101
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Taha MO, Habash M, Al-Hadidi Z, Al-Bakri A, Younis K, Sisan S. Docking-based comparative intermolecular contacts analysis as new 3-D QSAR concept for validating docking studies and in silico screening: NMT and GP inhibitors as case studies. J Chem Inf Model 2011; 51:647-69. [PMID: 21370899 DOI: 10.1021/ci100368t] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The significant role played by docking algorithms in drug discovery combined with their serious pitfalls prompted us to envisage a novel concept for validating docking solutions, namely, docking-based comparative intermolecular contacts analysis (dbCICA). This novel approach is based on the number and quality of contacts between docked ligands and amino acid residues within the binding pocket. It assesses a particular docking configuration on the basis of its ability to align a set of ligands within a corresponding binding pocket in such a way that potent ligands come into contact with binding site spots distinct from those approached by low-affinity ligands and vice versa. In other words, dbCICA evaluates the consistency of docking by assessing the correlation between ligands' affinities and their contacts with binding site spots. Optimal dbCICA models can be translated into valid pharmacophore models that can be used as 3-D search queries to mine structural databases for new bioactive compounds. dbCICA was implemented to search for new inhibitors of candida N-myristoyl transferase as potential antifungal agents and glycogen phosphorylase (GP) inhibitors as potential antidiabetic agents. The process culminated in five selective micromolar antifungal leads and nine GP inhibitory leads.
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Affiliation(s)
- Mutasem O Taha
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Amman, Jordan.
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102
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103
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Abstract
Results of a previous docking study are reanalyzed and extended to include results from the docking program FRED and a detailed statistical analysis of both structure reproduction and virtual screening results. FRED is run both in a traditional docking mode and in a hybrid mode that makes use of the structure of a bound ligand in addition to the protein structure to screen molecules. This analysis shows that most docking programs are effective overall but highly inconsistent, tending to do well on one system and poorly on the next. Comparing methods, the difference in mean performance on DUD is found to be statistically significant (95% confidence) 61% of the time when using a global enrichment metric (AUC). Early enrichment metrics are found to have relatively poor statistical power, with 0.5% early enrichment only able to distinguish methods to 95% confidence 14% of the time.
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Affiliation(s)
- Mark McGann
- OpenEye Scientific Software, Santa Fe, New Mexico 87508, United States.
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104
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Swann SL, Brown SP, Muchmore SW, Patel H, Merta P, Locklear J, Hajduk PJ. A unified, probabilistic framework for structure- and ligand-based virtual screening. J Med Chem 2011; 54:1223-32. [PMID: 21309579 DOI: 10.1021/jm1013677] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a probabilistic framework for interpreting structure-based virtual screening that returns a quantitative likelihood of observing bioactivity and can be quantitatively combined with ligand-based screening methods to yield a cumulative prediction that consistently outperforms any single screening metric. The approach has been developed and validated on more than 30 different protein targets. Transforming structure-based in silico screening results into robust probabilities of activity enables the general fusion of multiple structure- and ligand-based approaches and returns a quantitative expectation of success that can be used to prioritize (or deprioritize) further discovery activities. This unified probabilistic framework offers a paradigm shift in how docking and scoring results are interpreted, which can enhance early lead-finding efforts by maximizing the value of in silico computational tools.
