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Schüß C, Vu O, Mishra NM, Tough IR, Du Y, Stichel J, Cox HM, Weaver CD, Meiler J, Emmitte KA, Beck-Sickinger AG. Structure-Activity Relationship Study of the High-Affinity Neuropeptide Y 4 Receptor Positive Allosteric Modulator VU0506013. J Med Chem 2023. [PMID: 37339079 DOI: 10.1021/acs.jmedchem.3c00383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Positive allosteric modulators targeting the Y4 receptor (Y4R), a G protein-coupled receptor (GPCR) involved in the regulation of satiety, offer great potential in anti-obesity research. In this study, we selected 603 compounds by using quantitative structure-activity relationship (QSAR) models and tested them in high-throughput screening (HTS). Here, the novel positive allosteric modulator (PAM) VU0506013 was identified, which exhibits nanomolar affinity and pronounced selectivity toward the Y4R in engineered cell lines and mouse descending colon mucosa natively expressing the Y4R. Based on this lead structure, we conducted a systematic SAR study in two regions of the scaffold and presented a series of 27 analogues with modifications in the N- and C-terminal heterocycles of the molecule to obtain insight into functionally relevant positions. By mutagenesis and computational docking, we present a potential binding mode of VU0506013 in the transmembrane core of the Y4R. VU0506013 presents a promising scaffold for developing in vivo tools to move toward anti-obesity drug research focused on the Y4R.
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Affiliation(s)
- Corinna Schüß
- Institute of Biochemistry, Leipzig University, Leipzig 04103, Germany
| | - Oanh Vu
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Nigam M Mishra
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Iain R Tough
- King's College London, Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology & Neuroscience, London SE1 1UL, U.K
| | - Yu Du
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jan Stichel
- Institute of Biochemistry, Leipzig University, Leipzig 04103, Germany
| | - Helen M Cox
- King's College London, Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology & Neuroscience, London SE1 1UL, U.K
| | - C David Weaver
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Institute for Drug Discovery, Leipzig University, Leipzig 04103, Germany
| | - Kyle A Emmitte
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
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Brown BP, Vu O, Geanes AR, Kothiwale S, Butkiewicz M, Lowe EW, Mueller R, Pape R, Mendenhall J, Meiler J. Introduction to the BioChemical Library (BCL): An Application-Based Open-Source Toolkit for Integrated Cheminformatics and Machine Learning in Computer-Aided Drug Discovery. Front Pharmacol 2022; 13:833099. [PMID: 35264967 PMCID: PMC8899505 DOI: 10.3389/fphar.2022.833099] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/24/2022] [Indexed: 01/31/2023] Open
Abstract
The BioChemical Library (BCL) cheminformatics toolkit is an application-based academic open-source software package designed to integrate traditional small molecule cheminformatics tools with machine learning-based quantitative structure-activity/property relationship (QSAR/QSPR) modeling. In this pedagogical article we provide a detailed introduction to core BCL cheminformatics functionality, showing how traditional tasks (e.g., computing chemical properties, estimating druglikeness) can be readily combined with machine learning. In addition, we have included multiple examples covering areas of advanced use, such as reaction-based library design. We anticipate that this manuscript will be a valuable resource for researchers in computer-aided drug discovery looking to integrate modular cheminformatics and machine learning tools into their pipelines.
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Affiliation(s)
- Benjamin P. Brown
- Chemical and Physical Biology Program, Medical Scientist Training Program, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
- *Correspondence: Jens Meiler, ; Jeffrey Mendenhall, ; Benjamin P. Brown,
| | - Oanh Vu
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Alexander R. Geanes
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Sandeepkumar Kothiwale
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Mariusz Butkiewicz
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Edward W. Lowe
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Ralf Mueller
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Richard Pape
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Jeffrey Mendenhall
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
- *Correspondence: Jens Meiler, ; Jeffrey Mendenhall, ; Benjamin P. Brown,
