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Gu S, Yang Y, Zhao Y, Qiu J, Wang X, Tong HHY, Liu L, Wan X, Liu H, Hou T, Kang Y. Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios. J Chem Inf Model 2024; 64:3630-3639. [PMID: 38630855 DOI: 10.1021/acs.jcim.3c01976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
The introduction of AlphaFold2 (AF2) has sparked significant enthusiasm and generated extensive discussion within the scientific community, particularly among drug discovery researchers. Although previous studies have addressed the performance of AF2 structures in virtual screening (VS), a more comprehensive investigation is still necessary considering the paramount importance of structural accuracy in drug design. In this study, we evaluate the performance of AF2 structures in VS across three common drug discovery scenarios: targets with holo, apo, and AF2 structures; targets with only apo and AF2 structures; and targets exclusively with AF2 structures. We utilized both the traditional physics-based Glide and the deep-learning-based scoring function RTMscore to rank the compounds in the DUD-E, DEKOIS 2.0, and DECOY data sets. The results demonstrate that, overall, the performance of VS on AF2 structures is comparable to that on apo structures but notably inferior to that on holo structures across diverse scenarios. Moreover, when a target has solely AF2 structure, selecting the holo structure of the target from different subtypes within the same protein family produces comparable results with the AF2 structure for VS on the data set of the AF2 structures, and significantly better results than the AF2 structures on its own data set. This indicates that utilizing AF2 structures for docking-based VS may not yield most satisfactory outcomes, even when solely AF2 structures are available. Moreover, we rule out the possibility that the variations in VS performance between the binding pockets of AF2 and holo structures arise from the differences in their biological assembly composition.
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Affiliation(s)
- Shukai Gu
- Faculty of Applied Science, Macao Polytechnic University, Macao 999078, SAR, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yuwei Yang
- Faculty of Applied Science, Macao Polytechnic University, Macao 999078, SAR, China
| | - Yihao Zhao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Jiayue Qiu
- Faculty of Applied Science, Macao Polytechnic University, Macao 999078, SAR, China
| | - Xiaorui Wang
- State Key Laboratory of Quality Re-search in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao 999078, China
| | - Henry Hoi Yee Tong
- Faculty of Applied Science, Macao Polytechnic University, Macao 999078, SAR, China
| | - Liwei Liu
- Advanced Computing and Storage Laboratory, Central Research Institute, 2012 Laboratories, Huawei Technologies Co., Ltd., Nanjing 210000, Jiangsu, China
| | - Xiaozhe Wan
- Advanced Computing and Storage Laboratory, Central Research Institute, 2012 Laboratories, Huawei Technologies Co., Ltd., Nanjing 210000, Jiangsu, China
| | - Huanxiang Liu
- Faculty of Applied Science, Macao Polytechnic University, Macao 999078, SAR, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
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Callil-Soares PH, Biasi LCK, Pessoa Filho PDA. Effect of preprocessing and simulation parameters on the performance of molecular docking studies. J Mol Model 2023; 29:251. [PMID: 37452150 DOI: 10.1007/s00894-023-05637-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023]
Abstract
CONTEXT Molecular docking is an important and rapid tool that provides a comprehensive view of different molecular mechanisms. It is often used to verify the binding interactions of many pairs of molecules and is much faster than more rigorous approaches. However, its application requires carefully preprocessing each molecule and selecting a series of simulation parameters, which is not always done correctly. We show how preprocessing and simulation parameters can positively or negatively impact molecular docking performance. For example, the inclusion of hydrogen atoms leads to better redocking scores, but molecular dynamics simulations must be performed under certain constraints; otherwise, it may worsen performance rather than improve it. This study clarifies the importance and influence of these different parameters in the simulation results. METHODS We analyzed the influence of different parameters on the predictive ability of molecular docking techniques using two software packages: AutoDock Vina and AutoDock-GPU. Thus, 90 receptor-ligand complexes were redocked, evaluating the root mean square deviation (RMSD) between the original position of the ligand (receptor-ligand complex obtained experimentally) and that obtained by the software for every analysis. We investigated the influence of hydrogen atoms (on the receptor and on the receptor-ligand complex), partial charges (QEq, QTPIE, EEM, EEM2015ha, MMFF94, Gasteiger-Marsili, and no charge), search boxes (size and exhaustiveness), ligand characteristics (size and number of torsions), and the use of molecular dynamics (of the receptor or the receptor-ligand complex) before docking analyses.
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Affiliation(s)
- Pedro Henrique Callil-Soares
- Chemical Engineering Department, Polytechnic School of the University of São Paulo, Av. Lineu Prestes, 580, São Paulo, 05508-000, Brazil
| | - Lilian Caroline Kramer Biasi
- Chemical Engineering Department, Polytechnic School of the University of São Paulo, Av. Lineu Prestes, 580, São Paulo, 05508-000, Brazil.
| | - Pedro de Alcântara Pessoa Filho
- Chemical Engineering Department, Polytechnic School of the University of São Paulo, Av. Lineu Prestes, 580, São Paulo, 05508-000, Brazil
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3
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Nazir S, Anwar F, Saleem U, Ahmad B, Raza Z, Sanawar M, Rehman AU, Ismail T. Drotaverine Inhibitor of PDE4: Reverses the Streptozotocin Induced Alzheimer's Disease in Mice. Neurochem Res 2021; 46:1814-1829. [PMID: 33877499 DOI: 10.1007/s11064-021-03327-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/24/2021] [Accepted: 04/09/2021] [Indexed: 11/26/2022]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease associated with decline in memory and cognitive impairments. Phosphodiesterase IV (PDE4) protein, an intracellular cAMP levels regulator, when inhibited act as potent neuroprotective agents by virtue of ceasing the activity of Pro-inflammatory mediators. The complexity of AD etiology has ever since compelled the researchers to discover multifunctional compounds to combat the AD and neurodegeneration. The aim of this study was to probe into role of drotaverine a PDE4 inhibitor in the management of AD. Albino mice were divided into seven groups (n = 10). Group 1 control group received carboxy methyl cellulose (CMC 1 mL/kg), group II diseased group treated with streptozotocin (STZ 3 mg/kg) by intracerebroventricular (ICV) route, group III administered standard drug Piracetam 200 mg/kg and groups IV-VII were given drotaverine (10, 20, 40, and 80 mg/kg i/p respectively). Groups II-VII were given STZ (3 mg/kg, ICV) on 1st and 3rd day of treatment to induce AD. All the groups were given their respective treatments for 23 days. Improvement in learning and memory was evaluated by using behavioral tests like open field test, elevated plus maze test, Morris water maze test and passive avoidance test. Furthermore, brain levels of biochemical markers of oxidative stress, neurotransmitters, β-amyloid and tau protein were also measured. Drotaverine showed statistically significant dose dependent improvement in behavioral and biochemical markers of AD: the maximum response was achieved at a dose level of 80 mg/kg. The Study concluded that drotaverine ameliorates cognitive impairment and as well as exhibited modulated the brain levels of neurotransmitters.
