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Olmedo DA, Durant-Archibold AA, López-Pérez JL, Medina-Franco JL. Design and Diversity Analysis of Chemical Libraries in Drug Discovery. Comb Chem High Throughput Screen 2024; 27:502-515. [PMID: 37409545 DOI: 10.2174/1386207326666230705150110] [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: 04/05/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 07/07/2023]
Abstract
Chemical libraries and compound data sets are among the main inputs to start the drug discovery process at universities, research institutes, and the pharmaceutical industry. The approach used in the design of compound libraries, the chemical information they possess, and the representation of structures, play a fundamental role in the development of studies: chemoinformatics, food informatics, in silico pharmacokinetics, computational toxicology, bioinformatics, and molecular modeling to generate computational hits that will continue the optimization process of drug candidates. The prospects for growth in drug discovery and development processes in chemical, biotechnological, and pharmaceutical companies began a few years ago by integrating computational tools with artificial intelligence methodologies. It is anticipated that it will increase the number of drugs approved by regulatory agencies shortly.
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Affiliation(s)
- Dionisio A Olmedo
- Centro de Investigaciones Farmacognósticas de la Flora Panameña (CIFLORPAN), Facultad de Farmacia, Universidad de Panamá, Ciudad de Panamá, Apartado, 0824-00178, Panamá
- Sistema Nacional de Investigación (SNI), Secretaria Nacional de Ciencia, Tecnología e Innovación (SENACYT), Ciudad del Saber, Clayton, Panamá
| | - Armando A Durant-Archibold
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Apartado, 0843-01103, Panamá
- Departamento de Bioquímica, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Ciudad de Panamá, Panamá
| | - José Luis López-Pérez
- CESIFAR, Departamento de Farmacología, Facultad de Medicina, Universidad de Panamá, Ciudad de Panamá, Panamá
- Departamento de Ciencias Farmacéuticas, Facultad de Farmacia, Universidad de Salamanca, Avda. Campo Charro s/n, 37071 Salamanca, España
| | - José Luis Medina-Franco
- DIFACQUIM Grupo de Investigación, Departamento de Farmacia, Escuela de Química, Universidad Nacional Autónoma de México, Ciudad de México, Apartado, 04510, México
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2
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Tran-Nguyen VK, Junaid M, Simeon S, Ballester PJ. A practical guide to machine-learning scoring for structure-based virtual screening. Nat Protoc 2023; 18:3460-3511. [PMID: 37845361 DOI: 10.1038/s41596-023-00885-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/03/2023] [Indexed: 10/18/2023]
Abstract
Structure-based virtual screening (SBVS) via docking has been used to discover active molecules for a range of therapeutic targets. Chemical and protein data sets that contain integrated bioactivity information have increased both in number and in size. Artificial intelligence and, more concretely, its machine-learning (ML) branch, including deep learning, have effectively exploited these data sets to build scoring functions (SFs) for SBVS against targets with an atomic-resolution 3D model (e.g., generated by X-ray crystallography or predicted by AlphaFold2). Often outperforming their generic and non-ML counterparts, target-specific ML-based SFs represent the state of the art for SBVS. Here, we present a comprehensive and user-friendly protocol to build and rigorously evaluate these new SFs for SBVS. This protocol is organized into four sections: (i) using a public benchmark of a given target to evaluate an existing generic SF; (ii) preparing experimental data for a target from public repositories; (iii) partitioning data into a training set and a test set for subsequent target-specific ML modeling; and (iv) generating and evaluating target-specific ML SFs by using the prepared training-test partitions. All necessary code and input/output data related to three example targets (acetylcholinesterase, HMG-CoA reductase, and peroxisome proliferator-activated receptor-α) are available at https://github.com/vktrannguyen/MLSF-protocol , can be run by using a single computer within 1 week and make use of easily accessible software/programs (e.g., Smina, CNN-Score, RF-Score-VS and DeepCoy) and web resources. Our aim is to provide practical guidance on how to augment training data to enhance SBVS performance, how to identify the most suitable supervised learning algorithm for a data set, and how to build an SF with the highest likelihood of discovering target-active molecules within a given compound library.
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Affiliation(s)
| | - Muhammad Junaid
- Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Saw Simeon
- Centre de Recherche en Cancérologie de Marseille, Marseille, France
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3
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Srinivasan B. Non-equilibrium modalities of inhibition: Characterizing irreversible inhibition for the ErbB receptor family members. Methods Enzymol 2023; 690:85-108. [PMID: 37858541 DOI: 10.1016/bs.mie.2023.08.004] [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] [Indexed: 10/21/2023]
Abstract
Most drug target interactions for clinically approved small-molecules are non-equilibrium slow-onset, tight-binding or irreversible in nature, with pronounced element of time-dependence of inhibition. Analysis of such modality of inhibition requires a continuous enzyme kinetic measurement that can yield complete progress curves and an automated high-throughput analysis pipeline. Given the increasing emphasis on designing non-equilibrium modes of inhibiting an enzyme target (especially irreversible), the above specified pipeline for data generation and analysis is essential for extracting parameters to guide decisions in early drug discovery. In this manuscript, the methodology and data analysis protocol from our irreversible inhibitor characterization campaigns for the ErbB receptor family members is presented. Guidance is provided on the appropriate design of assay to generate quality data, setting up the analysis and estimation of inactivation rate (kinact) and the pseudo-equilibrium binding affinity (KI) constant (or their ratio kinact/KI) in a high-throughput manner for the inhibitor interacting with the protein target of interest.
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Affiliation(s)
- Bharath Srinivasan
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom.
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4
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Sheridan R, Spelman K. Polyphenolic promiscuity, inflammation-coupled selectivity: Whether PAINs filters mask an antiviral asset. Front Pharmacol 2022; 13:909945. [PMID: 36339544 PMCID: PMC9634583 DOI: 10.3389/fphar.2022.909945] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/03/2022] [Indexed: 11/26/2023] Open
Abstract
The Covid-19 pandemic has elicited much laboratory and clinical research attention on vaccines, mAbs, and certain small-molecule antivirals against SARS-CoV-2 infection. By contrast, there has been comparatively little attention on plant-derived compounds, especially those that are understood to be safely ingested at common doses and are frequently consumed in the diet in herbs, spices, fruits and vegetables. Examining plant secondary metabolites, we review recent elucidations into the pharmacological activity of flavonoids and other polyphenolic compounds and also survey their putative frequent-hitter behavior. Polyphenols, like many drugs, are glucuronidated post-ingestion. In an inflammatory milieu such as infection, a reversion back to the active aglycone by the release of β-glucuronidase from neutrophils and macrophages allows cellular entry of the aglycone. In the context of viral infection, virions and intracellular virus particles may be exposed to promiscuous binding by the polyphenol aglycones resulting in viral inhibition. As the mechanism's scope would apply to the diverse range of virus species that elicit inflammation in infected hosts, we highlight pre-clinical studies of polyphenol aglycones, such as luteolin, isoginkgetin, quercetin, quercetagetin, baicalein, curcumin, fisetin and hesperetin that reduce virion replication spanning multiple distinct virus genera. It is hoped that greater awareness of the potential spatial selectivity of polyphenolic activation to sites of pathogenic infection will spur renewed research and clinical attention for natural products antiviral assaying and trialing over a wide array of infectious viral diseases.
