Universitat Pompeu Fabra, Pare de Recerca Biomèdica (PRBB), Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Maria C. Carrascosa
- Chemogenomics Laboratory, Research Unit on Biomedical Informatics, Institut Municipal d'Investigació Mèdica and Universitat Pompeu Fabra, Pare de Recerca Biomèdica (PRBB), Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Tudor I. Oprea
- Division of Biocomputing, Department of Biochemistry & Molecular Biology and UNM Center for Molecular Discovery, University of New Mexico School of Medicine, MSC11 6145, Albuquerque NM 87131, USA
| | - Jordi Mestres
- Chemogenomics Laboratory, Research Unit on Biomedical Informatics, Institut Municipal d'Investigació Mèdica and Universitat Pompeu Fabra, Pare de Recerca Biomèdica (PRBB), Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
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Abstract
The aim of this chapter is to describe the stages of early drug discovery that can be assisted by techniques commonly used in the field of cheminformatics. In fact, cheminformatics tools can be applied all the way from the design of compound libraries and the analysis of HTS results, to the discovery of functional relationships between compounds and their targets.
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Affiliation(s)
- Anne Kümmel
- Novartis Institutes for BioMedical Research, Basel, Switzerland
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Venhorst J, Núñez S, Kruse CG. Design of a high fragment efficiency library by molecular graph theory. ACS Med Chem Lett 2010; 1:499-503. [PMID: 24900238 DOI: 10.1021/ml100163s] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 09/01/2010] [Indexed: 11/28/2022] Open
Abstract
Molecular graph theory was used to design a unique and diverse, high-efficiency fragment screening collection. A data set retrieved from the annotated database AurSCOPE GPS was used as the reference set, and the GDB-13 database, a virtual library of enumerated organic molecules, was used as a source for the fragment selection. The data graph collection of Discngine as implemented in PipelinePilot was applied to perform the graph pharmacophore similarity matching between the reference and the GDB-13 data sets, leading to the ultimate fragment screening library. The relevance of this unique fragment collection was demonstrated by means of a virtual screening exercise using human trypsin as a test case. Several novel entities with high similarity to known trypsin inhibitors were identified in the in silico exercise. The application of this unique, high fragment efficiency collection to other protein targets in the framework of fragment-based drug discovery is warranted.
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Affiliation(s)
| | - Sara Núñez
- Abbott Healthcare Products, 1381 CP Weesp, The Netherlands
| | - Chris G. Kruse
- Abbott Healthcare Products, 1381 CP Weesp, The Netherlands
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Abstract
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Molecular biology now dominates pharmacology so thoroughly that it is difficult to recall that only a generation ago the field was very different. To understand drug action today, we characterize the targets through which they act and new drug leads are discovered on the basis of target structure and function. Until the mid-1980s the information often flowed in reverse: investigators began with organic molecules and sought targets, relating receptors not by sequence or structure but by their ligands. Recently, investigators have returned to this chemical view of biology, bringing to it systematic and quantitative methods of relating targets by their ligands. This has allowed the discovery of new targets for established drugs, suggested the bases for their side effects, and predicted the molecular targets underlying phenotypic screens. The bases for these new methods, some of their successes and liabilities, and new opportunities for their use are described.
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Affiliation(s)
- Michael J Keiser
- Department of Pharmaceutical Chemistry, University of California-San Francisco, 1700 4th Street, San Francisco, CA 94158-2558, USA
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35
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Lead generation and optimization based on protein-ligand complementarity. Molecules 2010; 15:4382-400. [PMID: 20657448 PMCID: PMC6264460 DOI: 10.3390/molecules15064382] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 06/07/2010] [Indexed: 01/16/2023] Open
Abstract
This work proposes a computational procedure for structure-based lead generation and optimization, which relies on the complementarity of the protein-ligand interactions. This procedure takes as input the known structure of a protein-ligand complex. Retaining the positions of the ligand heavy atoms in the protein binding site it designs structurally similar compounds considering all possible combinations of atomic species (N, C, O, CH3, NH, etc). Compounds are ranked based on a score which incorporates energetic contributions evaluated using molecular mechanics force fields. This procedure was used to design new inhibitor molecules for three serine/threonine protein kinases (p38 MAP kinase, p42 MAP kinase (ERK2), and c-Jun N-terminal kinase 3 (JNK3)). For each enzyme, the calculations produce a set of potential inhibitors whose scores are in agreement with IC50 data and Ki values. Furthermore, the native ligands for each protein target, scored within the five top-ranking compounds predicted by our method, one of the top-ranking compounds predicted to inhibit JNK3 was synthesized and his inhibitory activity confirmed against ATP hydrolysis. Our computational procedure is therefore deemed to be a useful tool for generating chemically diverse molecules active against known target proteins.