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Affiliation(s)
- Samra Nazir
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Lahore Campus, Lahore, 54000, Pakistan
| | - Fareeha Anwar
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Lahore Campus, Lahore, 54000, Pakistan.
| | - Uzma Saleem
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad, Pakistan
| | - Bashir Ahmad
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Lahore Campus, Lahore, 54000, Pakistan
| | - Zohaib Raza
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Lahore Campus, Lahore, 54000, Pakistan
| | - Maham Sanawar
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Lahore Campus, Lahore, 54000, Pakistan
| | - Artta Ur Rehman
- Department of Pharmacy, Faculty of Natural Sciences, Forman Christian College, Lahore, Pakistan
| | - Tariq Ismail
- Department of Pharmacy, COMSAT University, Abottabad, Pakistan
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Abstract
The majority of biological processes are regulated by enzymes, precise control over specific enzymes could create the potential for controlling cellular processes remotely. We show that the thermophilic enzyme thermolysin can be remotely activated in 17.76 MHz radiofrequency (RF) fields when covalently attached to 6.1 nm gold coated magnetite nanoparticles. Without raising the bulk solution temperature, we observe enzyme activity as if the solution was 16 ± 2 °C warmer in RF fields-an increase in enzymatic rate of 129 ± 8%. Kinetics studies show that the activity increase of the enzyme is consistent with the induced fit of a hot enzyme with cold substrate.
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Saikia S, Bordoloi M. Molecular Docking: Challenges, Advances and its Use in Drug Discovery Perspective. Curr Drug Targets 2020; 20:501-521. [PMID: 30360733 DOI: 10.2174/1389450119666181022153016] [Citation(s) in RCA: 203] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/08/2018] [Accepted: 08/28/2018] [Indexed: 01/21/2023]
Abstract
Molecular docking is a process through which small molecules are docked into the macromolecular structures for scoring its complementary values at the binding sites. It is a vibrant research area with dynamic utility in structure-based drug-designing, lead optimization, biochemical pathway and for drug designing being the most attractive tools. Two pillars for a successful docking experiment are correct pose and affinity prediction. Each program has its own advantages and drawbacks with respect to their docking accuracy, ranking accuracy and time consumption so a general conclusion cannot be drawn. Moreover, users don't always consider sufficient diversity in their test sets which results in certain programs to outperform others. In this review, the prime focus has been laid on the challenges of docking and troubleshooters in existing programs, underlying algorithmic background of docking, preferences regarding the use of docking programs for best results illustrated with examples, comparison of performance for existing tools and algorithms, state of art in docking, recent trends of diseases and current drug industries, evidence from clinical trials and post-marketing surveillance are discussed. These aspects of the molecular drug designing paradigm are quite controversial and challenging and this review would be an asset to the bioinformatics and drug designing communities.
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Affiliation(s)
- Surovi Saikia
- Natural Products Chemistry Group, CSIR North East Institute of Science & Technology, Jorhat-785006, Assam, India
| | - Manobjyoti Bordoloi
- Natural Products Chemistry Group, CSIR North East Institute of Science & Technology, Jorhat-785006, Assam, India
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Abstract
Molecular Docking is used to positioning the computer-generated 3D structure of small
ligands into a receptor structure in a variety of orientations, conformations and positions. This
method is useful in drug discovery and medicinal chemistry providing insights into molecular
recognition. Docking has become an integral part of Computer-Aided Drug Design and Discovery
(CADDD). Traditional docking methods suffer from limitations of semi-flexible or static treatment
of targets and ligand. Over the last decade, advances in the field of computational, proteomics and
genomics have also led to the development of different docking methods which incorporate
protein-ligand flexibility and their different binding conformations. Receptor flexibility accounts
for more accurate binding pose predictions and a more rational depiction of protein binding
interactions with the ligand. Protein flexibility has been included by generating protein ensembles
or by dynamic docking methods. Dynamic docking considers solvation, entropic effects and also
fully explores the drug-receptor binding and recognition from both energetic and mechanistic point
of view. Though in the fast-paced drug discovery program, dynamic docking is computationally
expensive but is being progressively used for screening of large compound libraries to identify the
potential drugs. In this review, a quick introduction is presented to the available docking methods
and their application and limitations in drug discovery.
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Affiliation(s)
- Ritu Jakhar
- Center for Bioinformatics, Maharshi Dayanand University, Rohtak, India
| | - Mehak Dangi
- Center for Bioinformatics, Maharshi Dayanand University, Rohtak, India
| | - Alka Khichi
- Center for Bioinformatics, Maharshi Dayanand University, Rohtak, India
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Gómez-Castro CZ, López-Martínez M, Hernández-Pineda J, Trujillo-Ferrara JG, Padilla-Martínez II. Profiling the interaction of 1-phenylbenzimidazoles to cyclooxygenases. J Mol Recognit 2019; 32:e2801. [PMID: 31353677 DOI: 10.1002/jmr.2801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/03/2019] [Accepted: 06/03/2019] [Indexed: 11/12/2022]
Abstract
In the design of 1-phenylbenzimidazoles as model cyclooxygenase (COX) inhibitors, docking to a series of crystallographic COX structures was performed to evaluate their potential for high-affinity binding and to reproduce the interaction profile of well-known COX inhibitors. The effect of ligand-specific induced fit on the calculations was also studied. To quantitatively compare the pattern of interactions of model compounds to the profile of several cocrystallized COX inhibitors, a geometric parameter, denominated ligand-receptor contact distance (LRCD), was developed. The interaction profile of several model complexes showed similarity to the profile of COX complexes with inhibitors such as iodosuprofen, iodoindomethacin, diclofenac, and flurbiprofen. Shaping of high-affinity binding sites upon ligand-specific induced fit mostly determined both the affinity and the binding mode of the ligands in the docking calculations. The results suggest potential of 1-phenylbenzimidazole derivatives as COX inhibitors on the basis of their predicted affinity and interaction profile to COX enzymes. The analyses also provided insights into the role of induced fit in COX enzymes. While inhibitors produce different local structural changes at the COX ligand binding site, induced fit allows inhibitors in diverse chemical classes to share characteristic interaction patterns that ensure key contacts to be achieved. Different interaction patterns may also be associated with different inhibitory mechanisms.