| | - Jens Meiler
- Department of Chemistry, Departments of Pharmacology and Biomedical Informatics, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
- *Correspondence: Jens Meiler, ; Jeffrey Mendenhall, ; Benjamin P. Brown,
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Rudolf S, Kaempf K, Vu O, Meiler J, Beck‐Sickinger AG, Coin I. Binding of Natural Peptide Ligands to the Neuropeptide Y
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Receptor. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202108738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sarina Rudolf
- Institute of Biochemistry Faculty of Life Science Leipzig University 04103 Leipzig Germany
| | - Kerstin Kaempf
- Institute of Biochemistry Faculty of Life Science Leipzig University 04103 Leipzig Germany
| | - Oanh Vu
- Chemistry Department Vanderbilt University Nashville TN 37212 USA
| | - Jens Meiler
- Chemistry Department Vanderbilt University Nashville TN 37212 USA
- Center for Structural Biology Department of Biological Sciences Vanderbilt University Nashville TN 37212 USA
- Institute of Drug Design Faculty of Medicine Leipzig University 04103 Leipzig Germany
| | | | - Irene Coin
- Institute of Biochemistry Faculty of Life Science Leipzig University 04103 Leipzig Germany
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Rudolf S, Kaempf K, Vu O, Meiler J, Beck-Sickinger AG, Coin I. Binding of Natural Peptide Ligands to the Neuropeptide Y 5 Receptor. Angew Chem Int Ed Engl 2022; 61:e202108738. [PMID: 34822209 PMCID: PMC8766924 DOI: 10.1002/anie.202108738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Indexed: 01/28/2023]
Abstract
The binding mode of natural peptide ligands to the Y5 G protein-coupled receptor (Y5 R), an attractive therapeutic target for the treatment of obesity, is largely unknown. Here, we apply complementary biochemical and computational approaches, including scanning of the receptor surface with a genetically encoded crosslinker, Ala-scanning of the ligand and double-cycle mutagenesis, to map interactions in the ligand-receptor interface and build a structural model of the NPY-Y5 R complex guided by the experimental data. In the model, the carboxyl (C)-terminus of bound NPY is placed close to the extracellular loop (ECL) 3, whereas the characteristic α-helical segment of the ligand drapes over ECL1 and is tethered towards ECL2 by a hydrophobic cluster. We further show that the other two natural ligands of Y5 R, peptide YY (PYY) and pancreatic polypeptide (PP) dock to the receptor in a similar pose.
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Affiliation(s)
- Sarina Rudolf
- Institute of Biochemistry, Faculty of Life Science, Leipzig University, Leipzig 04103, Germany
| | - Kerstin Kaempf
- Institute of Biochemistry, Faculty of Life Science, Leipzig University, Leipzig 04103, Germany
| | - Oanh Vu
- Chemistry Department, Vanderbilt University, Nashville, Tennessee 37212, U.S.A
| | - Jens Meiler
- Chemistry Department, Vanderbilt University, Nashville, Tennessee 37212, U.S.A
- Center for Structural Biology, Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37212, U.S.A
- Institute of Drug Design, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | | | - Irene Coin
- Institute of Biochemistry, Faculty of Life Science, Leipzig University, Leipzig 04103, Germany
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Zimmermann A, Vu O, Brüser A, Sliwoski G, Marnett LJ, Meiler J, Schöneberg T. Mapping the binding sites of UDP and prostaglandin E2 glyceryl ester in the nucleotide receptor P2Y6. ChemMedChem 2022; 17:e202100683. [PMID: 35034430 PMCID: PMC9305961 DOI: 10.1002/cmdc.202100683] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/14/2022] [Indexed: 12/02/2022]
Abstract
Cyclooxygenase‐2 catalyzes the biosynthesis of prostaglandins from arachidonic acid and the biosynthesis of prostaglandin glycerol esters (PG‐Gs) from 2‐arachidonoylglycerol. PG‐Gs are mediators of several biological actions such as macrophage activation, hyperalgesia, synaptic plasticity, and intraocular pressure. Recently, the human UDP receptor P2Y6 was identified as a target for the prostaglandin E2 glycerol ester (PGE2‐G). Here, we show that UDP and PGE2‐G are evolutionary conserved endogenous agonists at vertebrate P2Y6 orthologs. Using sequence comparison of P2Y6 orthologs, homology modeling, and ligand docking studies, we proposed several receptor positions participating in agonist binding. Site‐directed mutagenesis and functional analysis of these P2Y6 mutants revealed that both UDP and PGE2‐G share in parts one ligand‐binding site. Thus, the convergent signaling of these two chemically very different agonists has already been manifested in the evolutionary design of the ligand‐binding pocket.