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Affiliation(s)
- Steven L Swann
- Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Illinois 60064, United States
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105
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Gandhi NS, Mancera RL. Molecular Dynamics Simulations of CXCL-8 and Its Interactions with a Receptor Peptide, Heparin Fragments, and Sulfated Linked Cyclitols. J Chem Inf Model 2011; 51:335-58. [DOI: 10.1021/ci1003366] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Neha S. Gandhi
- Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, ‡School of Biomedical Sciences, and §School of Pharmacy, Curtin University, GPO Box U1987, Perth WA 6845, Australia
| | - Ricardo L. Mancera
- Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, ‡School of Biomedical Sciences, and §School of Pharmacy, Curtin University, GPO Box U1987, Perth WA 6845, Australia
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106
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Wu J, Wang J, Li M, Yang Y, Wang B, Zheng YG. Small molecule inhibitors of histone acetyltransferase Tip60. Bioorg Chem 2011; 39:53-8. [PMID: 21186043 PMCID: PMC3144758 DOI: 10.1016/j.bioorg.2010.11.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 11/26/2010] [Accepted: 11/29/2010] [Indexed: 12/13/2022]
Abstract
Tip60 is a key member of the MYST family of histone acetyltransferases and involved in a broad spectrum of cellular pathways and disease conditions. So far, small molecule inhibitors of Tip60 and other members of MYST HATs are rarely reported. To discover new small molecule inhibitors of Tip60 as mechanistic tools for functional study and as chemical leads for therapeutic development, we performed virtual screening using the crystal structure of Esa1 (the yeast homolog of Tip60) on a small molecule library database. Radioactive acetylation assays were carried out to further evaluate the virtual screen hits. Several compounds with new structural scaffolds were identified with micromolar inhibition potency for Tip60 from the biochemical studies. Further, computer modeling and kinetic assays suggest that these molecules target the acetyl-CoA binding site in Tip60. These new inhibitors provide valuable chemical hits to develop further potent inhibitors for the MYST HATs.
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Affiliation(s)
- Jiang Wu
- Department of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, PO Box 4098, Atlanta, GA 30302, USA
| | - Juxian Wang
- Department of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, PO Box 4098, Atlanta, GA 30302, USA
| | - Minyong Li
- Department of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, PO Box 4098, Atlanta, GA 30302, USA
| | - Yutao Yang
- Department of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, PO Box 4098, Atlanta, GA 30302, USA
| | - Binghe Wang
- Department of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, PO Box 4098, Atlanta, GA 30302, USA
| | - Y. George Zheng
- Department of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, PO Box 4098, Atlanta, GA 30302, USA
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107
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Mazanetz MP, Ichihara O, Law RJ, Whittaker M. Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method. J Cheminform 2011; 3:2. [PMID: 21219630 PMCID: PMC3032746 DOI: 10.1186/1758-2946-3-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 01/10/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The reliable and robust estimation of ligand binding affinity continues to be a challenge in drug design. Many current methods rely on molecular mechanics (MM) calculations which do not fully explain complex molecular interactions. Full quantum mechanical (QM) computation of the electronic state of protein-ligand complexes has recently become possible by the latest advances in the development of linear-scaling QM methods such as the ab initio fragment molecular orbital (FMO) method. This approximate molecular orbital method is sufficiently fast that it can be incorporated into the development cycle during structure-based drug design for the reliable estimation of ligand binding affinity. Additionally, the FMO method can be combined with approximations for entropy and solvation to make it applicable for binding affinity prediction for a broad range of target and chemotypes. RESULTS We applied this method to examine the binding affinity for a series of published cyclin-dependent kinase 2 (CDK2) inhibitors. We calculated the binding affinity for 28 CDK2 inhibitors using the ab initio FMO method based on a number of X-ray crystal structures. The sum of the pair interaction energies (PIE) was calculated and used to explain the gas-phase enthalpic contribution to binding. The correlation of the ligand potencies to the protein-ligand interaction energies gained from FMO was examined and was seen to give a good correlation which outperformed three MM force field based scoring functions used to appoximate the free energy of binding. Although the FMO calculation allows for the enthalpic component of binding interactions to be understood at the quantum level, as it is an in vacuo single point calculation, the entropic component and solvation terms are neglected. For this reason a more accurate and predictive estimate for binding free energy was desired. Therefore, additional terms used to describe the protein-ligand interactions were then calculated to improve the correlation of the FMO derived values to experimental free energies of binding. These terms were used to account for the polar and non-polar solvation of the molecule estimated by the Poisson-Boltzmann equation and the solvent accessible surface area (SASA), respectively, as well as a correction term for ligand entropy. A quantitative structure-activity relationship (QSAR) model obtained by Partial Least Squares projection to latent structures (PLS) analysis of the ligand potencies and the calculated terms showed a strong correlation (r2 = 0.939, q2 = 0.896) for the 14 molecule test set which had a Pearson rank order correlation of 0.97. A training set of a further 14 molecules was well predicted (r2 = 0.842), and could be used to obtain meaningful estimations of the binding free energy. CONCLUSIONS Our results show that binding energies calculated with the FMO method correlate well with published data. Analysis of the terms used to derive the FMO energies adds greater understanding to the binding interactions than can be gained by MM methods. Combining this information with additional terms and creating a scaled model to describe the data results in more accurate predictions of ligand potencies than the absolute values obtained by FMO alone.