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Affiliation(s)
- Carlos Z Gómez-Castro
- CONACyT Research Fellow, Universidad Autónoma del Estado de Hidalgo, Instituto de Ciencias Básicas e Ingeniería, Área Académica de Química, Mexico
| | - Margarita López-Martínez
- Laboratorio de Farmacología Experimental, Instituto Nacional de Perinatología, Ciudad de México, Mexico
| | - Jessica Hernández-Pineda
- Laboratorio de Farmacología Experimental, Instituto Nacional de Perinatología, Ciudad de México, Mexico
| | - José G Trujillo-Ferrara
- Sección de Estudios de Posgrado e Investigación, Departamento de Farmacología, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Itzia I Padilla-Martínez
- Laboratorio de Química Supramolecular y Nanociencias, Unidad Profesional Interdisciplinaria de Biotecnología del Instituto Politécnico Nacional, Ciudad de México, Mexico
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8
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Lee HS, Im W. Stalis: A Computational Method for Template-Based Ab Initio Ligand Design. J Comput Chem 2019; 40:1622-1632. [PMID: 30829435 DOI: 10.1002/jcc.25813] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/23/2019] [Accepted: 02/17/2019] [Indexed: 12/20/2022]
Abstract
Proteins interact with small molecules through specific molecular recognition, which is central to essential biological functions in living systems. Therefore, understanding such interactions is crucial for basic sciences and drug discovery. Here, we present Structure template-based ab initio ligand design solution (Stalis), a knowledge-based approach that uses structure templates from the Protein Data Bank libraries of whole ligands and their fragments and generates a set of molecules (virtual ligands) whose structures represent the pocket shape and chemical features of a given target binding site. Our benchmark performance evaluation shows that ligand structure-based virtual screening using virtual ligands from Stalis outperforms a receptor structure-based virtual screening using AutoDock Vina, demonstrating reliable overall screening performance applicable to computational high-throughput screening. However, virtual ligands from Stalis are worse in recognizing active compounds at the small fraction of a rank-ordered list of screened library compounds than crystal ligands, due to the low resolution of the virtual ligand structures. In conclusion, Stalis can facilitate drug discovery research by designing virtual ligands that can be used for fast ligand structure-based virtual screening. Moreover, Stalis provides actual three-dimensional ligand structures that likely bind to a target protein, enabling to gain structural insight into potential ligands. Stalis can be an efficient computational platform for high-throughput ligand design for fundamental biological study and drug discovery research at the proteomic level. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Hui Sun Lee
- Departments of Biological Sciences and Bioengineering, Lehigh University, 111 Research Drive, Bethlehem, Pennsylvania 18015
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University, 111 Research Drive, Bethlehem, Pennsylvania 18015
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9
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Clark JJ, Benson ML, Smith RD, Carlson HA. Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures. PLoS Comput Biol 2019; 15:e1006705. [PMID: 30699115 PMCID: PMC6370239 DOI: 10.1371/journal.pcbi.1006705] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 02/11/2019] [Accepted: 12/07/2018] [Indexed: 11/18/2022] Open
Abstract
Understanding how ligand binding influences protein flexibility is important, especially in rational drug design. Protein flexibility upon ligand binding is analyzed herein using 305 proteins with 2369 crystal structures with ligands (holo) and 1679 without (apo). Each protein has at least two apo and two holo structures for analysis. The inherent variation in structures with and without ligands is first established as a baseline. This baseline is then compared to the change in conformation in going from the apo to holo states to probe induced flexibility. The inherent backbone flexibility across the apo structures is roughly the same as the variation across holo structures. The induced backbone flexibility across apo-holo pairs is larger than that of the apo or holo states, but the increase in RMSD is less than 0.5 Å. Analysis of χ1 angles revealed a distinctly different pattern with significant influences seen for ligand binding on side-chain conformations in the binding site. Within the apo and holo states themselves, the variation of the χ1 angles is the same. However, the data combining both apo and holo states show significant displacements. Upon ligand binding, χ1 angles are frequently pushed to new orientations outside the range seen in the apo states. Influences on binding-site variation could not be easily attributed to features such as ligand size or x-ray structure resolution. By combining these findings, we find that most binding site flexibility is compatible with the common practice in flexible docking, where backbones are kept rigid and side chains are allowed some degree of flexibility.
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Affiliation(s)
- Jordan J. Clark
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Mark L. Benson
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Richard D. Smith
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Heather A. Carlson
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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10
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Shiri F, Pirhadi S, Ghasemi JB. Dynamic structure based pharmacophore modeling of the Acetylcholinesterase reveals several potential inhibitors. J Biomol Struct Dyn 2018; 37:1800-1812. [PMID: 29695192 DOI: 10.1080/07391102.2018.1468281] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Acetylcholinesterase is a critical enzyme that regulates neurotransmission by catalyzing the breakdown of neurotransmitter acetylcholine in synapses of the nervous system. It is an important target for therapeutic drugs that treat Alzheimer's disease. Since, the degree of flexibility of the side chains of the residues in the active-site gorge of Acetylcholinesterase is diverse it results in different bound ligand conformations. The side-chain conformations of Ser293, Tyr341, Leu76, and Val73 are flexible, while the side-chain conformations of Tyr72, Tyr 124, Ser125, Phe295, and Arg296 appear to be fixed. In this study, multi-conformation dynamic pharmacophore models from the donepezyl-binding pocket based on highly populated structures chosen from molecular dynamics simulations were used for screening compounds that can properly bind acetylcholinesterase. Based on these structures, three pharmacophore models were generated. Consequently, 14 hits were retrieved as final candidates by utilizing virtual screening of ZINC database and molecular docking.
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Affiliation(s)
- Fereshteh Shiri
- a Department of Chemistry , University of Zabol , Zabol , Iran
| | - Somayeh Pirhadi
- b Medicinal and Natural Products Chemistry Research Center , Shiraz University of Medical Sciences , Shiraz , Iran
| | - Jahan B Ghasemi
- c School of Chemistry , University College of Science, University of Tehran , Tehran , Iran
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11
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Velazquez HA, Riccardi D, Xiao Z, Quarles LD, Yates CR, Baudry J, Smith JC. Ensemble docking to difficult targets in early-stage drug discovery: Methodology and application to fibroblast growth factor 23. Chem Biol Drug Des 2018; 91:491-504. [PMID: 28944571 PMCID: PMC7983124 DOI: 10.1111/cbdd.13110] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/30/2017] [Accepted: 09/02/2017] [Indexed: 12/23/2022]
Abstract
Ensemble docking is now commonly used in early-stage in silico drug discovery and can be used to attack difficult problems such as finding lead compounds which can disrupt protein-protein interactions. We give an example of this methodology here, as applied to fibroblast growth factor 23 (FGF23), a protein hormone that is responsible for regulating phosphate homeostasis. The first small-molecule antagonists of FGF23 were recently discovered by combining ensemble docking with extensive experimental target validation data (Science Signaling, 9, 2016, ra113). Here, we provide a detailed account of how ensemble-based high-throughput virtual screening was used to identify the antagonist compounds discovered in reference (Science Signaling, 9, 2016, ra113). Moreover, we perform further calculations, redocking those antagonist compounds identified in reference (Science Signaling, 9, 2016, ra113) that performed well on drug-likeness filters, to predict possible binding regions. These predicted binding modes are rescored with the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) approach to calculate the most likely binding site. Our findings suggest that the antagonist compounds antagonize FGF23 through the disruption of protein-protein interactions between FGF23 and fibroblast growth factor receptor (FGFR).
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Affiliation(s)
- Hector A. Velazquez
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Demian Riccardi
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Zhousheng Xiao
- Department of Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Leigh Darryl Quarles
- Department of Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Charless Ryan Yates
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jerome Baudry
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
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12
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Uehara S, Tanaka S. Cosolvent-Based Molecular Dynamics for Ensemble Docking: Practical Method for Generating Druggable Protein Conformations. J Chem Inf Model 2017; 57:742-756. [PMID: 28388074 DOI: 10.1021/acs.jcim.6b00791] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Protein flexibility is a major hurdle in current structure-based virtual screening (VS). In spite of the recent advances in high-performance computing, protein-ligand docking methods still demand tremendous computational cost to take into account the full degree of protein flexibility. In this context, ensemble docking has proven its utility and efficiency for VS studies, but it still needs a rational and efficient method to select and/or generate multiple protein conformations. Molecular dynamics (MD) simulations are useful to produce distinct protein conformations without abundant experimental structures. In this study, we present a novel strategy that makes use of cosolvent-based molecular dynamics (CMD) simulations for ensemble docking. By mixing small organic molecules into a solvent, CMD can stimulate dynamic protein motions and induce partial conformational changes of binding pocket residues appropriate for the binding of diverse ligands. The present method has been applied to six diverse target proteins and assessed by VS experiments using many actives and decoys of DEKOIS 2.0. The simulation results have revealed that the CMD is beneficial for ensemble docking. Utilizing cosolvent simulation allows the generation of druggable protein conformations, improving the VS performance compared with the use of a single experimental structure or ensemble docking by standard MD with pure water as the solvent.