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36
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Langdon SR, Ertl P, Brown N. Bioisosteric Replacement and Scaffold Hopping in Lead Generation and Optimization. Mol Inform 2010; 29:366-85. [PMID: 27463193 DOI: 10.1002/minf.201000019] [Citation(s) in RCA: 145] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 04/01/2010] [Indexed: 11/09/2022]
Abstract
Bioisosteric replacement and scaffold hopping are twin methods used in drug design to improve the synthetic accessibility, potency and drug like properties of a compound and to move into novel chemical space. Bioisosteric replacement involves swapping functional groups of a molecule with other functional groups that have similar biological properties. Scaffold hopping is the replacement of the core framework of a molecule with another scaffold that will improve the properties of the molecule or to find similar potent compounds that exist in novel chemical space. This review outlines the key concepts, importance and challenges of both methods using examples and comparisons of techniques available for finding bioisosteric replacements and scaffold hops. There are many methods available for bioisosteric replacement and scaffold hopping, all with their own advantages and disadvantages. Drug design projects would benefit from a combination of these methods to retrieve diverse and complimentary results. Continuing progress in these fields will allow further validation of both methods as well as the accumulation of knowledge on bioisosteres and possible scaffold replacements.
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Affiliation(s)
- Sarah R Langdon
- In Silico Medicinal Chemistry, Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, SM2 5NG, UK phone/fax: +44 (0) 20 8722 4033/+44 (0) 20 8722 4205
| | - Peter Ertl
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Nathan Brown
- In Silico Medicinal Chemistry, Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, SM2 5NG, UK phone/fax: +44 (0) 20 8722 4033/+44 (0) 20 8722 4205.
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37
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Mueller R, Rodriguez AL, Dawson ES, Butkiewicz M, Nguyen TT, Oleszkiewicz S, Bleckmann A, Weaver CD, Lindsley CW, Conn PJ, Meiler J. Identification of Metabotropic Glutamate Receptor Subtype 5 Potentiators Using Virtual High-Throughput Screening. ACS Chem Neurosci 2010; 1:288-305. [PMID: 20414370 PMCID: PMC2857954 DOI: 10.1021/cn9000389] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 01/04/2010] [Indexed: 11/30/2022] Open
Abstract
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Selective potentiators of glutamate response at metabotropic glutamate receptor subtype 5 (mGluR5) have exciting potential for the development of novel treatment strategies for schizophrenia. A total of 1,382 compounds with positive allosteric modulation (PAM) of the mGluR5 glutamate response were identified through high-throughput screening (HTS) of a diverse library of 144,475 substances utilizing a functional assay measuring receptor-induced intracellular release of calcium. Primary hits were tested for concentration-dependent activity, and potency data (EC50 values) were used for training artificial neural network (ANN) quantitative structure−activity relationship (QSAR) models that predict biological potency from the chemical structure. While all models were trained to predict EC50, the quality of the models was assessed by using both continuous measures and binary classification. Numerical descriptors of chemical structure were used as input for the machine learning procedure and optimized in an iterative protocol. The ANN models achieved theoretical enrichment ratios of up to 38 for an independent data set not used in training the model. A database of ∼450,000 commercially available drug-like compounds was targeted in a virtual screen. A set of 824 compounds was obtained for testing based on the highest predicted potency values. Biological testing found 28.2% (232/824) of these compounds with various activities at mGluR5 including 177 pure potentiators and 55 partial agonists. These results represent an enrichment factor of 23 for pure potentiation of the mGluR5 glutamate response and 30 for overall mGluR5 modulation activity when compared with those of the original mGluR5 experimental screening data (0.94% hit rate). The active compounds identified contained 72% close derivatives of previously identified PAMs as well as 28% nontrivial derivatives of known active compounds.
