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Gorgulla C, Çınaroğlu SS, Fischer PD, Fackeldey K, Wagner G, Arthanari H. VirtualFlow Ants-Ultra-Large Virtual Screenings with Artificial Intelligence Driven Docking Algorithm Based on Ant Colony Optimization. Int J Mol Sci 2021; 22:5807. [PMID: 34071676 PMCID: PMC8199267 DOI: 10.3390/ijms22115807] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 01/09/2023] Open
Abstract
The docking program PLANTS, which is based on ant colony optimization (ACO) algorithm, has many advanced features for molecular docking. Among them are multiple scoring functions, the possibility to model explicit displaceable water molecules, and the inclusion of experimental constraints. Here, we add support of PLANTS to VirtualFlow (VirtualFlow Ants), which adds a valuable method for primary virtual screenings and rescoring procedures. Furthermore, we have added support of ligand libraries in the MOL2 format, as well as on the fly conversion of ligand libraries which are in the PDBQT format to the MOL2 format to endow VirtualFlow Ants with an increased flexibility regarding the ligand libraries. The on the fly conversion is carried out with Open Babel and the program SPORES. We applied VirtualFlow Ants to a test system involving KEAP1 on the Google Cloud up to 128,000 CPUs, and the observed scaling behavior is approximately linear. Furthermore, we have adjusted several central docking parameters of PLANTS (such as the speed parameter or the number of ants) and screened 10 million compounds for each of the 10 resulting docking scenarios. We analyzed their docking scores and average docking times, which are key factors in virtual screenings. The possibility of carrying out ultra-large virtual screening with PLANTS via VirtualFlow Ants opens new avenues in computational drug discovery.
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Affiliation(s)
- Christoph Gorgulla
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; (P.D.F.); (G.W.)
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA
| | | | - Patrick D. Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; (P.D.F.); (G.W.)
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Konstantin Fackeldey
- Zuse Institute Berlin, 14195 Berlin, Germany;
- Institute of Mathematics, Technical University Berlin, 10623 Berlin, Germany
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; (P.D.F.); (G.W.)
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; (P.D.F.); (G.W.)
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA
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Wang Y, Kim J, Hilty C. Determination of protein-ligand binding modes using fast multi-dimensional NMR with hyperpolarization. Chem Sci 2020; 11:5935-5943. [PMID: 32874513 PMCID: PMC7441707 DOI: 10.1039/d0sc00266f] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/05/2020] [Indexed: 11/21/2022] Open
Abstract
Elucidation of small molecule-protein interactions provides essential information for understanding biological processes such as cellular signaling, as well as for rational drug development. Here, multi-dimensional NMR with sensitivity enhancement by dissolution dynamic nuclear polarization (D-DNP) is shown to allow the determination of the binding epitope of folic acid when complexed with the target dihydrofolate reductase. Protein signals are selectively enhanced by polarization transfer from the hyperpolarized ligand. A pseudo three-dimensional data acquisition with ligand-side Hadamard encoding results in protein-side [13C, 1H] chemical shift correlations that contain intermolecular nuclear Overhauser effect (NOE) information. A scoring function based on this data is used to select pre-docked ligand poses. The top five poses are within 0.76 Å root-mean-square deviation from a reference structure for the encoded five protons, showing improvements compared with the poses selected by an energy-based scoring function without experimental inputs. The sensitivity enhancement provided by the D-DNP combined with multi-dimensional NMR increases the speed and potentially the selectivity of structure elucidation of ligand binding epitopes.
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Affiliation(s)
- Yunyi Wang
- Department of Chemistry , Texas A&M University , 3255 TAMU , College Station , TX 77843 , USA .
| | - Jihyun Kim
- Department of Chemistry , Texas A&M University , 3255 TAMU , College Station , TX 77843 , USA .
| | - Christian Hilty
- Department of Chemistry , Texas A&M University , 3255 TAMU , College Station , TX 77843 , USA .
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Fu DY, Meiler J. Predictive Power of Different Types of Experimental Restraints in Small Molecule Docking: A Review. J Chem Inf Model 2018; 58:225-233. [PMID: 29286651 DOI: 10.1021/acs.jcim.7b00418] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Incorporating experimental restraints is a powerful method of increasing accuracy in computational protein small molecule docking simulations. Different algorithms integrate distinct forms of biochemical data during the docking and/or scoring stages. These so-called hybrid methods make use of receptor-based information such as nuclear magnetic resonance (NMR) restraints or small molecule-based information such as structure-activity relationships (SARs). A third class of methods directly interrogates contacts between the protein receptor and the small molecule. This work reviews the current state of using such restraints in docking simulations, evaluates their feasibility across broad systems, and identifies potential areas of algorithm development.
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Affiliation(s)
- Darwin Y Fu
- Department of Chemistry Vanderbilt University Nashville, Tennessee 37235, United States
| | - Jens Meiler
- Department of Chemistry Vanderbilt University Nashville, Tennessee 37235, United States
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Nitsche C, Otting G. NMR studies of ligand binding. Curr Opin Struct Biol 2017; 48:16-22. [PMID: 29017071 DOI: 10.1016/j.sbi.2017.09.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/15/2017] [Accepted: 09/18/2017] [Indexed: 12/17/2022]
Abstract
NMR spectroscopy is an established tool in drug discovery, but its strength is commonly regarded to be largely confined to the early stages of hit discovery and fragment based drug design, where NMR offers unique capabilities of characterizing the binding modes of ligand molecules that bind sufficiently weakly to be in rapid exchange between bound and free state. Here we, first, provide a meta-review of recent reviews on NMR studies of ligand binding and, second, review recent progress towards NMR characterization of the ligand binding mode in stable protein-ligand complexes, with particular emphasis on the global positioning system (GPS) approach enabled by paramagnetic lanthanide tags.