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Affiliation(s)
- Shota Uehara
- Department of Computational Science, Graduate School of System Informatics, Kobe University , 1-1 Rokkodai, Nada, Kobe, Hyogo 657-8501, Japan
| | - Shigenori Tanaka
- Department of Computational Science, Graduate School of System Informatics, Kobe University , 1-1 Rokkodai, Nada, Kobe, Hyogo 657-8501, Japan
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13
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Hamzeh-Mivehroud M, Sokouti B, Dastmalchi S. Molecular Docking at a Glance. Oncology 2017. [DOI: 10.4018/978-1-5225-0549-5.ch030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The current chapter introduces different aspects of molecular docking technique in order to give an overview to the readers about the topics which will be dealt with throughout this volume. Like many other fields of science, molecular docking studies has experienced a lagging period of slow and steady increase in terms of acquiring attention of scientific community as well as its frequency of application, followed by a pronounced era of exponential expansion in theory, methodology, areas of application and performance due to developments in related technologies such as computational resources and theoretical as well as experimental biophysical methods. In the following sections the evolution of molecular docking will be reviewed and its different components including methods, search algorithms, scoring functions, validation of the methods, and area of applications plus few case studies will be touched briefly.
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Affiliation(s)
| | | | - Siavoush Dastmalchi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Iran & School of Pharmacy, Tabriz University of Medical Sciences, Iran
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14
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Rapid activity prediction of HIV-1 integrase inhibitors: harnessing docking energetic components for empirical scoring by chemometric and artificial neural network approaches. J Comput Aided Mol Des 2016; 30:471-88. [DOI: 10.1007/s10822-016-9917-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 06/13/2016] [Indexed: 12/22/2022]
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15
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Bolia A, Ozkan SB. Adaptive BP-Dock: An Induced Fit Docking Approach for Full Receptor Flexibility. J Chem Inf Model 2016; 56:734-46. [PMID: 26971620 DOI: 10.1021/acs.jcim.5b00587] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We present an induced fit docking approach called Adaptive BP-Dock that integrates perturbation response scanning (PRS) with the flexible docking protocol of RosettaLigand in an adaptive manner. We first perturb the binding pocket residues of a receptor and obtain a new conformation based on the residue response fluctuation profile using PRS. Next, we dock a ligand to this new conformation by RosettaLigand, where we repeat these steps for several iterations. We test this approach on several protein test sets including difficult unbound docking cases such as HIV-1 reverse transcriptase and HIV-1 protease. Adaptive BP-Dock results show better correlation with experimental binding affinities compared to other docking protocols. Overall, the results imply that Adaptive BP-Dock can easily capture binding induced conformational changes by simultaneous sampling of protein and ligand conformations. This can provide faster and efficient docking of novel targets for rational drug design.
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Affiliation(s)
- Ashini Bolia
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
| | - S Banu Ozkan
- Department of Physics, Center for Biological Physics, Arizona State University , Tempe, Arizona 85287, United States
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16
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Binding of phenothiazines into allosteric hydrophobic pocket of human thioredoxin 1. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 45:279-86. [PMID: 26820562 DOI: 10.1007/s00249-016-1113-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/25/2015] [Accepted: 01/10/2016] [Indexed: 10/22/2022]
Abstract
Thioredoxins are multifunctional oxidoreductase proteins implicated in the antioxidant cellular apparatus and oxidative stress. They are involved in several pathologies and are promising anticancer targets. Identification of noncatalytic binding sites is of great interest for designing new allosteric inhibitors of thioredoxin. In a recent work, we predicted normal mode motions of human thioredoxin 1 and identified two major putative hydrophobic binding sites. In this work we investigated noncovalent interactions of human thioredoxin 1 with three phenotiazinic drugs acting as prooxidant compounds by using molecular docking and circular dichroism spectrometry to probe ligand binding into the previously predicted allosteric hydrophobic pockets. Our in silico and CD spectrometry experiments suggested one preferred allosteric binding site involving helix 3 and adopting the best druggable conformation identified by NMA. The CD spectra showed binding of thioridazine into thioredoxin 1 and suggested partial helix unfolding, which most probably concerns helix 3. Taken together, these data support the strategy to design thioredoxin inhibitors targeting a druggable allosteric binding site.
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17
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Gamaleldin Elsadig Karar M, Matei MF, Jaiswal R, Illenberger S, Kuhnert N. Neuraminidase inhibition of Dietary chlorogenic acids and derivatives – potential antivirals from dietary sources. Food Funct 2016; 7:2052-9. [DOI: 10.1039/c5fo01412c] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Plants rich in chlorogenic acids (CGAs), caffeic acids and their derivatives have been found to exert antiviral effects against influenza virus neuroaminidase.
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Affiliation(s)
| | - Marius-Febi Matei
- Department of Life Sciences and Chemistry
- Jacobs University Bremen
- 28759 Bremen
- Germany
| | - Rakesh Jaiswal
- Department of Life Sciences and Chemistry
- Jacobs University Bremen
- 28759 Bremen
- Germany
| | - Susanne Illenberger
- Department of Life Sciences and Chemistry
- Jacobs University Bremen
- 28759 Bremen
- Germany
| | - Nikolai Kuhnert
- Department of Life Sciences and Chemistry
- Jacobs University Bremen
- 28759 Bremen
- Germany
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18
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Cerqueira NMFSA, Gesto D, Oliveira EF, Santos-Martins D, Brás NF, Sousa SF, Fernandes PA, Ramos MJ. Receptor-based virtual screening protocol for drug discovery. Arch Biochem Biophys 2015; 582:56-67. [PMID: 26045247 DOI: 10.1016/j.abb.2015.05.011] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 12/12/2022]
Abstract
Computational aided drug design (CADD) is presently a key component in the process of drug discovery and development as it offers great promise to drastically reduce cost and time requirements. In the pharmaceutical arena, virtual screening is normally regarded as the top CADD tool to screen large libraries of chemical structures and reduce them to a key set of likely drug candidates regarding a specific protein target. This chapter provides a comprehensive overview of the receptor-based virtual screening process and of its importance in the present drug discovery and development paradigm. Following a focused contextualization on the subject, the main stages of a virtual screening campaign, including its strengths and limitations, are the subject of particular attention in this review. In all of these stages special consideration will be given to practical issues that are normally the Achilles heel of the virtual screening process.
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Affiliation(s)
- Nuno M F S A Cerqueira
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Diana Gesto
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Eduardo F Oliveira
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Diogo Santos-Martins
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Natércia F Brás
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Sérgio F Sousa
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Pedro A Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Maria J Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal.
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19
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Choudhury C, Priyakumar UD, Sastry GN. Dynamics based pharmacophore models for screening potential inhibitors of mycobacterial cyclopropane synthase. J Chem Inf Model 2015; 55:848-60. [PMID: 25751016 DOI: 10.1021/ci500737b] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The therapeutic challenges in the treatment of tuberculosis demand multidisciplinary approaches for the identification of potential drug targets as well as fast and accurate techniques to screen huge chemical libraries. Mycobacterial cyclopropane synthase (CmaA1) has been shown to be essential for the survival of the bacteria due to its critical role in the synthesis of mycolic acids. The present study proposes pharmacophore models based on the structure of CmaA1 taking into account its various states in the cyclopropanation process, and their dynamic nature as assessed using molecular dynamics (MD) simulations. The qualities of these pharmacophore models were validated by mapping 23 molecules that have been previously reported to exhibit inhibitory activities on CmaA1. Additionally, 1398 compounds that have been shown to be inactive for tuberculosis were collected from the ChEMBL database and were screened against the models for validation. The models were further validated by comparing the results from pharmacophore mapping with the results obtained from docking these molecules with the respective protein structures. The best models are suggested by validating all the models based on their screening abilities and by comparing with docking results. The models generated from the MD trajectories were found to perform better than the one generated based on the crystal structure demonstrating the importance of incorporating receptor flexibility in drug design.