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Affiliation(s)
| | | | - Eric S. Dawson
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232-6600
| | | | | | | | | | | | - Craig W. Lindsley
- Department of Chemistry
- Department of Pharmacology
- Institute for Chemical Biology
| | | | - Jens Meiler
- Department of Chemistry
- Department of Pharmacology
- Institute for Chemical Biology
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232-6600
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Van Drie JH. History of 3D pharmacophore searching: commercial, academic and open-source tools. DRUG DISCOVERY TODAY. TECHNOLOGIES 2010; 7:e203-e270. [PMID: 24103801 DOI: 10.1016/j.ddtec.2010.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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39
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van Hoorn WP, Bell AS. Searching Chemical Space with the Bayesian Idea Generator. J Chem Inf Model 2009; 49:2211-20. [DOI: 10.1021/ci900072g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Willem P. van Hoorn
- Department of Chemistry, Pfizer Global Research and Development, Sandwich Laboratories, Sandwich, Kent CT13 9NJ, United Kingdom
| | - Andrew S. Bell
- Department of Chemistry, Pfizer Global Research and Development, Sandwich Laboratories, Sandwich, Kent CT13 9NJ, United Kingdom
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40
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Vasudevan SR, Churchill GC. Mining free compound databases to identify candidates selected by virtual screening. Expert Opin Drug Discov 2009; 4:901-6. [DOI: 10.1517/17460440903190953] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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41
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Yongye AB, Appel JR, Giulianotti MA, Dooley CT, Medina-Franco JL, Nefzi A, Houghten RA, Martínez-Mayorga K. Identification, structure-activity relationships and molecular modeling of potent triamine and piperazine opioid ligands. Bioorg Med Chem 2009; 17:5583-97. [PMID: 19576786 DOI: 10.1016/j.bmc.2009.06.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Revised: 06/11/2009] [Accepted: 06/13/2009] [Indexed: 11/27/2022]
Abstract
Opioid receptors are important targets for pain management. Here, we report the synthesis and biological evaluation of three positional scanning combinatorial libraries, consisting of linear triamines and piperazines. A highly potent (14 nM) and selective (IC(50(mu))/IC(50(kappa))=71; IC(50(delta))/IC(50(kappa))=714) triamine for the kappa-opioid receptor was found. In addition, non-selective mu-kappa binders were obtained, with binding affinities of 54 nM and 22 nM for mu- and kappa-opioid receptors, respectively. Structure-activity relationships of each subset are described. 3D molecular alignments based on shape similarity to internal and external query molecules were carried out. For the combinatorial chemistry dataset studied here a 1.3 similarity cut-off value was observed to be efficient in the rocs-based alignment method. Interactions from the overlays analyzed in the binding sites of homology models of the receptors revealed specific substitution patterns for enhancing binding affinity in the piperazine series. Pharmacophore modeling of the compounds found from the three combinatorial libraries was also performed. The pharmacophore model indicated that the important feature for receptor binding activity with the mu-receptor was the presence of at least one hydrogen bond acceptor and one aromatic hydrophobic group. Whereas for the kappa-receptor two binding modes emerged with one set of compounds employing the hydrogen bond acceptor and aromatic hydrophobic group, and a second set possibly via interactions with the receptor by hydrophobic and ionic salt-bridges.
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Affiliation(s)
- Austin B Yongye
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Room 132, Port St. Lucie, FL 34987, USA
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42
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Computational fragment-based drug design to explore the hydrophobic sub-pocket of the mitotic kinesin Eg5 allosteric binding site. J Comput Aided Mol Des 2009; 23:571-82. [DOI: 10.1007/s10822-009-9286-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Accepted: 05/19/2009] [Indexed: 10/20/2022]
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Nigsch F, Macaluso NJM, Mitchell JBO, Zmuidinavicius D. Computational toxicology: an overview of the sources of data and of modelling methods. Expert Opin Drug Metab Toxicol 2009; 5:1-14. [PMID: 19236225 DOI: 10.1517/17425250802660467] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Toxicology has the goal of ensuring the safety of humans, animals and the environment. Computational toxicology is an area of active development and great potential. There are tangible reasons for the emerging interest in this discipline from academia, industry, regulatory bodies and governments. RESULTS Pharmaceuticals, personal health care products, nutritional ingredients and products of the chemical industries are all potential hazards and need to be assessed. Toxicological tests for these products are costly, frequently use laboratory animals and are time-consuming. This delays end-user access to improved products or, conversely, the timely withdrawal of dangerous substances from the market. The aim of computational toxicology is to accelerate the assessment of potentially dangerous substances through in silico models. CONCLUSIONS In this review, we provide an overview of the development of models for computational toxicology. Addressing the significant divide between the experimental and computational worlds-believed to be a prime hindrance to computational toxicology-we briefly consider the fundamental issue of toxicological data and the assays they stem from. Different kinds of models that can be built using such data are presented: computational filters, models for specific toxicological endpoints and tools for the generation of testable hypotheses.
