1
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Multi-Phase In Silico Discovery of Potential SARS-CoV-2 RNA-Dependent RNA Polymerase Inhibitors among 3009 Clinical and FDA-Approved Related Drugs. Processes (Basel) 2022. [DOI: 10.3390/pr10030530] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Proceeding our prior studies of SARS-CoV-2, the inhibitory potential against SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) has been investigated for a collection of 3009 clinical and FDA-approved drugs. A multi-phase in silico approach has been employed in this study. Initially, a molecular fingerprint experiment of Remdesivir (RTP), the co-crystallized ligand of the examined protein, revealed the most similar 150 compounds. Among them, 30 compounds were selected after a structure similarity experiment. Subsequently, the most similar 30 compounds were docked against SARS-CoV-2 RNA-dependent RNA polymerase (PDB ID: 7BV2). Aloin 359, Baicalin 456, Cefadroxil 1273, Sophoricoside 1459, Hyperoside 2109, and Vitexin 2286 exhibited the most precise binding modes, as well as the best binding energies. To confirm the obtained results, MD simulations experiments have been conducted for Hyperoside 2109, the natural flavonoid glycoside that exhibited the best docking scores, against RdRp (PDB ID: 7BV2) for 100 ns. The achieved results authenticated the correct binding of 2109, showing low energy and optimum dynamics. Our team presents these outcomes for scientists all over the world to advance in vitro and in vivo examinations against COVID-19 for the promising compounds.
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2
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Takács G, Sándor M, Szalai Z, Kiss R, Balogh GT. Analysis of the uncharted, druglike property space by self-organizing maps. Mol Divers 2021; 26:2427-2441. [PMID: 34709525 PMCID: PMC9532340 DOI: 10.1007/s11030-021-10343-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/15/2021] [Indexed: 12/29/2022]
Abstract
Physicochemical properties are fundamental to predict the pharmacokinetic and pharmacodynamic behavior of drug candidates. Easily calculated descriptors such as molecular weight and logP have been found to correlate with the success rate of clinical trials. These properties have been previously shown to highlight a sweet-spot in the chemical space associated with favorable pharmacokinetics, which is superior against other regions during hit identification and optimization. In this study, we applied self-organizing maps (SOMs) trained on sixteen calculated properties of a subset of known drugs for the analysis of commercially available compound databases, as well as public biological and chemical databases frequently used for drug discovery. Interestingly, several regions of the property space have been identified that are highly overrepresented by commercially available chemical libraries, while we found almost completely unoccupied regions of the maps (commercially neglected chemical space resembling the properties of known drugs). Moreover, these underrepresented portions of the chemical space are compatible with most rigorous property filters applied by the pharma industry in medicinal chemistry optimization programs. Our results suggest that SOMs may be directly utilized in the strategy of library design for drug discovery to sample previously unexplored parts of the chemical space to aim at yet-undruggable targets.
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Affiliation(s)
- Gergely Takács
- Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, Műegyetem rakpart 3, Budapest, 1111, Hungary
- Mcule.com Kft, Bartók Béla út 105-113, Budapest, 1115, Hungary
| | - Márk Sándor
- Mcule.com Kft, Bartók Béla út 105-113, Budapest, 1115, Hungary
| | - Zoltán Szalai
- Mcule.com Kft, Bartók Béla út 105-113, Budapest, 1115, Hungary
| | - Róbert Kiss
- Mcule.com Kft, Bartók Béla út 105-113, Budapest, 1115, Hungary.
| | - György T Balogh
- Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, Műegyetem rakpart 3, Budapest, 1111, Hungary.
- Department of Pharmacodynamics and Biopharmacy, University of Szeged, Szeged, 6720, Hungary.