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Affiliation(s)
- Chinmayee Choudhury
- †Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information and Technology, Hyderabad 500032, India
- ‡Centre for Molecular Modeling, Indian Institute of Chemical Technology, Hyderabad 500007, India
| | - U Deva Priyakumar
- †Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information and Technology, Hyderabad 500032, India
| | - G Narahari Sastry
- ‡Centre for Molecular Modeling, Indian Institute of Chemical Technology, Hyderabad 500007, India
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20
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Zhang H, Wang Y, Xu F. Impact of the subtle differences in MMP-12 structure on Glide-based molecular docking for pose prediction of inhibitors. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Ardakani A, Ghasemi JB. Identification of novel inhibitors of HIV-1 integrase using pharmacophore-based virtual screening combined with molecular docking strategies. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0545-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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Abstract
Virtual screening has become a standard tool in drug discovery to identify novel lead compounds that target a biomolecule of interest. I present several concepts in ligand-based and structure-based virtual screening and discuss some of the current shortcomings and new developments. I also highlight approaches that combine concepts from structure- and ligand-based design.
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Affiliation(s)
- Markus Lill
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
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23
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Jayaram B, Singh T, Mukherjee G, Mathur A, Shekhar S, Shekhar V. Sanjeevini: a freely accessible web-server for target directed lead molecule discovery. BMC Bioinformatics 2012; 13 Suppl 17:S7. [PMID: 23282245 PMCID: PMC3521208 DOI: 10.1186/1471-2105-13-s17-s7] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Background Computational methods utilizing the structural and functional information help to understand specific molecular recognition events between the target biomolecule and candidate hits and make it possible to design improved lead molecules for the target. Results Sanjeevini represents a massive on-going scientific endeavor to provide to the user, a freely accessible state of the art software suite for protein and DNA targeted lead molecule discovery. It builds in several features, including automated detection of active sites, scanning against a million compound library for identifying hit molecules, all atom based docking and scoring and various other utilities to design molecules with desired affinity and specificity against biomolecular targets. Each of the modules is thoroughly validated on a large dataset of protein/DNA drug targets. Conclusions The article presents Sanjeevini, a freely accessible user friendly web-server, to aid in drug discovery. It is implemented on a tera flop cluster and made accessible via a web-interface at http://www.scfbio-iitd.res.in/sanjeevini/sanjeevini.jsp. A brief description of various modules, their scientific basis, validation, and how to use the server to develop in silico suggestions of lead molecules is provided.
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Affiliation(s)
- B Jayaram
- Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India.
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24
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Beier C, Zacharias M. Tackling the challenges posed by target flexibility in drug design. Expert Opin Drug Discov 2012; 5:347-59. [PMID: 22823087 DOI: 10.1517/17460441003713462] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
IMPORTANCE OF THE FIELD Current computational docking methods are often effective in predicting accurate drug-binding geometries in cases of relatively rigid target structures. However, binding of drug-like ligands to protein receptor molecules frequently involves or even requires conformational adaptation. Realistic prediction of ligand-receptor binding geometries and complex stability needs in many cases an appropriate inclusion of conformational changes, not only for the ligand, but also for the receptor molecule. AREAS COVERED IN THIS REVIEW Recent approaches to efficiently account for target receptor flexibility during docking simulations are reviewed. WHAT THE READER WILL GAIN The reader will gain insights into methods to efficiently treat protein side-chain flexibility and approaches for continuous adaptation of backbone conformations in pre-calculated essential or soft collective degrees of freedom. In addition, molecular dynamics or Monte Carlo based methods providing simultaneous inclusion of receptor and ligand flexibility are discussed as well as promising new developments to generate conformationally diverse ensembles of a protein structure. The large variety of possible conformational changes in proteins on ligand binding is illustrated for the enzyme reverse transcriptase of HIV-1, which is an important drug target. TAKE HOME MESSAGE If the backbone conformation of the binding site does not change, current docking programs can perform well by taking side-chain reorientations into account only. Future progress to account for full target flexibility in docking requires both accurate prediction of the essential modes of backbone motion and improvements in scoring to enhance selectivity. Thus, the scoring function should realistically cover energetic and particularly entropic contributions to binding, which would allow more realistic estimates of binding free energies.
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Affiliation(s)
- Christian Beier
- Jacobs University Bremen, School of Engineering and Science, Campus Ring 1, D-28759 Bremen, Germany
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25
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Flick J, Tristram F, Wenzel W. Modeling loop backbone flexibility in receptor-ligand docking simulations. J Comput Chem 2012; 33:2504-15. [DOI: 10.1002/jcc.23087] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Revised: 06/15/2012] [Accepted: 07/09/2012] [Indexed: 12/20/2022]
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26
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Abstract
Structure-based drug design has become an essential tool for rapid lead discovery and optimization. As available structural information has increased, researchers have become increasingly aware of the importance of protein flexibility for accurate description of the native state. Typical protein-ligand docking efforts still rely on a single rigid receptor, which is an incomplete representation of potential binding conformations of the protein. These rigid docking efforts typically show the best performance rates between 50 and 75%, while fully flexible docking methods can enhance pose prediction up to 80-95%. This review examines the current toolbox for flexible protein-ligand docking and receptor surface mapping. Present limitations and possibilities for future development are discussed.
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Affiliation(s)
- Katrina W. Lexa
- Department of Medicinal Chemistry, University of Michigan, 428 Church Street, Ann Arbor, MI 48109-1065, USA
| | - Heather A. Carlson
- Department of Medicinal Chemistry, University of Michigan, 428 Church Street, Ann Arbor, MI 48109-1065, USA
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27
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Korb O, Olsson TSG, Bowden SJ, Hall RJ, Verdonk ML, Liebeschuetz JW, Cole JC. Potential and limitations of ensemble docking. J Chem Inf Model 2012; 52:1262-74. [PMID: 22482774 DOI: 10.1021/ci2005934] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A major problem in structure-based virtual screening applications is the appropriate selection of a single or even multiple protein structures to be used in the virtual screening process. A priori it is unknown which protein structure(s) will perform best in a virtual screening experiment. We investigated the performance of ensemble docking, as a function of ensemble size, for eight targets of pharmaceutical interest. Starting from single protein structure docking results, for each ensemble size up to 500,000 combinations of protein structures were generated, and, for each ensemble, pose prediction and virtual screening results were derived. Comparison of single to multiple protein structure results suggests improvements when looking at the performance of the worst and the average over all single protein structures to the performance of the worst and average over all protein ensembles of size two or greater, respectively. We identified several key factors affecting ensemble docking performance, including the sampling accuracy of the docking algorithm, the choice of the scoring function, and the similarity of database ligands to the cocrystallized ligands of ligand-bound protein structures in an ensemble. Due to these factors, the prospective selection of optimum ensembles is a challenging task, shown by a reassessment of published ensemble selection protocols.
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Affiliation(s)
- Oliver Korb
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK.
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28
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A reverse combination of structure-based and ligand-based strategies for virtual screening. J Comput Aided Mol Des 2012; 26:319-27. [DOI: 10.1007/s10822-012-9558-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 02/24/2012] [Indexed: 10/28/2022]
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29
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Singh T, Biswas D, Jayaram B. AADS--an automated active site identification, docking, and scoring protocol for protein targets based on physicochemical descriptors. J Chem Inf Model 2011; 51:2515-27. [PMID: 21877713 DOI: 10.1021/ci200193z] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report here a robust automated active site detection, docking, and scoring (AADS) protocol for proteins with known structures. The active site finder identifies all cavities in a protein and scores them based on the physicochemical properties of functional groups lining the cavities in the protein. The accuracy realized on 620 proteins with sizes ranging from 100 to 600 amino acids with known drug active sites is 100% when the top ten cavity points are considered. These top ten cavity points identified are then submitted for an automated docking of an input ligand/candidate molecule. The docking protocol uses an all atom energy based Monte Carlo method. Eight low energy docked structures corresponding to different locations and orientations of the candidate molecule are stored at each cavity point giving 80 docked structures overall which are then ranked using an effective free energy function and top five structures are selected. The predicted structure and energetics of the complexes agree quite well with experiment when tested on a data set of 170 protein-ligand complexes with known structures and binding affinities. The AADS methodology is implemented on an 80 processor cluster and presented as a freely accessible, easy to use tool at http://www.scfbio-iitd.res.in/dock/ActiveSite_new.jsp .