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Affiliation(s)
- Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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Fredriksson K, Lottmann P, Hinz S, Onila I, Shymanets A, Harteneck C, Müller CE, Griesinger C, Exner TE. Nanodiscs for INPHARMA NMR Characterization of GPCRs: Ligand Binding to the Human A2A Adenosine Receptor. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Kai Fredriksson
- Institute of Pharmacy; Eberhard Karls Universität Tübingen; Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Chemistry and Zukunftskolleg; Universität Konstanz; 78457 Konstanz Germany
- Present address: Fakultät für Chemie; Technische Universität München; Lichtenbergstraße 4 85748 Garching Germany
| | - Philip Lottmann
- Max Planck Institute for Biophysical Chemistry; Am Faßberg 11 37077 Göttingen Germany
| | - Sonja Hinz
- Universität Bonn; Pharma-Zentrum Bonn; Pharmazeutisches Institut; Pharmazeutische Chemie; An der Immenburg 4 53121 Bonn Germany
| | - Iounut Onila
- Institute of Pharmacy; Eberhard Karls Universität Tübingen; Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Chemistry and Zukunftskolleg; Universität Konstanz; 78457 Konstanz Germany
| | - Aliaksei Shymanets
- Department of Pharmacology and Experimental Therapy; Institute of Experimental and Clinical Pharmacology and Toxicology; Interfaculty Center of Pharmacogenomics and Pharmaceutical Research (ICePhA); University of Tübingen; Tübingen Germany
| | - Christian Harteneck
- Department of Pharmacology and Experimental Therapy; Institute of Experimental and Clinical Pharmacology and Toxicology; Interfaculty Center of Pharmacogenomics and Pharmaceutical Research (ICePhA); University of Tübingen; Tübingen Germany
| | - Christa E. Müller
- Universität Bonn; Pharma-Zentrum Bonn; Pharmazeutisches Institut; Pharmazeutische Chemie; An der Immenburg 4 53121 Bonn Germany
| | - Christian Griesinger
- Max Planck Institute for Biophysical Chemistry; Am Faßberg 11 37077 Göttingen Germany
| | - Thomas E. Exner
- Institute of Pharmacy; Eberhard Karls Universität Tübingen; Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Chemistry and Zukunftskolleg; Universität Konstanz; 78457 Konstanz Germany
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Fredriksson K, Lottmann P, Hinz S, Onila I, Shymanets A, Harteneck C, Müller CE, Griesinger C, Exner TE. Nanodiscs for INPHARMA NMR Characterization of GPCRs: Ligand Binding to the Human A2A Adenosine Receptor. Angew Chem Int Ed Engl 2017; 56:5750-5754. [PMID: 28429411 DOI: 10.1002/anie.201612547] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 02/09/2017] [Indexed: 11/11/2022]
Abstract
G-protein-coupled-receptors (GPCRs) are of fundamental importance for signal transduction through cell membranes. This makes them important drug targets, but structure-based drug design (SBDD) is still hampered by the limitations for structure determination of unmodified GPCRs. We show that the interligand NOEs for pharmacophore mapping (INPHARMA) method can provide valuable information on ligand poses inside the binding site of the unmodified human A2A adenosine receptor reconstituted in nanodiscs. By comparing experimental INPHARMA spectra with back-calculated spectra based on ligand poses obtained from molecular dynamics simulations, a complex structure for A2A R with the low-affinity ligand 3-pyrrolidin-1-ylquinoxalin-2-amine was determined based on the X-ray structure of ligand ZM-241,358 in complex with a modified A2A R.
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Affiliation(s)
- Kai Fredriksson
- Institute of Pharmacy, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,Department of Chemistry and Zukunftskolleg, Universität Konstanz, 78457, Konstanz, Germany.,Present address: Fakultät für Chemie, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Philip Lottmann
- Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Sonja Hinz
- Universität Bonn, Pharma-Zentrum Bonn, Pharmazeutisches Institut, Pharmazeutische Chemie, An der Immenburg 4, 53121, Bonn, Germany
| | - Iounut Onila
- Institute of Pharmacy, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,Department of Chemistry and Zukunftskolleg, Universität Konstanz, 78457, Konstanz, Germany
| | - Aliaksei Shymanets
- Department of Pharmacology and Experimental Therapy, Institute of Experimental and Clinical Pharmacology and Toxicology, Interfaculty Center of Pharmacogenomics and Pharmaceutical Research (ICePhA), University of Tübingen, Tübingen, Germany
| | - Christian Harteneck
- Department of Pharmacology and Experimental Therapy, Institute of Experimental and Clinical Pharmacology and Toxicology, Interfaculty Center of Pharmacogenomics and Pharmaceutical Research (ICePhA), University of Tübingen, Tübingen, Germany
| | - Christa E Müller
- Universität Bonn, Pharma-Zentrum Bonn, Pharmazeutisches Institut, Pharmazeutische Chemie, An der Immenburg 4, 53121, Bonn, Germany
| | - Christian Griesinger
- Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Thomas E Exner
- Institute of Pharmacy, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,Department of Chemistry and Zukunftskolleg, Universität Konstanz, 78457, Konstanz, Germany
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Frank AT. Can Holo NMR Chemical Shifts be Directly Used to Resolve RNA–Ligand Poses? J Chem Inf Model 2016; 56:368-76. [DOI: 10.1021/acs.jcim.5b00593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Aaron T. Frank
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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