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Affiliation(s)
| | - Kevin Spelman
- Massachusetts College of Pharmacy and Health Sciences, Boston, MA, United States
- Health Education and Research, Driggs, ID, United States
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5
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Lardos A, Aghaebrahimian A, Koroleva A, Sidorova J, Wolfram E, Anisimova M, Gil M. Computational Literature-based Discovery for Natural Products Research: Current State and Future Prospects. FRONTIERS IN BIOINFORMATICS 2022; 2:827207. [PMID: 36304281 PMCID: PMC9580913 DOI: 10.3389/fbinf.2022.827207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/28/2022] [Indexed: 11/21/2022] Open
Abstract
Literature-based discovery (LBD) mines existing literature in order to generate new hypotheses by finding links between previously disconnected pieces of knowledge. Although automated LBD systems are becoming widespread and indispensable in a wide variety of knowledge domains, little has been done to introduce LBD to the field of natural products research. Despite growing knowledge in the natural product domain, most of the accumulated information is found in detached data pools. LBD can facilitate better contextualization and exploitation of this wealth of data, for example by formulating new hypotheses for natural product research, especially in the context of drug discovery and development. Moreover, automated LBD systems promise to accelerate the currently tedious and expensive process of lead identification, optimization, and development. Focusing on natural product research, we briefly reflect the development of automated LBD and summarize its methods and principal data sources. In a thorough review of published use cases of LBD in the biomedical domain, we highlight the immense potential of this data mining approach for natural product research, especially in context with drug discovery or repurposing, mode of action, as well as drug or substance interactions. Most of the 91 natural product-related discoveries in our sample of reported use cases of LBD were addressed at a computer science audience. Therefore, it is the wider goal of this review to introduce automated LBD to researchers who work with natural products and to facilitate the dialogue between this community and the developers of automated LBD systems.
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Affiliation(s)
- Andreas Lardos
- Natural Product Chemistry and Phytopharmacy Research Group, Institute of Chemistry and Biotechnology, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Waedenswil, Switzerland
| | - Ahmad Aghaebrahimian
- Institute of Applied Simulation, School of Life Sciences and Facility Management, Zürich University of Applied Sciences (ZHAW), Waedenswil, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Anna Koroleva
- Institute of Applied Simulation, School of Life Sciences and Facility Management, Zürich University of Applied Sciences (ZHAW), Waedenswil, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Julia Sidorova
- Instituto de Tecnología del Conocimiento, Universidad Complutense de Madrid, Madrid, Spain
| | - Evelyn Wolfram
- Natural Product Chemistry and Phytopharmacy Research Group, Institute of Chemistry and Biotechnology, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Waedenswil, Switzerland
| | - Maria Anisimova
- Institute of Applied Simulation, School of Life Sciences and Facility Management, Zürich University of Applied Sciences (ZHAW), Waedenswil, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Manuel Gil
- Institute of Applied Simulation, School of Life Sciences and Facility Management, Zürich University of Applied Sciences (ZHAW), Waedenswil, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
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6
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Sun J, Zhong H, Wang K, Li N, Chen L. Gains from no real PAINS: Where 'Fair Trial Strategy' stands in the development of multi-target ligands. Acta Pharm Sin B 2021; 11:3417-3432. [PMID: 34900527 PMCID: PMC8642439 DOI: 10.1016/j.apsb.2021.02.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/15/2021] [Accepted: 02/25/2021] [Indexed: 12/26/2022] Open
Abstract
Compounds that selectively modulate multiple targets can provide clinical benefits and are an alternative to traditional highly selective agents for unique targets. High-throughput screening (HTS) for multitarget-directed ligands (MTDLs) using approved drugs, and fragment-based drug design has become a regular strategy to achieve an ideal multitarget combination. However, the unexpected presence of pan-assay interference compounds (PAINS) suspects in the development of MTDLs frequently results in nonspecific interactions or other undesirable effects leading to artefacts or false-positive data of biological assays. Publicly available filters can help to identify PAINS suspects; however, these filters cannot comprehensively conclude whether these suspects are "bad" or innocent. Additionally, these in silico approaches may inappropriately label a ligand as PAINS. More than 80% of the initial hits can be identified as PAINS by the filters if appropriate biochemical tests are not used resulting in false positive data that are unacceptable for medicinal chemists in manuscript peer review and future studies. Therefore, extensive offline experiments should be used after online filtering to discriminate "bad" PAINS and avoid incorrect evaluation of good scaffolds. We suggest that the use of "Fair Trial Strategy" to identify interesting molecules in PAINS suspects to provide certain structure‒function insight in MTDL development.
