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Abstract
We report on two fragment-based drug design protocols, SEED2XR and ALTA, which start by high-throughput docking. SEED2XR is a two-stage protocol for fragment-based drug design. The first stage is in silico and consists of the automatic docking of 103-104 fragments using SEED, which requires about 1 s per fragment. SEED is a docking software developed specifically for fragment docking and binding energy evaluation by a force field with implicit solvent. In the second stage of SEED2XR, the 10-102 fragments with the most favorable predicted binding energies are validated by protein X-ray crystallography. The recent applications of SEED2XR to bromodomains demonstrate that the whole SEED2XR protocol can be carried out in about a week of working time, with hit rates ranging from 10% to 40%. Information on fragment-target interactions generated by the SEED2XR protocol or directly from SEED docking has been used for the discovery of hundreds of hits. ALTA is a computational protocol for screening which identifies candidate ligands that preserve the interactions between the optimal SEED fragments and the protein target. Medicinal chemistry optimization of ligands predicted by ALTA has resulted in pre-clinical candidates for protein kinases and bromodomains. The high-throughput, very low cost, sustainability, and high hit rate of the SEED-based protocols, unreachable by purely experimental techniques, make them perfectly suitable for both academic and industrial drug discovery research.
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Affiliation(s)
- Jean-Rémy Marchand
- Department of Biochemistry, University of Zürich, CH-8057, Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, CH-8057, Zürich, Switzerland.
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2
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Abstract
Hydration has a significant impact on ligand binding within protein active sites. Specific water molecules and their placement within protein active sites have been shown to make specific contributions to the energetics of protein-ligand binding and need consideration in the design of efficient binding ligands. These specific nonbulk water molecules and their interactions are different and have more significant impact in ligand design than the generalized bulk solvation of ligand-protein systems. Proper theoretical description of the solvation effects of water within a ligand-binding pocket is a significant computational challenge. Recently, new computational methods have been developed which can more accurately describe the contribution of waters within a protein ligand site and lead to improved and enhanced ligand design and ranking in computational docking and to greater enrichment.
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4
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Yuriev E, Holien J, Ramsland PA. Improvements, trends, and new ideas in molecular docking: 2012-2013 in review. J Mol Recognit 2015; 28:581-604. [PMID: 25808539 DOI: 10.1002/jmr.2471] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 01/16/2015] [Accepted: 02/05/2015] [Indexed: 12/11/2022]
Abstract
Molecular docking is a computational method for predicting the placement of ligands in the binding sites of their receptor(s). In this review, we discuss the methodological developments that occurred in the docking field in 2012 and 2013, with a particular focus on the more difficult aspects of this computational discipline. The main challenges and therefore focal points for developments in docking, covered in this review, are receptor flexibility, solvation, scoring, and virtual screening. We specifically deal with such aspects of molecular docking and its applications as selection criteria for constructing receptor ensembles, target dependence of scoring functions, integration of higher-level theory into scoring, implicit and explicit handling of solvation in the binding process, and comparison and evaluation of docking and scoring methods.
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Affiliation(s)
- Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Jessica Holien
- ACRF Rational Drug Discovery Centre and Structural Biology Laboratory, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, 3065, Australia
| | - Paul A Ramsland
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, 3004, Australia.,Department of Surgery Austin Health, University of Melbourne, Melbourne, Victoria, 3084, Australia.,Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria, 3004, Australia.,School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, Western Australia, 6845, Australia
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5
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Abstract
Intelligent Automatic Design (IADE) is an expert system developed at Novartis to identify nonclassical bioisosteres. In addition to bioisostere searching, one could also use IADE to grow a fragment bound to a protein. Here we report an evaluation of IADE as a tool for fragment growing. Three examples from the literature served as test cases. In all three cases, IADE generated close analogues of the published compounds and reproduced their crystallographic binding modes. This exercise validated the use of the IADE system for fragment growing. We have also gained experience in optimizing the performance of IADE for this type of application.