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3
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Yang S, Ye Q, Ding J, Yin, Lu A, Chen X, Hou T, Cao D. Current advances in ligand‐based target prediction. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1504] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Su‐Qing Yang
- Xiangya School of Pharmaceutical Sciences Central South University Changsha Hunan China
| | - Qing Ye
- College of Pharmaceutical Sciences Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University Hangzhou, Zhejiang China
| | - Jun‐Jie Ding
- Beijing Institute of Pharmaceutical Chemistry Beijing China
| | - Yin
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital Central South University Changsha Hunan China
| | - Ai‐Ping Lu
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine Hong Kong Baptist University Hong Kong China
| | - Xiang Chen
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital Central South University Changsha Hunan China
| | - Ting‐Jun Hou
- College of Pharmaceutical Sciences Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University Hangzhou, Zhejiang China
| | - Dong‐Sheng Cao
- Xiangya School of Pharmaceutical Sciences Central South University Changsha Hunan China
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine Hong Kong Baptist University Hong Kong China
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4
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Abstract
Drugs modulate disease states through their actions on targets in the body. Determining these targets aids the focused development of new treatments, and helps to better characterize those already employed. One means of accomplishing this is through the deployment of in silico methodologies, harnessing computational analytical and predictive power to produce educated hypotheses for experimental verification. Here, we provide an overview of the current state of the art, describe some of the well-established methods in detail, and reflect on how they, and emerging technologies promoting the incorporation of complex and heterogeneous data-sets, can be employed to improve our understanding of (poly)pharmacology.
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Affiliation(s)
- Ryan Byrne
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland.
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5
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Schneider G, Schneider P. Macromolecular target prediction by self-organizing feature maps. Expert Opin Drug Discov 2016; 12:271-277. [DOI: 10.1080/17460441.2017.1274727] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Petra Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
- inSili.com LLC, Zurich, Switzerland
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6
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Kapoor S, Waldmann H, Ziegler S. Novel approaches to map small molecule–target interactions. Bioorg Med Chem 2016; 24:3232-45. [DOI: 10.1016/j.bmc.2016.05.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 10/24/2022]
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7
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Schneider P, Müller AT, Gabernet G, Button AL, Posselt G, Wessler S, Hiss JA, Schneider G. Hybrid Network Model for "Deep Learning" of Chemical Data: Application to Antimicrobial Peptides. Mol Inform 2016; 36. [PMID: 28124834 DOI: 10.1002/minf.201600011] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 02/24/2016] [Indexed: 01/26/2023]
Abstract
We present a "deep" network architecture for chemical data analysis and classification together with a prospective proof-of-concept application. The model features a self-organizing map (SOM) as the input layer of a feedforward neural network. The SOM converts molecular descriptors to a two-dimensional image for further processing. We implemented lateral neuron inhibition for contrast enhancement. The model achieved improved classification accuracy and predictive robustness compared to feedforward network classifiers lacking the SOM layer. By nonlinear dimensionality reduction the networks extracted meaningful chemical features from the data and outperformed linear principal component analysis (PCA). The learning machine was trained on the sequence-length independent recognition of antibacterial peptides and correctly predicted the killing activity of a synthetic test peptide against Staphylococcus aureus in an in vitro experiment.
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Affiliation(s)
- Petra Schneider
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland.,inSili.com LLC, Segantinisteig 3, CH-8049, Zurich, Switzerland
| | - Alex T Müller
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Gisela Gabernet
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Alexander L Button
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Gernot Posselt
- Paris-Lodron Universität Salzburg, Division of Microbiology, Billroth Str. 11, A-5020 Salzburg, Austria
| | - Silja Wessler
- Paris-Lodron Universität Salzburg, Division of Microbiology, Billroth Str. 11, A-5020 Salzburg, Austria
| | - Jan A Hiss
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Gisbert Schneider
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
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8
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Glaab E. Building a virtual ligand screening pipeline using free software: a survey. Brief Bioinform 2016; 17:352-66. [PMID: 26094053 PMCID: PMC4793892 DOI: 10.1093/bib/bbv037] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/20/2015] [Indexed: 12/17/2022] Open
Abstract
Virtual screening, the search for bioactive compounds via computational methods, provides a wide range of opportunities to speed up drug development and reduce the associated risks and costs. While virtual screening is already a standard practice in pharmaceutical companies, its applications in preclinical academic research still remain under-exploited, in spite of an increasing availability of dedicated free databases and software tools. In this survey, an overview of recent developments in this field is presented, focusing on free software and data repositories for screening as alternatives to their commercial counterparts, and outlining how available resources can be interlinked into a comprehensive virtual screening pipeline using typical academic computing facilities. Finally, to facilitate the set-up of corresponding pipelines, a downloadable software system is provided, using platform virtualization to integrate pre-installed screening tools and scripts for reproducible application across different operating systems.