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Key Words
- AD, Alzheimer disease
- ALARM NMR, a La assay to detect reactive molecules by nuclear magnetic resonance
- Biochemical experiment
- CADD, computer-aided drug design technology
- CoA, coenzyme A
- EGFR, epidermal growth factor receptor
- Fair trial strategy
- GSH, glutathione
- HER2, human epidermal growth factor receptor 2
- HTS, high-throughput screening
- In silico filtering
- LC−MS, liquid chromatography−mass spectrometry
- MTDLs, multitarget-directed ligands
- Multitarget-directed ligands
- PAINS suspects
- PAINS, pan-assay interference compounds
- QSAR, quantitative structure–activity relationship
- ROS, radicals and oxygen reactive species
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Affiliation(s)
- Jianbo Sun
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Hui Zhong
- Department of Pharmacology of Traditional Chinese Medicine, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Kun Wang
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Na Li
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Li Chen
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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Mukhtar A, Shah S, Kanwal, Khan KM, Khan SU, Zaib S, Iqbal J, Parveen S, Taha M, Hussain S, Hameed S, Khan NA, Siddiqui R, Anwar A. Synthesis of Chalcones as Potential
α
‐Glucosidase Inhibitors,
In‐Vitro
and
In‐Silico
Studies. ChemistrySelect 2021. [DOI: 10.1002/slct.202102434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Asma Mukhtar
- H. E. J. Research Institute of Chemistry International Center for Chemical and Biological Sciences University of Karachi Karachi 75270 Pakistan
| | - Shazia Shah
- H. E. J. Research Institute of Chemistry International Center for Chemical and Biological Sciences University of Karachi Karachi 75270 Pakistan
| | - Kanwal
- H. E. J. Research Institute of Chemistry International Center for Chemical and Biological Sciences University of Karachi Karachi 75270 Pakistan
- Institute of Marine Biotechnology Universiti Malaysia Terengganu 21030 Kuala Terengganu Malaysia
| | - Khalid Mohammed Khan
- H. E. J. Research Institute of Chemistry International Center for Chemical and Biological Sciences University of Karachi Karachi 75270 Pakistan
- Department of Clinical Pharmacy Institute for Research and Medical Consultations (IRMC) Imam Abdulrahman Bin Faisal University P.O. Box 1982 Dammam 31441 Saudi Arabia
| | - Shahid Ullah Khan
- Centre for Advanced Drug Research COMSATS University Islamabad Abbottabad Campus Abbottabad 22060 Pakistan
| | - Sumera Zaib
- Centre for Advanced Drug Research COMSATS University Islamabad Abbottabad Campus Abbottabad 22060 Pakistan
| | - Jamshed Iqbal
- Centre for Advanced Drug Research COMSATS University Islamabad Abbottabad Campus Abbottabad 22060 Pakistan
| | - Shahnaz Parveen
- PCSIR Laboratories Complex Karachi, Shahra-e-Dr. Salimuzzaman Siddiqui Karachi 75280 Pakistan
| | - Muhammad Taha
- Department of Clinical Pharmacy Institute for Research and Medical Consultations (IRMC) Imam Abdulrahman Bin Faisal University P.O. Box 1982 Dammam 31441 Saudi Arabia
| | - Shafqat Hussain
- Department of Chemistry University of Baltistan, Skardu, Main Campus Husainabad Kargil Road, Skardu Gilgit-Baltistan Pakistan
| | - Shahryar Hameed
- H. E. J. Research Institute of Chemistry International Center for Chemical and Biological Sciences University of Karachi Karachi 75270 Pakistan
| | - Naveed Ahmed Khan
- Department of Clinical Sciences College of Medicine University of Sharjah Sharjah 27272 United Arab Emirates
| | - Ruqaiyyah Siddiqui
- College of Arts and Sciences American University of Sharjah Sharjah 26666 United Arab Emirates
| | - Ayaz Anwar
- Department of Biological Sciences School of Medical and Life Sciences Sunway University Petaling Jaya 47500 Selangor Malaysia
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8
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Kell DB. The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes. Molecules 2021; 26:5629. [PMID: 34577099 PMCID: PMC8470029 DOI: 10.3390/molecules26185629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological membranes in vivo is vanishingly low. This is because (i) most real biomembranes are mostly protein, not lipid, (ii) unlike purely lipid bilayers that can form transient aqueous channels, the high concentrations of proteins serve to stop such activity, (iii) natural evolution long ago selected against transport methods that just let any undesirable products enter a cell, (iv) transporters have now been identified for all kinds of molecules (even water) that were once thought not to require them, (v) many experiments show a massive variation in the uptake of drugs between different cells, tissues, and organisms, that cannot be explained if lipid bilayer transport is significant or if efflux were the only differentiator, and (vi) many experiments that manipulate the expression level of individual transporters as an independent variable demonstrate their role in drug and nutrient uptake (including in cytotoxicity or adverse drug reactions). This makes such transporters valuable both as a means of targeting drugs (not least anti-infectives) to selected cells or tissues and also as drug targets. The same considerations apply to the exploitation of substrate uptake and product efflux transporters in biotechnology. We are also beginning to recognise that transporters are more promiscuous, and antiporter activity is much more widespread, than had been realised, and that such processes are adaptive (i.e., were selected by natural evolution). The purpose of the present review is to summarise the above, and to rehearse and update readers on recent developments. These developments lead us to retain and indeed to strengthen our contention that for transmembrane pharmaceutical drug transport "phospholipid bilayer transport is negligible".
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Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St, Liverpool L69 7ZB, UK;
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs Lyngby, Denmark
- Mellizyme Biotechnology Ltd., IC1, Liverpool Science Park, Mount Pleasant, Liverpool L3 5TF, UK
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9
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Täger J, Wissinger B, Kohl S, Reuter P. Identification of Chemical and Pharmacological Chaperones for Correction of Trafficking-Deficient Mutant Cyclic Nucleotide-Gated A3 Channels. Mol Pharmacol 2021; 99:460-468. [PMID: 33827965 DOI: 10.1124/molpharm.120.000180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 03/30/2021] [Indexed: 12/19/2022] Open
Abstract
Trafficking deficiency caused by missense mutations is a well known phenomenon that occurs for mutant, misfolded proteins. Typically, the misfolded protein is retained by the protein quality-control system and degraded by the endoplasmic reticulum-associated protein degradation pathway and thus does not reach its destination, although residual function of the protein may be preserved. Chemical and pharmacological chaperones can improve the targeting of trafficking-deficient proteins and thus may be promising candidates for therapeutic applications. Here, we report the application of a cellular bioassay based on the bioluminescent calcium reporter aequorin to quantify surface expression of mutant CNGA3 channels associated with the autosomal recessively inherited retinal disease achromatopsia. A screening of 77 compounds enabled the identification of effective chemical and pharmacological chaperones that result in a 1.5- to 4.8-fold increase of surface expression of mutant CNGA3. Using selected compounds, we confirmed that the rescue of the defective trafficking is not limited to a single mutation in CNGA3. Active compounds and our structure-activity correlated data for the dihydropyridine compound class may provide valuable information for developing a treatment of the trafficking defect in achromatopsia. SIGNIFICANCE STATEMENT: This study describes a novel luminescence-based assay to detect the surface expression of mutant trafficking-deficient CNGA3 channels based on the calcium-sensitive photoprotein aequorin. Using this assay for a compound screening, this study identifies novel chemical and pharmacological chaperones that restore the surface localization of mutant trafficking-deficient CNGA3 channels. The results from this work may serve as starting point for the development of potent compounds that rescue trafficking deficiencies in the autosomal recessively inherited retinal disease achromatopsia.