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Affiliation(s)
- Michael P Mazanetz
- Evotec (UK) limited, 114 Milton Park, Abingdon, Oxfordshire, OX14 4SA, UK
| | - Osamu Ichihara
- Evotec (UK) limited, 114 Milton Park, Abingdon, Oxfordshire, OX14 4SA, UK
| | - Richard J Law
- Evotec (UK) limited, 114 Milton Park, Abingdon, Oxfordshire, OX14 4SA, UK
| | - Mark Whittaker
- Evotec (UK) limited, 114 Milton Park, Abingdon, Oxfordshire, OX14 4SA, UK
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108
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Tang YT, Marshall GR. PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements. J Chem Inf Model 2011; 51:214-28. [PMID: 21214225 DOI: 10.1021/ci100257s] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Binding affinity prediction is one of the most critical components to computer-aided structure-based drug design. Despite advances in first-principle methods for predicting binding affinity, empirical scoring functions that are fast and only relatively accurate are still widely used in structure-based drug design. With the increasing availability of X-ray crystallographic structures in the Protein Data Bank and continuing application of biophysical methods such as isothermal titration calorimetry to measure thermodynamic parameters contributing to binding free energy, sufficient experimental data exists that scoring functions can now be derived by separating enthalpic (ΔH) and entropic (TΔS) contributions to binding free energy (ΔG). PHOENIX, a scoring function to predict binding affinities of protein-ligand complexes, utilizes the increasing availability of experimental data to improve binding affinity predictions by the following: model training and testing using high-resolution crystallographic data to minimize structural noise, independent models of enthalpic and entropic contributions fitted to thermodynamic parameters assumed to be thermodynamically biased to calculate binding free energy, use of shape and volume descriptors to better capture entropic contributions. A set of 42 descriptors and 112 protein-ligand complexes were used to derive functions using partial least-squares for change of enthalpy (ΔH) and change of entropy (TΔS) to calculate change of binding free energy (ΔG), resulting in a predictive r2 (r(pred)2) of 0.55 and a standard error (SE) of 1.34 kcal/mol. External validation using the 2009 version of the PDBbind "refined set" (n = 1612) resulted in a Pearson correlation coefficient (R(p)) of 0.575 and a mean error (ME) of 1.41 pK(d). Enthalpy and entropy predictions were of limited accuracy individually. However, their difference resulted in a relatively accurate binding free energy. While the development of an accurate and applicable scoring function was an objective of this study, the main focus was evaluation of the use of high-resolution X-ray crystal structures with high-quality thermodynamic parameters from isothermal titration calorimetry for scoring function development. With the increasing application of structure-based methods in molecular design, this study suggests that using high-resolution crystal structures, separating enthalpy and entropy contributions to binding free energy, and including descriptors to better capture entropic contributions may prove to be effective strategies toward rapid and accurate calculation of binding affinity.