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9
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Hughes TB, Miller GP, Swamidass SJ. Site of reactivity models predict molecular reactivity of diverse chemicals with glutathione. Chem Res Toxicol 2015; 28:797-809. [PMID: 25742281 DOI: 10.1021/acs.chemrestox.5b00017] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Drug toxicity is often caused by electrophilic reactive metabolites that covalently bind to proteins. Consequently, the quantitative strength of a molecule's reactivity with glutathione (GSH) is a frequently used indicator of its toxicity. Through cysteine, GSH (and proteins) scavenges reactive molecules to form conjugates in the body. GSH conjugates to specific atoms in reactive molecules: their sites of reactivity. The value of knowing a molecule's sites of reactivity is unexplored in the literature. This study tests the value of site of reactivity data that identifies the atoms within 1213 reactive molecules that conjugate to GSH and builds models to predict molecular reactivity with glutathione. An algorithm originally written to model sites of cytochrome P450 metabolism (called XenoSite) finds clear patterns in molecular structure that identify sites of reactivity within reactive molecules with 90.8% accuracy and separate reactive and unreactive molecules with 80.6% accuracy. Furthermore, the model output strongly correlates with quantitative GSH reactivity data in chemically diverse, external data sets. Site of reactivity data is nearly unstudied in the literature prior to our efforts, yet it contains a strong signal for reactivity that can be utilized to more accurately predict molecule reactivity and, eventually, toxicity.
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Affiliation(s)
- Tyler B Hughes
- †Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 S. Euclid Ave., St. Louis, Missouri 63110, United States
| | - Grover P Miller
- ‡Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - S Joshua Swamidass
- †Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 S. Euclid Ave., St. Louis, Missouri 63110, United States
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10
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Lin YC, Hiss JA, Schneider P, Thelesklaf P, Lim YF, Pillong M, Koehler FM, Dittrich PS, Halin C, Wessler S, Schneider G. Piloting the membranolytic activities of peptides with a self-organizing map. Chembiochem 2014; 15:2225-31. [PMID: 25204788 DOI: 10.1002/cbic.201402231] [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: 05/13/2014] [Indexed: 01/01/2023]
Abstract
Antimicrobial peptides (AMPs) show remarkable selectivity toward lipid membranes and possess promising antibiotic potential. Their modes of action are diverse and not fully understood, and innovative peptide design strategies are needed to generate AMPs with improved properties. We present a de novo peptide design approach that resulted in new AMPs possessing low-nanomolar membranolytic activities. Thermal analysis revealed an entropy-driven mechanism of action. The study demonstrates sustained potential of advanced computational methods for designing peptides with the desired activity.
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Affiliation(s)
- Yen-Chu Lin
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
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11
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Reker D, Seet M, Pillong M, Koch CP, Schneider P, Witschel MC, Rottmann M, Freymond C, Brun R, Schweizer B, Illarionov B, Bacher A, Fischer M, Diederich F, Schneider G. Identifizierung von Pyrrolopyrazinen als polypotente Liganden mit Antimalariawirkung. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201311162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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12
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Reker D, Seet M, Pillong M, Koch CP, Schneider P, Witschel MC, Rottmann M, Freymond C, Brun R, Schweizer B, Illarionov B, Bacher A, Fischer M, Diederich F, Schneider G. Deorphaning pyrrolopyrazines as potent multi-target antimalarial agents. Angew Chem Int Ed Engl 2014; 53:7079-84. [PMID: 24895172 DOI: 10.1002/anie.201311162] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 03/06/2014] [Indexed: 11/10/2022]
Abstract
The discovery of pyrrolopyrazines as potent antimalarial agents is presented, with the most effective compounds exhibiting EC50 values in the low nanomolar range against asexual blood stages of Plasmodium falciparum in human red blood cells, and Plasmodium berghei liver schizonts, with negligible HepG2 cytotoxicity. Their potential mode of action is uncovered by predicting macromolecular targets through avant-garde computer modeling. The consensus prediction method suggested a functional resemblance between ligand binding sites in non-homologous target proteins, linking the observed parasite elimination to IspD, an enzyme from the non-mevalonate pathway of isoprenoid biosynthesis, and multi-kinase inhibition. Further computational analysis suggested essential P. falciparum kinases as likely targets of our lead compound. The results obtained validate our methodology for ligand- and structure-based target prediction, expand the bioinformatics toolbox for proteome mining, and provide unique access to deciphering polypharmacological effects of bioactive chemical agents.