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Affiliation(s)
- Joachim Täger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research (J.T., B.W., S.K., P.R.), and Graduate School of Cellular and Molecular Neuroscience (J.T.), University of Tübingen, Tübingen, Germany
| | - Bernd Wissinger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research (J.T., B.W., S.K., P.R.), and Graduate School of Cellular and Molecular Neuroscience (J.T.), University of Tübingen, Tübingen, Germany
| | - Susanne Kohl
- Molecular Genetics Laboratory, Institute for Ophthalmic Research (J.T., B.W., S.K., P.R.), and Graduate School of Cellular and Molecular Neuroscience (J.T.), University of Tübingen, Tübingen, Germany
| | - Peggy Reuter
- Molecular Genetics Laboratory, Institute for Ophthalmic Research (J.T., B.W., S.K., P.R.), and Graduate School of Cellular and Molecular Neuroscience (J.T.), University of Tübingen, Tübingen, Germany
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10
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Schuffenhauer A, Schneider N, Hintermann S, Auld D, Blank J, Cotesta S, Engeloch C, Fechner N, Gaul C, Giovannoni J, Jansen J, Joslin J, Krastel P, Lounkine E, Manchester J, Monovich LG, Pelliccioli AP, Schwarze M, Shultz MD, Stiefl N, Baeschlin DK. Evolution of Novartis' Small Molecule Screening Deck Design. J Med Chem 2020; 63:14425-14447. [PMID: 33140646 DOI: 10.1021/acs.jmedchem.0c01332] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This article summarizes the evolution of the screening deck at the Novartis Institutes for BioMedical Research (NIBR). Historically, the screening deck was an assembly of all available compounds. In 2015, we designed a first deck to facilitate access to diverse subsets with optimized properties. We allocated the compounds as plated subsets on a 2D grid with property based ranking in one dimension and increasing structural redundancy in the other. The learnings from the 2015 screening deck were applied to the design of a next generation in 2019. We found that using traditional leadlikeness criteria (mainly MW, clogP) reduces the hit rates of attractive chemical starting points in subset screening. Consequently, the 2019 deck relies on solubility and permeability to select preferred compounds. The 2019 design also uses NIBR's experimental assay data and inferred biological activity profiles in addition to structural diversity to define redundancy across the compound sets.
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Affiliation(s)
- Ansgar Schuffenhauer
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Nadine Schneider
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Samuel Hintermann
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Douglas Auld
- Novartis Institutes for BioMedical Research Inc., 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jutta Blank
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Simona Cotesta
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Caroline Engeloch
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Nikolas Fechner
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Christoph Gaul
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Jerome Giovannoni
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Johanna Jansen
- Novartis Institutes for BioMedical Research-Emeryville, 5300 Chiron Way, Emeryville, California 94608-2916, United States
| | - John Joslin
- Genomics Institute of the Novartis Foundation, San Diego, California 92121, United States
| | - Philipp Krastel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Eugen Lounkine
- Novartis Institutes for BioMedical Research Inc., 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - John Manchester
- Novartis Institutes for BioMedical Research Inc., 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Lauren G Monovich
- Novartis Institutes for BioMedical Research Inc., 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Anna Paola Pelliccioli
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Manuel Schwarze
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Michael D Shultz
- Novartis Institutes for BioMedical Research Inc., 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Nikolaus Stiefl
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Daniel K Baeschlin
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
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11
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Benchmarking Data Sets from PubChem BioAssay Data: Current Scenario and Room for Improvement. Int J Mol Sci 2020; 21:ijms21124380. [PMID: 32575564 PMCID: PMC7352161 DOI: 10.3390/ijms21124380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 11/17/2022] Open
Abstract
Developing realistic data sets for evaluating virtual screening methods is a task that has been tackled by the cheminformatics community for many years. Numerous artificially constructed data collections were developed, such as DUD, DUD-E, or DEKOIS. However, they all suffer from multiple drawbacks, one of which is the absence of experimental results confirming the impotence of presumably inactive molecules, leading to possible false negatives in the ligand sets. In light of this problem, the PubChem BioAssay database, an open-access repository providing the bioactivity information of compounds that were already tested on a biological target, is now a recommended source for data set construction. Nevertheless, there exist several issues with the use of such data that need to be properly addressed. In this article, an overview of benchmarking data collections built upon experimental PubChem BioAssay input is provided, along with a thorough discussion of noteworthy issues that one must consider during the design of new ligand sets from this database. The points raised in this review are expected to guide future developments in this regard, in hopes of offering better evaluation tools for novel in silico screening procedures.
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12
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Saravanan KM, Zhang H, Zhang H, Xi W, Wei Y. On the Conformational Dynamics of β-Amyloid Forming Peptides: A Computational Perspective. Front Bioeng Biotechnol 2020; 8:532. [PMID: 32656188 PMCID: PMC7325929 DOI: 10.3389/fbioe.2020.00532] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/04/2020] [Indexed: 12/12/2022] Open
Abstract
Understanding the conformational dynamics of proteins and peptides involved in important functions is still a difficult task in computational structural biology. Because such conformational transitions in β-amyloid (Aβ) forming peptides play a crucial role in many neurological disorders, researchers from different scientific fields have been trying to address issues related to the folding of Aβ forming peptides together. Many theoretical models have been proposed in the recent years for studying Aβ peptides using mathematical, physicochemical, and molecular dynamics simulation, and machine learning approaches. In this article, we have comprehensively reviewed the developmental advances in the theoretical models for Aβ peptide folding and interactions, particularly in the context of neurological disorders. Furthermore, we have extensively reviewed the advances in molecular dynamics simulation as a tool used for studying the conversions between polymorphic amyloid forms and applications of using machine learning approaches in predicting Aβ peptides and aggregation-prone regions in proteins. We have also provided details on the theoretical advances in the study of Aβ peptides, which would enhance our understanding of these peptides at the molecular level and eventually lead to the development of targeted therapies for certain acute neurological disorders such as Alzheimer's disease in the future.
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Affiliation(s)
| | | | | | - Wenhui Xi
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yanjie Wei
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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13
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Yang Y, Zhang Y, Hua Y, Chen X, Fan Y, Wang Y, Liang L, Deng C, Lu T, Chen Y, Liu H. In Silico Design and Analysis of a Kinase-Focused Combinatorial Library Considering Diversity and Quality. J Chem Inf Model 2020; 60:92-107. [PMID: 31886658 DOI: 10.1021/acs.jcim.9b00841] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A structurally diverse, high-quality, and kinase-focused database plays a critical role in finding hits or leads in kinase drug discovery. Here, we propose a workflow for designing a virtual kinase-focused combinatorial library using existing structures. Based on the analysis of known protein kinase inhibitors (PKIs), detailed fragment optimization, fragment selection, fragment linking, and a molecular filtering scheme were defined. Quick recognition of core fragments that can possibly form dual hydrogen bonds with the hinge region of the ATP-pocket was proposed. Furthermore, three diversity and four quality metrics were chosen for compound library analysis, which can be applied to databases with over 30 million structures. Compared with 13 commercial libraries, our protocol demonstrates a special advantage in terms of good skeleton diversity, acceptable fingerprint diversity, balanced scaffold distribution, and high quality, which can work well not only on existing PKIs, but also on four chosen commercial libraries. Overall, the strategy can greatly facilitate the expansion of a desirable chemical space for kinase drug discovery.