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Affiliation(s)
- Anne Zimmermann
- Leipzig University: Universitat Leipzig Rudolf Schönheimer Institute of Biochemistry GERMANY
| | - Oanh Vu
- Vanderbilt University Department of Chemistry UNITED STATES
| | - Antje Brüser
- Leipzig University: Universitat Leipzig Rudolf Schönheimer Institute of Biochemistry GERMANY
| | - Gregory Sliwoski
- Vanderbilt University School of Medicine Department of Biomedical Informatics UNITED STATES
| | - Lawrence J. Marnett
- Vanderbilt University School of Medicine Department of Biochemistry UNITED STATES
| | - Jens Meiler
- Leipzig University: Universitat Leipzig Institute of Drug discovery GERMANY
| | - Torsten Schöneberg
- Leipzig University: Universitat Leipzig Rudolf Schönheimer Institute of Biochemistry Johannisallee 30 04103 Leipzig GERMANY
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Vu O, Bender BJ, Pankewitz L, Huster D, Beck-Sickinger AG, Meiler J. The Structural Basis of Peptide Binding at Class A G Protein-Coupled Receptors. Molecules 2021; 27:molecules27010210. [PMID: 35011444 PMCID: PMC8746363 DOI: 10.3390/molecules27010210] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 12/15/2021] [Accepted: 12/18/2021] [Indexed: 11/16/2022] Open
Abstract
G protein-coupled receptors (GPCRs) represent the largest membrane protein family and a significant target class for therapeutics. Receptors from GPCRs’ largest class, class A, influence virtually every aspect of human physiology. About 45% of the members of this family endogenously bind flexible peptides or peptides segments within larger protein ligands. While many of these peptides have been structurally characterized in their solution state, the few studies of peptides in their receptor-bound state suggest that these peptides interact with a shared set of residues and undergo significant conformational changes. For the purpose of understanding binding dynamics and the development of peptidomimetic drug compounds, further studies should investigate the peptide ligands that are complexed to their cognate receptor.
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Affiliation(s)
- Oanh Vu
- Deparment of Chemistry, Vanderbilt University, Nashville, TN 37235, USA;
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; (B.J.B.); (L.P.)
| | - Brian Joseph Bender
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; (B.J.B.); (L.P.)
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
| | - Lisa Pankewitz
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; (B.J.B.); (L.P.)
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Medical Department, Leipzig University, Härtelstr. 16–18, D-04107 Leipzig, Germany;
| | - Annette G. Beck-Sickinger
- Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany;
| | - Jens Meiler
- Deparment of Chemistry, Vanderbilt University, Nashville, TN 37235, USA;
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; (B.J.B.); (L.P.)
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
- Leipzig University Medical Center, Institute for Drug Discovery, Departments of Chemistry and Computer Science, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
- Correspondence:
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Gershkovich MM, Groß VE, Vu O, Schoeder CT, Meiler J, Prömel S, Kaiser A. Structural Perspective on Ancient Neuropeptide Y-like System reveals Hallmark Features for Peptide Recognition and Receptor Activation. J Mol Biol 2021; 433:166992. [PMID: 33865871 PMCID: PMC8380825 DOI: 10.1016/j.jmb.2021.166992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/22/2021] [Accepted: 04/01/2021] [Indexed: 11/30/2022]
Abstract
The neuropeptide Y (NPY) family is a peptide-activated G protein-coupled receptor system conserved across all bilaterians, and is involved in food intake, learning, and behavior. We hypothesized that comparing the NPY system in evolutionarily ancient organisms can reveal structural determinants of peptide recognition and receptor activation conserved in evolution. To test this hypothesis, we investigated the homologous FLP/NPR system of the protostome C.elegans. For three prototypic peptide-receptor complexes representing different ligand types, we integrate extensive functional data into structural models of the receptors. Common features include acidic patches in the extracellular loops (ECLs) of the receptors that cooperatively 'draw' the peptide into the binding pocket, which was functionally validated in vivo. A structurally conserved glutamate in the ECL2 anchors the peptides by a conserved salt bridge to the arginine of the RFamide motif. Beyond this conserved interaction, peptide binding show variability enabled by receptor-specific interactions. The family-conserved residue Q3.32 is a key player for peptide binding and receptor activation. Altered interaction patterns at Q3.32 may drastically increase the efficacy to activate the receptor.
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Affiliation(s)
- Miron Mikhailowitsch Gershkovich
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany; Department of Chemistry, Center for Structural Biology, Vanderbilt University, 465 21st Ave South, BIOSCI/MRBIII, Nashville, TN 37235, USA
| | - Victoria Elisabeth Groß
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany
| | - Oanh Vu
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, 465 21st Ave South, BIOSCI/MRBIII, Nashville, TN 37235, USA
| | - Clara Tabea Schoeder
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, 465 21st Ave South, BIOSCI/MRBIII, Nashville, TN 37235, USA; Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, 465 21st Ave South, BIOSCI/MRBIII, Nashville, TN 37235, USA; Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Simone Prömel
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany
| | - Anette Kaiser
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany.