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Affiliation(s)
- Tanya Singh
- Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
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30
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Hassan S, Logambiga P, Raman AM, Subazini TK, Kumaraswami V, Hanna LE. MtbSD--a comprehensive structural database for Mycobacterium tuberculosis. Tuberculosis (Edinb) 2011; 91:556-62. [PMID: 21880546 DOI: 10.1016/j.tube.2011.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 08/06/2011] [Accepted: 08/08/2011] [Indexed: 11/25/2022]
Abstract
The Mycobacterium tuberculosis Structural Database (MtbSD) (http://bmi.icmr.org.in/mtbsd/MtbSD.php) is a relational database for the study of protein structures of M. tuberculosis. It currently holds information on description, reaction catalyzed and domains involved, active sites, structural homologues and similarities between bound and cognate ligands, for all the 857 protein structures that are available for M. tb proteins. The database will be a valuable resource for TB researchers to select the appropriate protein-ligand complex of a given protein for molecular modelling, docking, virtual screening and structure-based drug designing.
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Affiliation(s)
- Sameer Hassan
- National Institute for Research in Tuberculosis, Chetpet, Chennai 600 031, India
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31
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Cabrera ÁC, Gil-Redondo R, Perona A, Gago F, Morreale A. VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface. J Comput Aided Mol Des 2011; 25:813-24. [DOI: 10.1007/s10822-011-9465-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 08/01/2011] [Indexed: 10/17/2022]
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32
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Ahmed A, Rippmann F, Barnickel G, Gohlke H. A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins. J Chem Inf Model 2011; 51:1604-22. [PMID: 21639141 DOI: 10.1021/ci100461k] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A three-step approach for multiscale modeling of protein conformational changes is presented that incorporates information about preferred directions of protein motions into a geometric simulation algorithm. The first two steps are based on a rigid cluster normal-mode analysis (RCNMA). Low-frequency normal modes are used in the third step (NMSim) to extend the recently introduced idea of constrained geometric simulations of diffusive motions in proteins by biasing backbone motions of the protein, whereas side-chain motions are biased toward favorable rotamer states. The generated structures are iteratively corrected regarding steric clashes and stereochemical constraint violations. The approach allows performing three simulation types: unbiased exploration of conformational space; pathway generation by a targeted simulation; and radius of gyration-guided simulation. When applied to a data set of proteins with experimentally observed conformational changes, conformational variabilities are reproduced very well for 4 out of 5 proteins that show domain motions, with correlation coefficients r > 0.70 and as high as r = 0.92 in the case of adenylate kinase. In 7 out of 8 cases, NMSim simulations starting from unbound structures are able to sample conformations that are similar (root-mean-square deviation = 1.0-3.1 Å) to ligand bound conformations. An NMSim generated pathway of conformational change of adenylate kinase correctly describes the sequence of domain closing. The NMSim approach is a computationally efficient alternative to molecular dynamics simulations for conformational sampling of proteins. The generated conformations and pathways of conformational transitions can serve as input to docking approaches or as starting points for more sophisticated sampling techniques.
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Affiliation(s)
- Aqeel Ahmed
- Department of Biological Sciences, Molecular Bioinformatics Group, Goethe University, Frankfurt, Germany
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33
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Danielson ML, Desai PV, Mohutsky MA, Wrighton SA, Lill MA. Potentially increasing the metabolic stability of drug candidates via computational site of metabolism prediction by CYP2C9: The utility of incorporating protein flexibility via an ensemble of structures. Eur J Med Chem 2011; 46:3953-63. [PMID: 21703735 DOI: 10.1016/j.ejmech.2011.05.067] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 05/24/2011] [Accepted: 05/26/2011] [Indexed: 10/18/2022]
Abstract
Cytochrome P450 enzymes are responsible for metabolizing many endogenous and xenobiotic molecules encountered by the human body. It has been estimated that 75% of all drugs are metabolized by cytochrome P450 enzymes. Thus, predicting a compound's potential sites of metabolism (SOM) is highly advantageous early in the drug development process. We have combined molecular dynamics, AutoDock Vina docking, the neighboring atom type (NAT) reactivity model, and a solvent-accessible surface-area term to form a reactivity-accessibility model capable of predicting SOM for cytochrome P450 2C9 substrates. To investigate the importance of protein flexibility during the ligand-binding process, the results of SOM prediction using a static protein structure for docking were compared to SOM prediction using multiple protein structures in ensemble docking. The results reported here indicate that ensemble docking increases the number of ligands that can be docked in a bioactive conformation (ensemble: 96%, static: 85%) but only leads to a slight improvement (49% vs. 44%) in predicting an experimentally known SOM in the top-1 position for a ligand library of 75 CYP2C9 substrates. Using ensemble docking, the reactivity-accessibility model accurately predicts SOM in the top-1 ranked position for 49% of the ligand library and considering the top-3 predicted sites increases the prediction success rate to approximately 70% of the ligand library. Further classifying the substrate library according to K(m) values leads to an improvement in SOM prediction for substrates with low K(m) values (57% at top-1). While the current predictive power of the reactivity-accessibility model still leaves significant room for improvement, the results illustrate the usefulness of this method to identify key protein-ligand interactions and guide structural modifications of the ligand to increase its metabolic stability.
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Affiliation(s)
- Matthew L Danielson
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA
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34
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35
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Rognan D. Docking Methods for Virtual Screening: Principles and Recent Advances. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2011. [DOI: 10.1002/9783527633326.ch6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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36
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Kokh DB, Wade RC, Wenzel W. Receptor flexibility in small‐molecule docking calculations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.29] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Daria B. Kokh
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Heidelberg, Germany
| | - Rebecca C. Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Heidelberg, Germany
| | - Wolfgang Wenzel
- Karlsruhe Institute of Technology, Institute of Nanotechnology, Karlsruhe, Germany
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37
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Xu M, Lill MA. Significant enhancement of docking sensitivity using implicit ligand sampling. J Chem Inf Model 2011; 51:693-706. [PMID: 21375306 DOI: 10.1021/ci100457t] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The efficient and accurate quantification of protein-ligand interactions using computational methods is still a challenging task. Two factors strongly contribute to the failure of docking methods to predict free energies of binding accurately: the insufficient incorporation of protein flexibility coupled to ligand binding and the neglected dynamics of the protein-ligand complex in current scoring schemes. We have developed a new methodology, named the 'ligand-model' concept, to sample protein conformations that are relevant for binding structurally diverse sets of ligands. In the ligand-model concept, molecular-dynamics (MD) simulations are performed with a virtual ligand, represented by a collection of functional groups that binds to the protein and dynamically changes its shape and properties during the simulation. The ligand model essentially represents a large ensemble of different chemical species binding to the same target protein. Representative protein structures were obtained from the MD simulation, and docking was performed into this ensemble of protein conformation. Similar binding poses were clustered, and the averaged score was utilized to rerank the poses. We demonstrate that the ligand-model approach yields significant improvements in predicting native-like binding poses and quantifying binding affinities compared to static docking and ensemble docking simulations into protein structures generated from an apo MD simulation.