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Affiliation(s)
- Florian Nigsch
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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44
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Bergmann R, Liljefors T, Sørensen MD, Zamora I. SHOP: receptor-based scaffold HOPping by GRID-based similarity searches. J Chem Inf Model 2009; 49:658-69. [PMID: 19265417 DOI: 10.1021/ci800391v] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new field-derived 3D method for receptor-based scaffold hopping, implemented in the software SHOP, is presented. Information from a protein-ligand complex is utilized to substitute a fragment of the ligand with another fragment from a database of synthetically accessible scaffolds. A GRID-based interaction profile of the receptor and geometrical descriptions of a ligand scaffold are used to obtain new scaffolds with different structural features and are able to replace the original scaffold in the protein-ligand complex. An enrichment study was successfully performed verifying the ability of SHOP to find known active CDK2 scaffolds in a database. Additionally, SHOP was used for suggesting new inhibitors of p38 MAP kinase. Four p38 complexes were used to perform six scaffold searches. Several new scaffolds were suggested, and the resulting compounds were successfully docked into the query proteins.
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Affiliation(s)
- Rikke Bergmann
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen O, Denmark.
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45
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Medina-Franco JL, Martínez-Mayorga K, Bender A, Marín RM, Giulianotti MA, Pinilla C, Houghten RA. Characterization of activity landscapes using 2D and 3D similarity methods: consensus activity cliffs. J Chem Inf Model 2009; 49:477-91. [PMID: 19434846 DOI: 10.1021/ci800379q] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Activity landscape characterization has been demonstrated to be a valuable tool in lead optimization, virtual screening, and computational modeling of active compounds. In this work, we present a general protocol to explore systematically the activity landscape of a lead series using 11 2D and 3D structural representations. As a test case we employed a set of 48 bicyclic guanidines (BCGs) with kappa-opioid receptor binding affinity, identified in our group. MACCS keys, graph-based three point pharmacophores, circular fingerprints, ROCS shape descriptors, and the TARIS approach, that compares structures based on molecular electrostatic potentials, were employed as orthogonal descriptors. Based on 'activity cliffs' common to a series of descriptors, we introduce the concept of consensus activity cliffs. Results for the current test case suggest that the presence or absence of a methoxybenzyl group may lead to different modes of binding for the active BCGs with the kappa-opioid receptor. The most active compound (IC50 = 37 nM) is involved in a number of consensus cliffs making it a more challenge query for future virtual screening than would be expected from affinity alone. Results also reveal the importance of screening high density combinatorial libraries, especially in the "cliff-rich" regions of activity landscapes. The protocol presented here can be applied to other data sets to develop a consensus model of the activity landscape.
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Affiliation(s)
- Jose L Medina-Franco
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987, USA.
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46
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Oyarzabal J, Howe T, Alcazar J, Andrés JI, Alvarez RM, Dautzenberg F, Iturrino L, Martínez S, Van der Linden I. Novel Approach for Chemotype Hopping Based on Annotated Databases of Chemically Feasible Fragments and a Prospective Case Study: New Melanin Concentrating Hormone Antagonists. J Med Chem 2009; 52:2076-89. [DOI: 10.1021/jm8016199] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Julen Oyarzabal
- Departments of Molecular Informatics and Medicinal Chemistry, Johnson & Johnson Pharmaceutical R&D, Jarama 75, 45007 Toledo, Spain, and Department of Molecular Informatics and CNS Biology Department, Johnson & Johnson Pharmaceutical R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Trevor Howe
- Departments of Molecular Informatics and Medicinal Chemistry, Johnson & Johnson Pharmaceutical R&D, Jarama 75, 45007 Toledo, Spain, and Department of Molecular Informatics and CNS Biology Department, Johnson & Johnson Pharmaceutical R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Jesús Alcazar
- Departments of Molecular Informatics and Medicinal Chemistry, Johnson & Johnson Pharmaceutical R&D, Jarama 75, 45007 Toledo, Spain, and Department of Molecular Informatics and CNS Biology Department, Johnson & Johnson Pharmaceutical R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Jose Ignacio Andrés
- Departments of Molecular Informatics and Medicinal Chemistry, Johnson & Johnson Pharmaceutical R&D, Jarama 75, 45007 Toledo, Spain, and Department of Molecular Informatics and CNS Biology Department, Johnson & Johnson Pharmaceutical R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Rosa M. Alvarez
- Departments of Molecular Informatics and Medicinal Chemistry, Johnson & Johnson Pharmaceutical R&D, Jarama 75, 45007 Toledo, Spain, and Department of Molecular Informatics and CNS Biology Department, Johnson & Johnson Pharmaceutical R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Frank Dautzenberg