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Schüß C, Vu O, Schubert M, Du Y, Mishra NM, Tough IR, Stichel J, Weaver CD, Emmitte KA, Cox HM, Meiler J, Beck-Sickinger AG. Highly Selective Y 4 Receptor Antagonist Binds in an Allosteric Binding Pocket. J Med Chem 2021; 64:2801-2814. [PMID: 33595306 DOI: 10.1021/acs.jmedchem.0c02000] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Human neuropeptide Y receptors (Y1R, Y2R, Y4R, and Y5R) belong to the superfamily of G protein-coupled receptors and play an important role in the regulation of food intake and energy metabolism. We identified and characterized the first selective Y4R allosteric antagonist (S)-VU0637120, an important step toward validating Y receptors as therapeutic targets for metabolic diseases. To obtain insight into the antagonistic mechanism of (S)-VU0637120, we conducted a variety of in vitro, ex vivo, and in silico studies. These studies revealed that (S)-VU0637120 selectively inhibits native Y4R function and binds in an allosteric site located below the binding pocket of the endogenous ligand pancreatic polypeptide in the core of the Y4R transmembrane domains. Taken together, our studies provide a first-of-its-kind tool for probing Y4R function and improve the general understanding of allosteric modulation, ultimately contributing to the rational development of allosteric modulators for peptide-activated G protein-coupled receptors (GPCRs).
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Affiliation(s)
- Corinna Schüß
- Institute of Biochemistry, Leipzig University, Leipzig 04103, Germany
| | - Oanh Vu
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Mario Schubert
- Institute of Biochemistry, Leipzig University, Leipzig 04103, Germany
| | - Yu Du
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Nigam M Mishra
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Iain R Tough
- King's College London, Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology & Neuroscience, London SE1 1UL, U.K
| | - Jan Stichel
- Institute of Biochemistry, Leipzig University, Leipzig 04103, Germany
| | - C David Weaver
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States.,Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Kyle A Emmitte
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Helen M Cox
- King's College London, Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology & Neuroscience, London SE1 1UL, U.K
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States.,Institute for Drug Discovery, Leipzig University, Leipzig 04103, Germany
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Vu O, Mendenhall J, Altarawy D, Meiler J. BCL::Mol2D-a robust atom environment descriptor for QSAR modeling and lead optimization. J Comput Aided Mol Des 2019; 33:477-486. [PMID: 30955193 PMCID: PMC6824857 DOI: 10.1007/s10822-019-00199-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 03/18/2019] [Indexed: 12/28/2022]
Abstract
Comparing fragment based molecular fingerprints of drug-like molecules is one of the most robust and frequently used approaches in computer-assisted drug discovery. Molprint2D, a popular atom environment (AE) descriptor, yielded the best enrichment of active compounds across a diverse set of targets in a recent large-scale study. We present here BCL::Mol2D descriptors that outperformed Molprint2D on nine PubChem datasets spanning a wide range of protein classes. Because BCL::Mol2D records the number of AEs from a universal AE library, a novel aspect of BCL::Mol2D over the Molprint2D is its reversibility. This property enables decomposition of prediction from machine learning models to particular molecular substructures. Artificial neural networks with dropout, when trained on BCL::Mol2D descriptors outperform those trained on Molprint2D descriptors by up to 26% in logAUC metric. When combined with the Reduced Short Range descriptor set, our previously published set of descriptors optimized for QSARs, BCL::Mol2D yields a modest improvement. Finally, we demonstrate how the reversibility of BCL::Mol2D enables visualization of a 'pharmacophore map' that could guide lead optimization for serine/threonine kinase 33 inhibitors.
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Affiliation(s)
- Oanh Vu
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN, 37235, USA
| | - Jeffrey Mendenhall
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN, 37235, USA
| | - Doaa Altarawy
- The Molecular Sciences Software Institute (MolSSI), 1880 Pratt Drive, Suite 1100, Blacksburg, VA, 24060, USA
- Department of Computer and Systems Engineering, Alexandria University, Alexandria, Egypt
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN, 37235, USA.
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Abstract
Background In ligand-based virtual screening experiments, a known active ligand is used in similarity searches to find putative active compounds for the same protein target. When there are several known active molecules, screening using all of them is more powerful than screening using a single ligand. A consensus query can be created by either screening serially with different ligands before merging the obtained similarity scores, or by combining the molecular descriptors (i.e. chemical fingerprints) of those ligands. Results We report on the discriminative power and speed of several consensus methods, on two datasets only made of experimentally verified molecules. The two datasets contain a total of 19 protein targets, 3776 known active and ~ 2 × 106 inactive molecules. Three chemical fingerprints are investigated: MACCS 166 bits, ECFP4 2048 bits and an unfolded version of MOLPRINT2D. Four different consensus policies and five consensus sizes were benchmarked. Conclusions The best consensus method is to rank candidate molecules using the maximum score obtained by each candidate molecule versus all known actives. When the number of actives used is small, the same screening performance can be approached by a consensus fingerprint. However, if the computational exploration of the chemical space is limited by speed (i.e. throughput), a consensus fingerprint allows to outperform this consensus of scores.
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Affiliation(s)
- Francois Berenger
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA. .,Division of System Cohort, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
| | - Oanh Vu
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
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