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Affiliation(s)
- Mengang Xu
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
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38
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Barakat K, Tuszynski J. Relaxed complex scheme suggests novel inhibitors for the lyase activity of DNA polymerase beta. J Mol Graph Model 2011; 29:702-16. [DOI: 10.1016/j.jmgm.2010.12.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 12/02/2010] [Accepted: 12/06/2010] [Indexed: 11/26/2022]
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39
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Brooijmans N, Cross JB, Humblet C. Biased retrieval of chemical series in receptor-based virtual screening. J Comput Aided Mol Des 2010; 24:1053-62. [DOI: 10.1007/s10822-010-9394-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 10/19/2010] [Indexed: 11/30/2022]
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40
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Brylinski M, Lee SY, Zhou H, Skolnick J. The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement. J Struct Biol 2010; 173:558-69. [PMID: 20850544 DOI: 10.1016/j.jsb.2010.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 09/08/2010] [Accepted: 09/10/2010] [Indexed: 01/01/2023]
Abstract
Exhaustive exploration of molecular interactions at the level of complete proteomes requires efficient and reliable computational approaches to protein function inference. Ligand docking and ranking techniques show considerable promise in their ability to quantify the interactions between proteins and small molecules. Despite the advances in the development of docking approaches and scoring functions, the genome-wide application of many ligand docking/screening algorithms is limited by the quality of the binding sites in theoretical receptor models constructed by protein structure prediction. In this study, we describe a new template-based method for the local refinement of ligand-binding regions in protein models using remotely related templates identified by threading. We designed a Support Vector Regression (SVR) model that selects correct binding site geometries in a large ensemble of multiple receptor conformations. The SVR model employs several scoring functions that impose geometrical restraints on the Cα positions, account for the specific chemical environment within a binding site and optimize the interactions with putative ligands. The SVR score is well correlated with the RMSD from the native structure; in 47% (70%) of the cases, the Pearson's correlation coefficient is >0.5 (>0.3). When applied to weakly homologous models, the average heavy atom, local RMSD from the native structure of the top-ranked (best of top five) binding site geometries is 3.1Å (2.9Å) for roughly half of the targets; this represents a 0.1 (0.3)Å average improvement over the original predicted structure. Focusing on the subset of strongly conserved residues, the average heavy atom RMSD is 2.6Å (2.3Å). Furthermore, we estimate the upper bound of template-based binding site refinement using only weakly related proteins to be ∼2.6Å RMSD. This value also corresponds to the plasticity of the ligand-binding regions in distant homologues. The Binding Site Refinement (BSR) approach is available to the scientific community as a web server that can be accessed at http://cssb.biology.gatech.edu/bsr/.
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Affiliation(s)
- Michal Brylinski
- Center for the Study of Systems Biology, Georgia Institute of Technology, Atlanta, GA 30318, USA
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Amaro RE, Li WW. Emerging methods for ensemble-based virtual screening. Curr Top Med Chem 2010; 10:3-13. [PMID: 19929833 DOI: 10.2174/156802610790232279] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Accepted: 09/16/2009] [Indexed: 02/06/2023]
Abstract
Ensemble based virtual screening refers to the use of conformational ensembles from crystal structures, NMR studies or molecular dynamics simulations. It has gained greater acceptance as advances in the theoretical framework, computational algorithms, and software packages enable simulations at longer time scales. Here we focus on the use of computationally generated conformational ensembles and emerging methods that use these ensembles for discovery, such as the Relaxed Complex Scheme or Dynamic Pharmacophore Model. We also discuss the more rigorous physics-based computational techniques such as accelerated molecular dynamics and thermodynamic integration and their applications in improving conformational sampling or the ranking of virtual screening hits. Finally, technological advances that will help make virtual screening tools more accessible to a wider audience in computer aided drug design are discussed.
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Affiliation(s)
- Rommie E Amaro
- Department of Pharmaceutical Sciences and Department of Information and Computer Science, University of California, Irvine, CA 92697, USA.
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42
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Brooijmans N, Humblet C. Chemical space sampling by different scoring functions and crystal structures. J Comput Aided Mol Des 2010; 24:433-47. [DOI: 10.1007/s10822-010-9356-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 04/05/2010] [Indexed: 10/19/2022]
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Abstract
The success of ligand docking calculations typically depends on the quality of the receptor structure. Given improvements in protein structure prediction approaches, approximate protein models now can be routinely obtained for the majority of gene products in a given proteome. Structure-based virtual screening of large combinatorial libraries of lead candidates against theoretically modeled receptor structures requires fast and reliable docking techniques capable of dealing with structural inaccuracies in protein models. Here, we present Q-Dock(LHM), a method for low-resolution refinement of binding poses provided by FINDSITE(LHM), a ligand homology modeling approach. We compare its performance to that of classical ligand docking approaches in ligand docking against a representative set of experimental (both holo and apo) as well as theoretically modeled receptor structures. Docking benchmarks reveal that unlike all-atom docking, Q-Dock(LHM) exhibits the desired tolerance to the receptor's structure deformation. Our results suggest that the use of an evolution-based approach to ligand homology modeling followed by fast low-resolution refinement is capable of achieving satisfactory performance in ligand-binding pose prediction with promising applicability to proteome-scale applications.
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Affiliation(s)
- Michal Brylinski
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, GA 30318
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, GA 30318
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Lee HS, Lee CS, Kim JS, Kim DH, Choe H. Improving virtual screening performance against conformational variations of receptors by shape matching with ligand binding pocket. J Chem Inf Model 2010; 49:2419-28. [PMID: 19852439 DOI: 10.1021/ci9002365] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this report, we present a novel virtual high-throughput screening methodology to assist in computer-aided drug discovery. Our method, designated as SLIM, involves ligand-free shape and chemical feature matching. The procedure takes advantage of a negative image of a binding pocket in a target receptor. The negative image is a set of virtual atoms representing the inner shape and chemical features of the binding pocket. Using this image, SLIM implements a shape-based similarity search based on molecular volume superposition for the ensemble of conformers of each molecule. The superposed structures, prioritized by shape similarity, are subjected to comparison of chemical feature similarities. To validate the merits of the SLIM method, we compared its performance with those of three distinct widely used tools ROCS, GLIDE, and GOLD. ROCS was selected as a representative of the ligand-centric methods, and docking programs GLIDE and GOLD as representatives of the receptor-centric methods. Our data suggest that SLIM has overall hit ranking ability that is comparable to that of the docking method, retaining the high computational speed of the ligand-centric method. It is notable that the SLIM method offers consistently reliable screening quality against conformational variations of receptors, whereas the docking methods have limited screening performance.