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Affiliation(s)
- Yan Yang
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yanmin Zhang
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yi Hua
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Xingye Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yuanrong Fan
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yuchen Wang
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Li Liang
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Chenglong Deng
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Tao Lu
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China.,State Key Laboratory of Natural Medicines , China Pharmaceutical University , 24 Tongjiaxiang , Nanjing 210009 , China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Haichun Liu
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
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14
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Abstract
Aim: The druggability of epigenetic targets has prompted researchers to develop small-molecule therapeutics. However, no systematic assessment has ever been done to investigate the chemical space of epigenetic modulators. Herein, we report a comprehensive chemoinformatic analysis of epigenetic ligands from EpiDBase, HEMD, ChEMBL and PubChem databases. Results: Nearly, 0.45 × 106 ligands were analyzed for assay interference compounds, target profiling, drug-like properties and hit prioritization. After eliminating approximately 96,000 problematic compounds, the remaining 0.36 × 106 compounds were studied for their physicochemical distributions, principal component analysis and hit prioritization. More than 30% of assay interference compounds were determined for many proteins. Conclusion: This systematic assessment of epigenetic ligands will help in the enrichment of screening libraries with high-quality compounds and thus, the generation of efficacious drug candidates.
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15
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Dantas RF, Evangelista TCS, Neves BJ, Senger MR, Andrade CH, Ferreira SB, Silva-Junior FP. Dealing with frequent hitters in drug discovery: a multidisciplinary view on the issue of filtering compounds on biological screenings. Expert Opin Drug Discov 2019; 14:1269-1282. [DOI: 10.1080/17460441.2019.1654453] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Rafael Ferreira Dantas
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Tereza Cristina Santos Evangelista
- LaSOPB – Laboratório de Síntese Orgânica e Prospecção Biológica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruno Junior Neves
- LabChem – Laboratory of Cheminformatics, Centro Universitário de Anápolis, UniEVANGÉLICA, Anápolis, Brazil
| | - Mario Roberto Senger
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Carolina Horta Andrade
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
| | - Sabrina Baptista Ferreira
- LaSOPB – Laboratório de Síntese Orgânica e Prospecção Biológica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Floriano Paes Silva-Junior
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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16
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Pereyra CE, Dantas RF, Ferreira SB, Gomes LP, Silva-Jr FP. The diverse mechanisms and anticancer potential of naphthoquinones. Cancer Cell Int 2019; 19:207. [PMID: 31388334 PMCID: PMC6679553 DOI: 10.1186/s12935-019-0925-8] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 07/23/2019] [Indexed: 12/15/2022] Open
Abstract
Cancer is one of the leading causes of death around the world and although the different clinical approaches have helped to increase survival rates, incidence is still high and so its mortality. Chemotherapy is the only approach which is systemic, reaching cancer cells in all body tissues and the search for new potent and selective drugs is still an attractive field within cancer research. Naphthoquinones, natural and synthetic, have garnered much attention in the scientific community due to their pharmacological properties, among them anticancer action, and potential therapeutic significance. Many mechanisms of action have been reported which also depend on structural differences among them. Here, we describe some of the most relevant mechanisms of action reported so far for naphthoquinones and highlight novel targets which are being described in the literature. Furthermore, we gather some of the most impressive efforts done by researchers to harness the anticancer properties of these compounds through specifically designed structural modifications.
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Affiliation(s)
- Carolina Escardó Pereyra
- 1Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Avenida Brasil 4365, Rio de Janeiro, Rio de Janeiro 21040-900 Brazil
| | - Rafael Ferreira Dantas
- 1Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Avenida Brasil 4365, Rio de Janeiro, Rio de Janeiro 21040-900 Brazil
| | - Sabrina Baptista Ferreira
- 2Laboratório de Síntese Orgânica e Prospecção Biológica, Instituto de Química, Universidade Federal do Rio de Janeiro, Ilha do Fundão, Rio de Janeiro, Rio de Janeiro 21949-900 Brazil
| | - Luciano Pinho Gomes
- 1Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Avenida Brasil 4365, Rio de Janeiro, Rio de Janeiro 21040-900 Brazil
| | - Floriano Paes Silva-Jr
- 1Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Avenida Brasil 4365, Rio de Janeiro, Rio de Janeiro 21040-900 Brazil
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17
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Chinsembu KC. Chemical diversity and activity profiles of HIV-1 reverse transcriptase inhibitors from plants. REVISTA BRASILEIRA DE FARMACOGNOSIA-BRAZILIAN JOURNAL OF PHARMACOGNOSY 2019. [DOI: 10.1016/j.bjp.2018.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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18
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Reker D, Bernardes GJL, Rodrigues T. Computational advances in combating colloidal aggregation in drug discovery. Nat Chem 2019; 11:402-418. [PMID: 30988417 DOI: 10.1038/s41557-019-0234-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 02/21/2019] [Indexed: 02/07/2023]
Abstract
Small molecule effectors are essential for drug discovery. Specific molecular recognition, reversible binding and dose-dependency are usually key requirements to ensure utility of a novel chemical entity. However, artefactual frequent-hitter and assay interference compounds may divert lead optimization and screening programmes towards attrition-prone chemical matter. Colloidal aggregates are the prime source of false positive readouts, either through protein sequestration or protein-scaffold mimicry. Nevertheless, assessment of colloidal aggregation remains somewhat overlooked and under-appreciated. In this Review, we discuss the impact of aggregation in drug discovery by analysing select examples from the literature and publicly-available datasets. We also examine and comment on technologies used to experimentally identify these potentially problematic entities. We focus on evidence-based computational filters and machine learning algorithms that may be swiftly deployed to flag chemical matter and mitigate the impact of aggregates in discovery programmes. We highlight the tools that can be used to scrutinize libraries, and identify and eliminate these problematic compounds.
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Affiliation(s)
- Daniel Reker
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. .,MIT-IBM Watson AI Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.,Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Tiago Rodrigues
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal.