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Affiliation(s)
- Bernard Pirard
- Novartis Institutes for BioMedical Research , Novartis Campus, CH-4056 Basel, Switzerland
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Vass M, Schmidt É, Horti F, Keserű GM. Virtual fragment screening on GPCRs: a case study on dopamine D3 and histamine H4 receptors. Eur J Med Chem 2014; 77:38-46. [PMID: 24607587 DOI: 10.1016/j.ejmech.2014.02.034] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 02/11/2014] [Accepted: 02/13/2014] [Indexed: 01/05/2023]
Abstract
Prospective structure based virtual fragment screening methodologies on two GPCR targets namely the dopamine D3 and the histamine H4 receptors with a library of 12,905 fragments were evaluated. Fragments were docked to the X-ray structure and the homology model of the D3 and H4 receptors, respectively. Representative receptor conformations for ensemble docking were obtained from molecular dynamics trajectories. In vitro confirmed hit rates ranged from 16% to 32%. Hits had high ligand efficiency (LE) values in the range of 0.31-0.74 and also acceptable lipophilic efficiency. The X-ray structure, the homology model and structural ensembles were all found suitable for docking based virtual screening of fragments against these GPCRs. However, there was little overlap among different hit sets and methodologies were thus complementary to each other.
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Affiliation(s)
- Márton Vass
- Gedeon Richter Plc, H-1475, P.O.B. 27, Budapest, Hungary
| | - Éva Schmidt
- Gedeon Richter Plc, H-1475, P.O.B. 27, Budapest, Hungary
| | - Ferenc Horti
- Gedeon Richter Plc, H-1475, P.O.B. 27, Budapest, Hungary
| | - György M Keserű
- Research Centre for Natural Sciences of the Hungarian Academy of Sciences, H-1525, P.O.B. 17, Budapest, Hungary.
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7
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Connors CR, Rosenman DJ, Lopes DHJ, Mittal S, Bitan G, Sorci M, Belfort G, Garcia A, Wang C. Tranilast binds to aβ monomers and promotes aβ fibrillation. Biochemistry 2013; 52:3995-4002. [PMID: 23679559 PMCID: PMC4082028 DOI: 10.1021/bi400426t] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The antiallergy and potential anticancer drug tranilast has been patented for treating Alzheimer's disease (AD), in which amyloid β-protein (Aβ) plays a key pathogenic role. We used solution NMR to determine that tranilast binds to Aβ40 monomers with ∼300 μM affinity. Remarkably, tranilast increases Aβ40 fibrillation more than 20-fold in the thioflavin T assay at a 1:1 molar ratio, as well as significantly reducing the lag time. Tranilast likely promotes fibrillation by shifting Aβ monomer conformations to those capable of seed formation and fibril elongation. Molecular docking results qualitatively agree with NMR chemical shift perturbation, which together indicate that hydrophobic interactions are the major driving force of the Aβ-tranilast interaction. These data suggest that AD may be a potential complication for tranilast usage in elderly patients.
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Affiliation(s)
- Christopher R. Connors
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute (RPI), Troy, New York 12180, United States
- Graduate Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute (RPI), Troy, New York 12180, United States
| | - David J. Rosenman
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute (RPI), Troy, New York 12180, United States
- Department of Biology, Rensselaer Polytechnic Institute (RPI), Troy, New York 12180, United States
| | - Dahabada H. J. Lopes
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Shivina Mittal
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, United States
- Brain Research Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Mirco Sorci
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute (RPI), Troy, New York 12180, United States
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute (RPI), Troy, New York 12180, United States
| | - Georges Belfort
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute (RPI), Troy, New York 12180, United States
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute (RPI), Troy, New York 12180, United States
| | - Angel Garcia
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute (RPI), Troy, New York 12180, United States
- Department of Physics, Rensselaer Polytechnic Institute (RPI), Troy, New York 12180, United States
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute (RPI), Troy, New York 12180, United States
- Graduate Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute (RPI), Troy, New York 12180, United States
- Department of Biology, Rensselaer Polytechnic Institute (RPI), Troy, New York 12180, United States
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