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Affiliation(s)
- Hui Sun Lee
- Department of Physiology, University of Ulsan College of Medicine, Seoul 138-736, South Korea
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45
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Seeliger D, de Groot BL. Conformational transitions upon ligand binding: holo-structure prediction from apo conformations. PLoS Comput Biol 2010; 6:e1000634. [PMID: 20066034 PMCID: PMC2796265 DOI: 10.1371/journal.pcbi.1000634] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 12/07/2009] [Indexed: 11/19/2022] Open
Abstract
Biological function of proteins is frequently associated with the formation of complexes with small-molecule ligands. Experimental structure determination of such complexes at atomic resolution, however, can be time-consuming and costly. Computational methods for structure prediction of protein/ligand complexes, particularly docking, are as yet restricted by their limited consideration of receptor flexibility, rendering them not applicable for predicting protein/ligand complexes if large conformational changes of the receptor upon ligand binding are involved. Accurate receptor models in the ligand-bound state (holo structures), however, are a prerequisite for successful structure-based drug design. Hence, if only an unbound (apo) structure is available distinct from the ligand-bound conformation, structure-based drug design is severely limited. We present a method to predict the structure of protein/ligand complexes based solely on the apo structure, the ligand and the radius of gyration of the holo structure. The method is applied to ten cases in which proteins undergo structural rearrangements of up to 7.1 A backbone RMSD upon ligand binding. In all cases, receptor models within 1.6 A backbone RMSD to the target were predicted and close-to-native ligand binding poses were obtained for 8 of 10 cases in the top-ranked complex models. A protocol is presented that is expected to enable structure modeling of protein/ligand complexes and structure-based drug design for cases where crystal structures of ligand-bound conformations are not available.
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Affiliation(s)
- Daniel Seeliger
- Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bert L. de Groot
- Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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Bhutoria S, Ghoshal N. Deciphering ligand dependent degree of binding site closure and its implication in inhibitor design: A modeling study on human adenosine kinase. J Mol Graph Model 2009; 28:577-91. [PMID: 20089430 DOI: 10.1016/j.jmgm.2009.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 12/04/2009] [Accepted: 12/08/2009] [Indexed: 11/26/2022]
Abstract
Protein flexibility plays a significant role in drug research due to its effect on accurate prediction of ligand binding mode and activity. Adenosine kinase (AK) represents a highly flexible binding site and is known to exhibit large conformational changes as a result of substrate or inhibitor binding. Here we propose a semi-open conformation for ligand binding in human AK, in addition to the known closed and open forms. The modeling study illustrates the necessity of thorough understanding of the conformational states of protein for docking and binding mode prediction. It has been shown that predicting activity in the context of correct binding mode can improve the insight into conserved interactions and mechanism of action for inhibition of AK. Integrating the knowledge about the binding modes of ligands in different conformational states of the protein, separate pharmacophore models were generated and used for virtual screening to explore potential novel hits. In addition, 2D descriptor based clustering was done to differentiate the ligands, binding to closed, semi-open and open conformations of human AK. The results indicated that binding of all AK inhibitors cannot be described by same rules, instead, they represent a rule based preference for inhibition. This inference about tubercidins binding to semi-open conformation of human AK may facilitate in finding much extensive space for AK inhibitors.
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Affiliation(s)
- Savita Bhutoria
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology (A unit of CSIR), 4 Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
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Barakat K, Mane J, Friesen D, Tuszynski J. Ensemble-based virtual screening reveals dual-inhibitors for the p53-MDM2/MDMX interactions. J Mol Graph Model 2009; 28:555-68. [PMID: 20056466 DOI: 10.1016/j.jmgm.2009.12.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 12/04/2009] [Accepted: 12/08/2009] [Indexed: 10/20/2022]
Abstract
The p53 protein, a guardian of the genome, is inactivated by mutations or deletions in approximately half of human tumors. While in the rest of human tumors, p53 is expressed in wild-type form, yet it is inhibited by over-expression of its cellular regulators MDM2 and MDMX proteins. Although the p53-binding sites within the MDMX and MDM2 proteins are closely related, known MDM2 small-molecule inhibitors have been shown experimentally not to bind to its homolog, MDMX. As a result, the activity of these inhibitors including Nutlin3 is compromised in tumor cells over-expressing MDMX, preventing these compounds from fully activating the p53 protein. Here, we applied the relaxed complex scheme (RCS) to allow for the full receptor flexibility in screening for dual-inhibitors that can mutually antagonize the two p53-regulator proteins. First, we filtered the NCI diversity set, DrugBank compounds and a derivative library for MDM2-inhibitors against 28 dominant MDM2-conformations. Then, we screened the MDM2 top hits against the binding site of p53 within the MDMX target. Results described herein identify a set of compounds that have been computationally predicted to ultimately activate the p53 pathway in tumor cells retaining the wild-type protein.
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Affiliation(s)
- Khaled Barakat
- Department of Physics, University of Alberta, Edmonton, AB, Canada
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Kazemi S, Krüger D, Sirockin F, Gohlke H. Elastic Potential Grids: Accurate and Efficient Representation of Intermolecular Interactions for Fully Flexible Docking. ChemMedChem 2009; 4:1264-8. [DOI: 10.1002/cmdc.200900146] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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49
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Juhl PB, Trodler P, Tyagi S, Pleiss J. Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking. BMC STRUCTURAL BIOLOGY 2009; 9:39. [PMID: 19493341 PMCID: PMC2699341 DOI: 10.1186/1472-6807-9-39] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 06/03/2009] [Indexed: 11/15/2022]
Abstract
Background Previously, ways to adapt docking programs that were developed for modelling inhibitor-receptor interaction have been explored. Two main issues were discussed. First, when trying to model catalysis a reaction intermediate of the substrate is expected to provide more valid information than the ground state of the substrate. Second, the incorporation of protein flexibility is essential for reliable predictions. Results Here we present a predictive and robust method to model substrate specificity and enantioselectivity of lipases and esterases that uses reaction intermediates and incorporates protein flexibility. Substrate-imprinted docking starts with covalent docking of reaction intermediates, followed by geometry optimisation of the resulting enzyme-substrate complex. After a second round of docking the same substrate into the geometry-optimised structures, productive poses are identified by geometric filter criteria and ranked by their docking scores. Substrate-imprinted docking was applied in order to model (i) enantioselectivity of Candida antarctica lipase B and a W104A mutant, (ii) enantioselectivity and substrate specificity of Candida rugosa lipase and Burkholderia cepacia lipase, and (iii) substrate specificity of an acetyl- and a butyrylcholine esterase toward the substrates acetyl- and butyrylcholine. Conclusion The experimentally observed differences in selectivity and specificity of the enzymes were reproduced with an accuracy of 81%. The method was robust toward small differences in initial structures (different crystallisation conditions or a co-crystallised ligand), although large displacements of catalytic residues often resulted in substrate poses that did not pass the geometric filter criteria.
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Affiliation(s)
- P Benjamin Juhl
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
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50
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Bolstad ESD, Anderson AC. In pursuit of virtual lead optimization: pruning ensembles of receptor structures for increased efficiency and accuracy during docking. Proteins 2009; 75:62-74. [PMID: 18781587 DOI: 10.1002/prot.22214] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Representing receptors as ensembles of protein conformations during docking is a powerful method to approximate protein flexibility and increase the accuracy of the resulting ranked list of compounds. Unfortunately, docking compounds against a large number of ensemble members can increase computational cost and time investment. In this article, we present an efficient method to evaluate and select the most contributive ensemble members prior to docking for targets with a conserved core of residues that bind a ligand moiety. We observed that ensemble members that preserve the geometry of the active site core are most likely to place ligands in the active site with a conserved orientation, generally rank ligands correctly and increase interactions with the receptor. A relative distance approach is used to quantify the preservation of the three-dimensional interatomic distances of the conserved ligand-binding atoms and prune large ensembles quickly. In this study, we investigate dihydrofolate reductase as an example of a protein with a conserved core; however, this method for accurately selecting relevant ensemble members a priori can be applied to any system with a conserved ligand-binding core, including HIV-1 protease, kinases, and acetylcholinesterase. Representing a drug target as a pruned ensemble during in silico screening should increase the accuracy and efficiency of high-throughput analyses of lead analogs.
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Affiliation(s)
- Erin S D Bolstad
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, USA
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