- Departments of Molecular Informatics and Medicinal Chemistry, Johnson & Johnson Pharmaceutical R&D, Jarama 75, 45007 Toledo, Spain, and Department of Molecular Informatics and CNS Biology Department, Johnson & Johnson Pharmaceutical R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Laura Iturrino
- Departments of Molecular Informatics and Medicinal Chemistry, Johnson & Johnson Pharmaceutical R&D, Jarama 75, 45007 Toledo, Spain, and Department of Molecular Informatics and CNS Biology Department, Johnson & Johnson Pharmaceutical R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Sonia Martínez
- Departments of Molecular Informatics and Medicinal Chemistry, Johnson & Johnson Pharmaceutical R&D, Jarama 75, 45007 Toledo, Spain, and Department of Molecular Informatics and CNS Biology Department, Johnson & Johnson Pharmaceutical R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Ilse Van der Linden
- Departments of Molecular Informatics and Medicinal Chemistry, Johnson & Johnson Pharmaceutical R&D, Jarama 75, 45007 Toledo, Spain, and Department of Molecular Informatics and CNS Biology Department, Johnson & Johnson Pharmaceutical R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
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47
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Fontaine F, Cross S, Plasencia G, Pastor M, Zamora I. SHOP: A Method For Structure-Based Fragment and Scaffold Hopping. ChemMedChem 2009; 4:427-39. [DOI: 10.1002/cmdc.200800355] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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48
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Identification of a chemical probe for NAADP by virtual screening. Nat Chem Biol 2009; 5:220-6. [PMID: 19234453 PMCID: PMC2659327 DOI: 10.1038/nchembio.150] [Citation(s) in RCA: 246] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Accepted: 01/29/2009] [Indexed: 11/17/2022]
Abstract
Research into the biological role of the Ca2+-releasing second messenger NAADP (nicotinic acid adenine dinucleotide phosphate) has been hampered by a lack of chemical probes. To find new chemical probes for exploring NAADP signaling, we turned to virtual screening, which can evaluate millions of molecules rapidly and inexpensively. We used NAADP as the query ligand to screen the chemical library ZINC for compounds with 3D-shape and electrostatic similarity. We tested the top-ranking hits in a sea urchin egg bioassay and found that one hit, Ned-19, blocks NAADP signaling at nanomolar concentrations. In intact cells, Ned-19 blocked NAADP signaling and fluorescently labeled NAADP receptors. Moreover, we show the utility of Ned-19 as a chemical probe by using it to demonstrate that NAADP is a key causal link between glucose sensing and Ca2+ increases in mouse pancreatic beta cells.
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49
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Jacoby E, Boettcher A, Mayr LM, Brown N, Jenkins JL, Kallen J, Engeloch C, Schopfer U, Furet P, Masuya K, Lisztwan J. Knowledge-based virtual screening: application to the MDM4/p53 protein-protein interaction. Methods Mol Biol 2009; 575:173-94. [PMID: 19727615 DOI: 10.1007/978-1-60761-274-2_7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chemogenomics knowledge-based drug discovery approaches aim to extract the knowledge gained from one target and to apply it for the discovery of ligands and hopefully drugs of a new target which is related to the parent target by homology or conserved molecular recognition. Herein, we demonstrate the potential of knowledge-based virtual screening by applying it to the MDM4-p53 protein-protein interaction where the MDM2-p53 protein-protein interaction constitutes the parent reference system; both systems are potentially relevant to cancer therapy. We show that a combination of virtual screening methods, including homology based similarity searching, QSAR (Quantitative Structure-Activity Relationship) methods, HTD (High Throughput Docking), and UNITY pharmacophore searching provide a successful approach to the discovery of inhibitors. The virtual screening hit list is of the magnitude of 50,000 compounds picked from the corporate compound library of approximately 1.2 million compounds. Emphasis is placed on the facts that such campaigns are only feasible because of the now existing HTCP (High throughput Cherry-Picking) automation systems in combination with robust MTS (Medium Throughput Screening) fluorescence-based assays. Given that the MDM2-p53 system constitutes the reference system, it is not surprising that significantly more and stronger hits are found for this interaction compared to the MDM4-p53 system. Novel, selective and dual hits are discovered for both systems. A hit rate analysis will be provided compared to the full HTS (High-throughput Screening).
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Affiliation(s)
- Edgar Jacoby
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
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50
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Cao W, Zhang H, Chen J, Deng H, Shao M, Lei L, Qian J, Zhu Y. A facile preparation of trans-1,2-cyclopropanes containing p-trifluoromethylphenyl group and its application to the construction of pyrazole and cyclopropane ring fused pyridazinone derivatives. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.05.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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