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Affiliation(s)
- Daniel Reker
- Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog-Weg 3-4, 8093 Zürich (Switzerland)
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13
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Identifying the macromolecular targets of de novo-designed chemical entities through self-organizing map consensus. Proc Natl Acad Sci U S A 2014; 111:4067-72. [PMID: 24591595 DOI: 10.1073/pnas.1320001111] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
De novo molecular design and in silico prediction of polypharmacological profiles are emerging research topics that will profoundly affect the future of drug discovery and chemical biology. The goal is to identify the macromolecular targets of new chemical agents. Although several computational tools for predicting such targets are publicly available, none of these methods was explicitly designed to predict target engagement by de novo-designed molecules. Here we present the development and practical application of a unique technique, self-organizing map-based prediction of drug equivalence relationships (SPiDER), that merges the concepts of self-organizing maps, consensus scoring, and statistical analysis to successfully identify targets for both known drugs and computer-generated molecular scaffolds. We discovered a potential off-target liability of fenofibrate-related compounds, and in a comprehensive prospective application, we identified a multitarget-modulating profile of de novo designed molecules. These results demonstrate that SPiDER may be used to identify innovative compounds in chemical biology and in the early stages of drug discovery, and help investigate the potential side effects of drugs and their repurposing options.
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14
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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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15
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Lötsch J, Schneider G, Reker D, Parnham MJ, Schneider P, Geisslinger G, Doehring A. Common non-epigenetic drugs as epigenetic modulators. Trends Mol Med 2013; 19:742-53. [PMID: 24054876 DOI: 10.1016/j.molmed.2013.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 12/15/2022]
Abstract
Epigenetic effects are exerted by a variety of factors and evidence increases that common drugs such as opioids, cannabinoids, valproic acid, or cytostatics may induce alterations in DNA methylation patterns or histone conformations. These effects occur via chemical structural interactions with epigenetic enzymes, through interactions with DNA repair mechanisms. Computational predictions indicate that one-twentieth of all drugs might potentially interact with human histone deacetylase, which was prospectively experimentally verified for the compound with the highest predicted interaction probability. These epigenetic effects add to wanted and unwanted drug effects, contributing to mechanisms of drug resistance or disease-related and unrelated phenotypes. Because epigenetic changes might be transmitted to offspring, the need for reliable and cost-effective epigenetic screening tools becomes acute.
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Affiliation(s)
- Jörn Lötsch
- Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany; Fraunhofer Institute of Molecular Biology and Applied Ecology - Project Group Translational Medicine and Pharmacology (IME-TMP), Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany.
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16
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Yang M, Chen JL, Xu LW, Ji G. Navigating traditional chinese medicine network pharmacology and computational tools. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2013; 2013:731969. [PMID: 23983798 PMCID: PMC3747450 DOI: 10.1155/2013/731969] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 07/04/2013] [Indexed: 12/17/2022]
Abstract
The concept of "network target" has ushered in a new era in the field of traditional Chinese medicine (TCM). As a new research approach, network pharmacology is based on the analysis of network models and systems biology. Taking advantage of advancements in systems biology, a high degree of integration data analysis strategy and interpretable visualization provides deeper insights into the underlying mechanisms of TCM theories, including the principles of herb combination, biological foundations of herb or herbal formulae action, and molecular basis of TCM syndromes. In this study, we review several recent developments in TCM network pharmacology research and discuss their potential for bridging the gap between traditional and modern medicine. We briefly summarize the two main functional applications of TCM network models: understanding/uncovering and predicting/discovering. In particular, we focus on how TCM network pharmacology research is conducted and highlight different computational tools, such as network-based and machine learning algorithms, and sources that have been proposed and applied to the different steps involved in the research process. To make network pharmacology research commonplace, some basic network definitions and analysis methods are presented.