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19
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Gilberg E, Gütschow M, Bajorath J. Promiscuous Ligands from Experimentally Determined Structures, Binding Conformations, and Protein Family-Dependent Interaction Hotspots. ACS OMEGA 2019; 4:1729-1737. [PMID: 31459430 PMCID: PMC6648413 DOI: 10.1021/acsomega.8b03481] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/10/2019] [Indexed: 05/06/2023]
Abstract
Compound promiscuity is often attributed to nonspecific binding or assay artifacts. On the other hand, it is well-known that many pharmaceutically relevant compounds are capable of engaging multiple targets in vivo, giving rise to polypharmacology. To explore and better understand promiscuous binding characteristics of small molecules, we have searched X-ray structures (and very few qualifying solution structures) for ligands that bind to multiple distantly related or unrelated target proteins. Experimental structures of a given ligand bound to different targets represent high-confidence data for exploring promiscuous binding events. A total of 192 ligands were identified that formed crystallographic complexes with proteins from different families and for which activity data were available. These "multifamily" compounds included endogenous ligands and were often more polar than other bound compounds and active in the submicromolar range. Unexpectedly, many promiscuous ligands displayed conserved or similar binding conformations in different active sites. Others were found to conformationally adjust to binding sites of different architectures. A comprehensive analysis of ligand-target interactions revealed that multifamily ligands frequently formed different interaction hotspots in binding sites, even if their bound conformations were similar, thus providing a rationale for promiscuous binding events at the molecular level of detail. As a part of this work, all multifamily ligands we have identified and associated activity data are made freely available.
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Affiliation(s)
- Erik Gilberg
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
- Pharmaceutical
Institute, Rheinische Friedrich-Wilhelms-Universität, An der Immenburg 4, D-53121 Bonn, Germany
| | - Michael Gütschow
- Pharmaceutical
Institute, Rheinische Friedrich-Wilhelms-Universität, An der Immenburg 4, D-53121 Bonn, Germany
| | - Jürgen Bajorath
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
- E-mail: .
Phone: 49-228-2699-306 (J.B.)
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20
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Mauney CH, Perrino FW, Hollis T. Identification of Inhibitors of the dNTP Triphosphohydrolase SAMHD1 Using a Novel and Direct High-Throughput Assay. Biochemistry 2018; 57:6624-6636. [PMID: 30380297 DOI: 10.1021/acs.biochem.8b01038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dNTP triphosphohydrolase SAMHD1 is a regulator of cellular dNTP pools. Given its central role in nucleotide metabolism, SAMHD1 performs important functions in cellular homeostasis, cell cycle regulation, and innate immunity. It therefore represents a high-profile target for small molecule drug design. SAMHD1 has a complex mechanism of catalytic activation that makes the design of an activating compound challenging. However, an inhibitor of SAMHD1 could serve multiple therapeutic roles, including the potentiation of antiviral and anticancer drug regimens. The lack of high-throughput screens that directly measure SAMHD1 catalytic activity has impeded efforts to identify inhibitors of SAMHD1. Here we describe a novel high-throughput screen that directly measures SAMHD1 catalytic activity. This assay results in a colorimetric end point that can be read spectrophotometrically and utilizes bis(4-nitrophenyl) phosphate as the substrate and Mn2+ as the activating cation that facilitates catalysis. When used to screen a library of Food and Drug Administration-approved drugs, this HTS identified multiple novel compounds that inhibited SAMHD1 dNTPase activity at micromolar concentrations.
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Affiliation(s)
- Christopher H Mauney
- Center for Structural Biology, Department of Biochemistry , Wake Forest School of Medicine , Winston-Salem , North Carolina 27157 , United States
| | - Fred W Perrino
- Center for Structural Biology, Department of Biochemistry , Wake Forest School of Medicine , Winston-Salem , North Carolina 27157 , United States
| | - Thomas Hollis
- Center for Structural Biology, Department of Biochemistry , Wake Forest School of Medicine , Winston-Salem , North Carolina 27157 , United States
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21
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Jasial S, Gilberg E, Blaschke T, Bajorath J. Machine Learning Distinguishes with High Accuracy between Pan-Assay Interference Compounds That Are Promiscuous or Represent Dark Chemical Matter. J Med Chem 2018; 61:10255-10264. [DOI: 10.1021/acs.jmedchem.8b01404] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Swarit Jasial
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Endenicher Allee 19c, Rheinische Friedrich-Wilhelms-Universität, D-53115 Bonn, Germany
| | - Erik Gilberg
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Endenicher Allee 19c, Rheinische Friedrich-Wilhelms-Universität, D-53115 Bonn, Germany
| | - Thomas Blaschke
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Endenicher Allee 19c, Rheinische Friedrich-Wilhelms-Universität, D-53115 Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Endenicher Allee 19c, Rheinische Friedrich-Wilhelms-Universität, D-53115 Bonn, Germany
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22
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Avram S, Curpan R, Bora A, Neanu C, Halip L. Enhancing Molecular Promiscuity Evaluation Through Assay Profiles. Pharm Res 2018; 35:240. [DOI: 10.1007/s11095-018-2523-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/10/2018] [Indexed: 10/28/2022]
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23
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Zhu M, Wang J, Xie J, Chen L, Wei X, Jiang X, Bao M, Qiu Y, Chen Q, Li W, Jiang C, Zhou X, Jiang L, Qiu P, Wu J. Design, synthesis, and evaluation of chalcone analogues incorporate α,β-Unsaturated ketone functionality as anti-lung cancer agents via evoking ROS to induce pyroptosis. Eur J Med Chem 2018; 157:1395-1405. [PMID: 30196062 DOI: 10.1016/j.ejmech.2018.08.072] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 08/24/2018] [Accepted: 08/25/2018] [Indexed: 12/22/2022]
Abstract
Chalcone, a natural structure, demonstrates many pharmacological activities including anticancer, and one promising mechanism is to modulate the generation of ROS. It has been known that pyroptosis is associated with anticancer effects, whereas there is fewer researches about ROS-mediated pyroptosis triggered by chemotherapy drugs. Moreover, incorporation of a α,β-unsaturated ketone unit into chalcone may be an effective strategy for development of chemotherapy drugs. Hence, a number of chalcone analogues bearing a α,β-unsaturated ketone were synthesized from chalcone analogues 1 with modest anticancer activities as the lead compound. Structure-activity relationship (SAR) studies confirmed the function of α,β-unsaturated ketone to improve anticancer activity. Notably, compound 8, bearing a α,β-unsaturated ketone, is the most potent inhibitor of cancer, with IC50 values on NCI-H460, A549 and H1975 cells of 2.3 ± 0.3, 3.2 ± 0.0 and 5.7 ± 1.4 μM, respectively. Besides, 8 showed antiproliferative ability against NCI-H460 cells in a time- and concentration-dependent manner through modulating ROS to induce caspase-3-mediated pyroptosis, and displayed a better safety profile in vivo. Overall, these results demonstrated that compound 8 is a candidate agent and a potential lead compound for development of chemotherapy drugs, and can be used as a probe to further examine the mechanism of ROS-dependent pyroptosis.
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Affiliation(s)
- Min Zhu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Jiabing Wang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China; Municipal Hospital Affiliated to Medical School of Taizhou University, Taizhou, Zhejiang, 318000, China
| | - Jingwen Xie
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Liping Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Xiaoyan Wei
- Department of Pharmacy, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, China; Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Xing Jiang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Miao Bao
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China; Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yanyi Qiu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Qian Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Wulan Li
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China; College of Information Science and Computer Engineering, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Chengxi Jiang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Xiaoou Zhou
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Liping Jiang
- Department of Parasitology, Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, China
| | - Peihong Qiu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
| | - Jianzhang Wu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
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24
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Abstract
‘Drug promiscuity’ refers to a drug that can act on multiple molecular targets, exhibiting similar or different pharmacological effects. Drugs may interact with unwanted targets, leading to off-target effects (one of the main reasons for side effects). Thus, intervention to prevent off-target effects in the early stages of drug discovery could reduce the risk of failure. The conversion between target and off-target effects is important for drug repurposing. Drug repurposing strategies could reduce research and development costs. This review details the research progress in the rational application of drug promiscuity for the discovery of multi-target drugs, drug repurposing and improving druggability in medicinal chemistry over the last 5 years.
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25
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Gilberg E, Stumpfe D, Bajorath J. X-ray-Structure-Based Identification of Compounds with Activity against Targets from Different Families and Generation of Templates for Multitarget Ligand Design. ACS OMEGA 2018; 3:106-111. [PMID: 30023769 PMCID: PMC6045467 DOI: 10.1021/acsomega.7b01849] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 12/18/2017] [Indexed: 05/22/2023]
Abstract
Compounds with multitarget activity (promiscuity) are increasingly sought in drug discovery. However, promiscuous compounds are often viewed controversially in light of potential assay artifacts that may give rise to false-positive activity annotations. We have reasoned that the strongest evidence for true multitarget activity of small molecules would be provided by experimentally determined structures of ligand-target complexes. Therefore, we have carried out a systematic search of currently available X-ray structures for compounds forming complexes with different targets. Rather unexpectedly, 1418 such crystallographic ligands were identified, including 702 that formed complexes with targets from different protein families (multifamily ligands). About half of these multifamily ligands originated from the medicinal chemistry literature, making it possible to consider additional target annotations and search for analogues. From 168 distinct series of analogues containing one or more multifamily ligands, 133 unique analogue-series-based scaffolds were isolated that can serve as templates for the design of new compounds with multitarget activity. As a part of our study, all of the multifamily ligands we have identified and the analogue-series-based scaffolds are made freely available.
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Affiliation(s)
- Erik Gilberg
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
- Pharmaceutical
Institute, Rheinische Friedrich-Wilhelms-Universität, An der Immenburg 4, D-53121 Bonn, Germany
| | - Dagmar Stumpfe
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
| | - Jürgen Bajorath
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
- Phone: 49-228-2699-306. E-mail:
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26
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Gilberg E, Gütschow M, Bajorath J. X-ray Structures of Target–Ligand Complexes Containing Compounds with Assay Interference Potential. J Med Chem 2018; 61:1276-1284. [DOI: 10.1021/acs.jmedchem.7b01780] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Erik Gilberg
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
- Pharmaceutical
Institute, Rheinische Friedrich-Wilhelms-Universität, An der Immenburg 4, D-53121 Bonn, Germany
| | - Michael Gütschow
- Pharmaceutical
Institute, Rheinische Friedrich-Wilhelms-Universität, An der Immenburg 4, D-53121 Bonn, Germany
| | - Jürgen Bajorath
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
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27
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Jacobson KA, Tosh DK, Toti KS, Ciancetta A. Polypharmacology of conformationally locked methanocarba nucleosides. Drug Discov Today 2017; 22:1782-1791. [PMID: 28781163 PMCID: PMC5705437 DOI: 10.1016/j.drudis.2017.07.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 06/13/2017] [Accepted: 07/26/2017] [Indexed: 12/13/2022]
Abstract
A single molecular scaffold can be adapted to interact with diverse targets, either separately or simultaneously. Nucleosides and nucleotides in which ribose is substituted with bicyclo[3.1.0]hexane are an example of a versatile drug-like scaffold for increasing selectivity at their classical targets: kinases, polymerases, adenosine and P2 receptors. Also, by applying structure-based functional group manipulations, rigidified adenosine derivatives can be repurposed to satisfy pharmacophoric requirements of various GPCRs, ion channels, enzymes and transporters, initially detected as off-target activities. Recent examples include 5HT2B serotonin receptor antagonists and novel dopamine transporter allosteric modulators. This directable target diversity establishes rigid nucleosides as privileged scaffolds.
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Affiliation(s)
- Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, Bldg 8A, Rm B1A-19, Bethesda, MD 20892-0810, USA.
| | - Dilip K Tosh
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, Bldg 8A, Rm B1A-19, Bethesda, MD 20892-0810, USA
| | - Kiran S Toti
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, Bldg 8A, Rm B1A-19, Bethesda, MD 20892-0810, USA
| | - Antonella Ciancetta
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, Bldg 8A, Rm B1A-19, Bethesda, MD 20892-0810, USA
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Gilberg E, Stumpfe D, Bajorath J. Towards a systematic assessment of assay interference: Identification of extensively tested compounds with high assay promiscuity. F1000Res 2017; 6. [PMID: 28928939 PMCID: PMC5596351 DOI: 10.12688/f1000research.12370.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/11/2017] [Indexed: 12/16/2022] Open
Abstract
A large-scale statistical analysis of hit rates of extensively assayed compounds is presented to provide a basis for a further assessment of assay interference potential and multi-target activities. A special feature of this investigation has been the inclusion of compound series information in activity analysis and the characterization of analog series using different parameters derived from assay statistics. No prior knowledge of compounds or targets was taken into consideration in the data-driven study of analog series. It was anticipated that taking large volumes of activity data, assay frequency, and assay overlap information into account would lead to statistically sound and chemically meaningful results. More than 6000 unique series of analogs with high hit rates were identified, more than 5000 of which did not contain known interference candidates, hence providing ample opportunities for follow-up analyses from a medicinal chemistry perspective.