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Affiliation(s)
- Ming Yang
- Longhua Hospital Affiliated to Shanghai University of TCM, Shanghai 200032, China
- Institute of Digestive Disease, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Jia-Lei Chen
- Longhua Hospital Affiliated to Shanghai University of TCM, Shanghai 200032, China
| | - Li-Wen Xu
- Longhua Hospital Affiliated to Shanghai University of TCM, Shanghai 200032, China
| | - Guang Ji
- Institute of Digestive Disease, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
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17
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Reutlinger M, Koch CP, Reker D, Todoroff N, Schneider P, Rodrigues T, Schneider G. Chemically Advanced Template Search (CATS) for Scaffold-Hopping and Prospective Target Prediction for 'Orphan' Molecules. Mol Inform 2013; 32:133-138. [PMID: 23956801 PMCID: PMC3743170 DOI: 10.1002/minf.201200141] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 01/18/2013] [Indexed: 02/04/2023]
Affiliation(s)
- Michael Reutlinger
- ETH, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences Wolfgang-Pauli-Str. 10, CH-8093 Zurich, Switzerland fax: +41 44 633 13 79, tel: +41 44 633 74 38
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18
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Schneider P, Stutz K, Kasper L, Haller S, Reutlinger M, Reisen F, Geppert T, Schneider G. Target Profile Prediction and Practical Evaluation of a Biginelli-Type Dihydropyrimidine Compound Library. Pharmaceuticals (Basel) 2011. [PMCID: PMC4058656 DOI: 10.3390/ph4091236] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We present a self-organizing map (SOM) approach to predicting macromolecular targets for combinatorial compound libraries. The aim was to study the usefulness of the SOM in combination with a topological pharmacophore representation (CATS) for selecting biologically active compounds from a virtual combinatorial compound collection, taking the multi-component Biginelli dihydropyrimidine reaction as an example. We synthesized a candidate compound from this library, for which the SOM model suggested inhibitory activity against cyclin-dependent kinase 2 (CDK2) and other kinases. The prediction was confirmed in an in vitro panel assay comprising 48 human kinases. We conclude that the computational technique may be used for ligand-based in silico pharmacology studies, off-target prediction, and drug re-purposing, thereby complementing receptor-based approaches.
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Affiliation(s)
| | | | | | | | | | | | | | - Gisbert Schneider
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +41-44-633-7438; Fax: +41-44-633-1379
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19
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Digles D, Ecker GF. Self-Organizing Maps for In Silico Screening and Data Visualization. Mol Inform 2011; 30:838-46. [PMID: 27468103 DOI: 10.1002/minf.201100082] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 08/05/2011] [Indexed: 02/04/2023]
Abstract
Self-organizing maps, which are unsupervised artificial neural networks, have become a very useful tool in a wide area of disciplines, including medicinal chemistry. Here, we will focus on two applications of self-organizing maps: the use of self-organizing maps for in silico screening and for clustering and visualisation of large datasets. Additionally, the importance of parameter selection is discussed and some modifications to the original algorithm are summarised.
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Affiliation(s)
- Daniela Digles
- Department of Medicinal Chemistry, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria phone/fax: +43-1-4277-55110/+43-1-4277-9551
| | - Gerhard F Ecker
- Department of Medicinal Chemistry, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria phone/fax: +43-1-4277-55110/+43-1-4277-9551.
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20
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Bieler M, Heilker R, Köppen H, Schneider G. Assay Related Target Similarity (ARTS) - Chemogenomics Approach for Quantitative Comparison of Biological Targets. J Chem Inf Model 2011; 51:1897-905. [DOI: 10.1021/ci200105t] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael Bieler
- Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach, Germany
| | - Ralf Heilker
- Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach, Germany
| | - Herbert Köppen
- Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach, Germany
| | - Gisbert Schneider
- Swiss Federal Institute of Technology (ETH), Institute of Pharmaceutical Sciences, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
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21
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Koutsoukas A, Simms B, Kirchmair J, Bond PJ, Whitmore AV, Zimmer S, Young MP, Jenkins JL, Glick M, Glen RC, Bender A. From in silico target prediction to multi-target drug design: current databases, methods and applications. J Proteomics 2011; 74:2554-74. [PMID: 21621023 DOI: 10.1016/j.jprot.2011.05.011] [Citation(s) in RCA: 186] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 04/10/2011] [Accepted: 05/06/2011] [Indexed: 01/31/2023]
Abstract
Given the tremendous growth of bioactivity databases, the use of computational tools to predict protein targets of small molecules has been gaining importance in recent years. Applications span a wide range, from the 'designed polypharmacology' of compounds to mode-of-action analysis. In this review, we firstly survey databases that can be used for ligand-based target prediction and which have grown tremendously in size in the past. We furthermore outline methods for target prediction that exist, both based on the knowledge of bioactivities from the ligand side and methods that can be applied in situations when a protein structure is known. Applications of successful in silico target identification attempts are discussed in detail, which were based partly or in whole on computational target predictions in the first instance. This includes the authors' own experience using target prediction tools, in this case considering phenotypic antibacterial screens and the analysis of high-throughput screening data. Finally, we will conclude with the prospective application of databases to not only predict, retrospectively, the protein targets of a small molecule, but also how to design ligands with desired polypharmacology in a prospective manner.