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Affiliation(s)
- Erik Gilberg
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, D-53113, Germany
| | - Dagmar Stumpfe
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, D-53113, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, D-53113, Germany
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29
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Gilberg E, Stumpfe D, Bajorath J. Towards a systematic assessment of assay interference: Identification of extensively tested compounds with high assay promiscuity. F1000Res 2017; 6. [PMID: 28928939 DOI: 10.12688/f1000research.12370.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/16/2017] [Indexed: 11/20/2022] Open
Abstract
A large-scale statistical analysis of hit rates of extensively assayed compounds is presented to provide a basis for a further assessment of assay interference potential and multi-target activities. A special feature of this investigation has been the inclusion of compound series information in activity analysis and the characterization of analog series using different parameters derived from assay statistics. No prior knowledge of compounds or targets was taken into consideration in the data-driven study of analog series. It was anticipated that taking large volumes of activity data, assay frequency, and assay overlap information into account would lead to statistically sound and chemically meaningful results. More than 6000 unique series of analogs with high hit rates were identified, more than 5000 of which did not contain known interference candidates, hence providing ample opportunities for follow-up analyses from a medicinal chemistry perspective.
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Affiliation(s)
- Erik Gilberg
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, D-53113, Germany
| | - Dagmar Stumpfe
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, D-53113, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, D-53113, Germany
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30
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Jasial S, Hu Y, Bajorath J. How Frequently Are Pan-Assay Interference Compounds Active? Large-Scale Analysis of Screening Data Reveals Diverse Activity Profiles, Low Global Hit Frequency, and Many Consistently Inactive Compounds. J Med Chem 2017; 60:3879-3886. [PMID: 28421750 DOI: 10.1021/acs.jmedchem.7b00154] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Undetected pan-assay interference compounds (PAINS) with false-positive activities in assays often propagate through medicinal chemistry programs and compromise their outcomes. Although a large number of PAINS have been classified, often on the basis of individual studies or chemical experience, little has been done so far to systematically assess their activity profiles. Herein we report a large-scale analysis of the behavior of PAINS in biological screening assays. More than 23 000 extensively tested compounds containing PAINS substructures were detected, and their hit rates were determined. Many consistently inactive compounds were identified. The hit frequency was low overall, with median values of two to five hits for PAINS tested in hundreds of assays. Only confined subsets of PAINS produced abundant hits. The same PAINS substructure was often found in consistently inactive and frequently active compounds, indicating that the structural context in which PAINS occur modulates their effects.
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Affiliation(s)
- Swarit Jasial
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität , Dahlmannstr. 2, D-53113 Bonn, Germany
| | - Ye Hu
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität , Dahlmannstr. 2, D-53113 Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität , Dahlmannstr. 2, D-53113 Bonn, Germany
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31
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Chemistry-based molecular signature underlying the atypia of clozapine. Transl Psychiatry 2017; 7:e1036. [PMID: 28221369 PMCID: PMC5438035 DOI: 10.1038/tp.2017.6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/06/2016] [Accepted: 12/29/2016] [Indexed: 12/21/2022] Open
Abstract
The central nervous system is functionally organized as a dynamic network of interacting neural circuits that underlies observable behaviors. At higher resolution, these behaviors, or phenotypes, are defined by the activity of a specific set of biomolecules within those circuits. Identification of molecules that govern psychiatric phenotypes is a major challenge. The only organic molecular entities objectively associated with psychiatric phenotypes in humans are drugs that induce psychiatric phenotypes and drugs used for treatment of specific psychiatric conditions. Here, we identified candidate biomolecules contributing to the organic basis for psychosis by deriving an in vivo biomolecule-tissue signature for the atypical pharmacologic action of the antipsychotic drug clozapine. Our novel in silico approach identifies the ensemble of potential drug targets based on the drug's chemical structure and the region-specific gene expression profile of each target in the central nervous system. We subtracted the signature of the action of clozapine from that of a typical antipsychotic, chlorpromazine. Our results implicate dopamine D4 receptors in the pineal gland and muscarinic acetylcholine M1 (CHRM1) and M3 (CHRM3) receptors in the prefrontal cortex (PFC) as significant and unique to clozapine, whereas serotonin receptors 5-HT2A in the PFC and 5-HT2C in the caudate nucleus were common significant sites of action for both drugs. Our results suggest that D4 and CHRM1 receptor activity in specific tissues may represent underappreciated drug targets to advance the pharmacologic treatment of schizophrenia. These findings may enhance our understanding of the organic basis of psychiatric disorders and help developing effective therapies.
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Tomohara K, Ito T, Onikata S, Kato A, Adachi I. Discovery of hyaluronidase inhibitors from natural products and their mechanistic characterization under DMSO-perturbed assay conditions. Bioorg Med Chem Lett 2017; 27:1620-1623. [PMID: 28202328 DOI: 10.1016/j.bmcl.2017.01.083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 01/24/2017] [Accepted: 01/27/2017] [Indexed: 12/19/2022]
Abstract
The present study discovered four novel hyaluronan-degrading enzyme (hyaluronidase) inhibitors including chikusetsusaponins and catechins through the activity-guided separation of Panax japonicus and Prunus salicina, respectively. Although the discovery resulted in identification of usual frequent hitters, subsequent mechanistic characterizations under our DMSO-perturbed assay conditions and related protocols revealed that chikusetusaponin IV would serve as an aggregating and non-specific binding inhibitor, while (-)-epicatechin would interact specifically with enzyme at the catalytic site or more likely at a kind of catechin-binding site with a relatively week inhibitory activity. The latter description might provide a possible explanation for the well-known fact that a series of catechin have been described as frequent hitters in biological assays with a moderate activity. Thus, the present study demonstrated a practical and robust methodology to characterize initial screening hits mechanistically molecule-by-molecule in the early stage of natural product-based drug discovery.
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Affiliation(s)
- Keisuke Tomohara
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
| | - Tomohiro Ito
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Saika Onikata
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Atsushi Kato
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Isao Adachi
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
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33
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Gilberg E, Stumpfe D, Bajorath J. Activity profiles of analog series containing pan assay interference compounds. RSC Adv 2017. [DOI: 10.1039/c7ra06736d] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Shown is the distribution of activity profiles (color-coded bars) of analog series containing PAINS substructures in a heatmap.
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Affiliation(s)
- Erik Gilberg
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
| | - Dagmar Stumpfe
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
| | - Jürgen Bajorath
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
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34
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Dimova D, Gilberg E, Bajorath J. Identification and analysis of promiscuity cliffs formed by bioactive compounds and experimental implications. RSC Adv 2017. [DOI: 10.1039/c6ra27247a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
For three promiscuity cliffs (enclosed), cliff compounds, their promiscuity degrees (PDs), and color-coded substitution sites are shown. Comparison of these cliffs suggests the design of a new analog to further explore promiscuity.
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Affiliation(s)
- Dilyana Dimova
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
| | - Erik Gilberg
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
| | - Jürgen Bajorath
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
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