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Affiliation(s)
- Alexios Koutsoukas
- Unilever Centre for Molecular Sciences Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Schneider G, Geppert T, Hartenfeller M, Reisen F, Klenner A, Reutlinger M, Hähnke V, Hiss JA, Zettl H, Keppner S, Spänkuch B, Schneider P. Reaction-driven de novo design, synthesis and testing of potential type II kinase inhibitors. Future Med Chem 2011; 3:415-24. [PMID: 21452978 DOI: 10.4155/fmc.11.8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
BACKGROUND De novo design of drug-like compounds with a desired pharmacological activity profile has become feasible through innovative computer algorithms. Fragment-based design and simulated chemical reactions allow for the rapid generation of candidate compounds as blueprints for organic synthesis. METHODS We used a combination of complementary virtual-screening tools for the analysis of de novo designed compounds that were generated with the aim to inhibit inactive polo-like kinase 1 (Plk1), a target for the development of cancer therapeutics. A homology model of the inactive state of Plk1 was constructed and the nucleotide binding pocket conformations in the DFG-in and DFG-out state were compared. The de novo-designed compounds were analyzed using pharmacophore matching, structure-activity landscape analysis, and automated ligand docking. One compound was synthesized and tested in vitro. RESULTS The majority of the designed compounds possess a generic architecture present in known kinase inhibitors. Predictions favor kinases as targets of these compounds but also suggest potential off-target effects. Several bioisosteric replacements were suggested, and de novo designed compounds were assessed by automated docking for potential binding preference toward the inactive (type II inhibitors) over the active conformation (type I inhibitors) of the kinase ATP binding site. One selected compound was successfully synthesized as suggested by the software. The de novo-designed compound exhibited inhibitory activity against inactive Plk1 in vitro, but did not show significant inhibition of active Plk1 and 38 other kinases tested. CONCLUSIONS Computer-based de novo design of screening candidates in combination with ligand- and receptor-based virtual screening generates motivated suggestions for focused library design in hit and lead discovery. Attractive, synthetically accessible compounds can be obtained together with predicted on- and off-target profiles and desired activities.
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Affiliation(s)
- Gisbert Schneider
- Swiss Federal Institute of Technology, Department of Chemistry & Applied Biosciences, 8093 Zürich, Switzerland.
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Zettl H, Weggen S, Schneider P, Schneider G. Exploring the chemical space of γ-secretase modulators. Trends Pharmacol Sci 2010; 31:402-10. [DOI: 10.1016/j.tips.2010.05.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 05/24/2010] [Accepted: 05/26/2010] [Indexed: 11/29/2022]
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Steri R, Schneider P, Klenner A, Rupp M, Kriegl JM, Schubert-Zsilavecz M, Schneider G. Target Profile Prediction: Cross-Activation of Peroxisome Proliferator-Activated Receptor (PPAR) and Farnesoid X Receptor (FXR). Mol Inform 2010; 29:287-92. [PMID: 27463055 DOI: 10.1002/minf.200900009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2009] [Accepted: 01/15/2010] [Indexed: 11/07/2022]
Affiliation(s)
- Ramona Steri
- Institute of Pharmaceutical Chemistry, LIFF, ZAFES, Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt a.M., Germany
| | - Petra Schneider
- Schneider Consulting GbR, George-C.-Marshall Ring 33, 61440 Oberursel, Germany
| | - Alexander Klenner
- Chair for Chem- and Bioinformatics, Goethe-University, LIFF, Siesmayerstr. 70, 60323 Frankfurt a.M., Germany
| | - Matthias Rupp
- Chair for Chem- and Bioinformatics, Goethe-University, LIFF, Siesmayerstr. 70, 60323 Frankfurt a.M., Germany.,Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Jan M Kriegl
- Boehringer-Ingelheim Pharma, Department of Lead Discovery, 88397 Biberach, Germany
| | - Manfred Schubert-Zsilavecz
- Institute of Pharmaceutical Chemistry, LIFF, ZAFES, Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt a.M., Germany
| | - Gisbert Schneider
- Chair for Chem- and Bioinformatics, Goethe-University, LIFF, Siesmayerstr. 70, 60323 Frankfurt a.M., Germany. .,Institute of Pharmaceutical Sciences, ETH Zürich, Wolfgang-Pauli-Str. 10, 8093 Zürich, Switzerland.
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