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Affiliation(s)
- Yat T Tang
- Center for Computational Biology, Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
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109
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Hinselmann G, Rosenbaum L, Jahn A, Fechner N, Ostermann C, Zell A. Large-Scale Learning of Structure−Activity Relationships Using a Linear Support Vector Machine and Problem-Specific Metrics. J Chem Inf Model 2011; 51:203-13. [DOI: 10.1021/ci100073w] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Georg Hinselmann
- Center for Bioinformatics (ZBIT), University of Tübingen, Tübingen, Germany
| | - Lars Rosenbaum
- Center for Bioinformatics (ZBIT), University of Tübingen, Tübingen, Germany
| | - Andreas Jahn
- Center for Bioinformatics (ZBIT), University of Tübingen, Tübingen, Germany
| | - Nikolas Fechner
- Center for Bioinformatics (ZBIT), University of Tübingen, Tübingen, Germany
| | | | - Andreas Zell
- Center for Bioinformatics (ZBIT), University of Tübingen, Tübingen, Germany
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110
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Abstract
The drug discovery process mainly relies on the experimental high-throughput screening of huge compound libraries in their pursuit of new active compounds. However, spiraling research and development costs and unimpressive success rates have driven the development of more rational, efficient, and cost-effective methods. With the increasing availability of protein structural information, advancement in computational algorithms, and faster computing resources, in silico docking-based methods are increasingly used to design smaller and focused compound libraries in order to reduce screening efforts and costs and at the same time identify active compounds with a better chance of progressing through the optimization stages. This chapter is a primer on the various docking-based methods developed for the purpose of structure-based library design. Our aim is to elucidate some basic terms related to the docking technique and explain the methodology behind several docking-based library design methods. This chapter also aims to guide the novice computational practitioner by laying out the general steps involved for such an exercise. Selected successful case studies conclude this chapter.
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Affiliation(s)
- Claudio N Cavasotto
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.
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111
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Kireev D, Wigle TJ, Norris-Drouin J, Herold JM, Janzen WP, Frye SV. Identification of non-peptide malignant brain tumor (MBT) repeat antagonists by virtual screening of commercially available compounds. J Med Chem 2010; 53:7625-31. [PMID: 20931980 DOI: 10.1021/jm1007374] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The malignant brain tumor (MBT) repeat is an important epigenetic-code "reader" and is functionally associated with differentiation, gene silencing, and tumor suppression. (1-3) Small molecule probes of MBT domains should enable a systematic study of MBT-containing proteins and potentially reveal novel druggable targets. We designed and applied a virtual screening strategy that identified potential MBT antagonists in a large database of commercially available compounds. A small set of virtual hits was purchased and submitted to experimental testing. Nineteen of the purchased compounds showed a specific dose-dependent protein binding and will provide critical structure-activity information for subsequent lead generation and optimization.
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Affiliation(s)
- Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina 27599-7363, United States.
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112
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Exploring the conformational changes of the ATP binding site of gyrase B from Escherichia coli complexed with different established inhibitors by using molecular dynamics simulation: protein-ligand interactions in the light of the alanine scanning and free energy decomposition methods. J Mol Graph Model 2010; 29:726-39. [PMID: 21216167 DOI: 10.1016/j.jmgm.2010.12.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 12/03/2010] [Accepted: 12/07/2010] [Indexed: 11/23/2022]
Abstract
Currently, bacterial diseases cause a death toll around 2 million people a year encouraging the search for new antimicrobial agents. DNA gyrase is a well-established antibacterial target consisting of two subunits, GyrA and GyrB, in a heterodimer A(2)B(2). GyrA is involved in DNA breakage and reunion and GyrB catalyzes the hydrolysis of ATP. The GyrB subunit from Escherichia coli has been investigated, namely the ATP binding pocket both considering the protein without ligands and bound with the inhibitors clorobiocin, novobiocin and 5'-adenylyl-β-γ-imidodiphosphate. The stability of the systems was studied by molecular dynamics simulation with the further analysis of the time dependent root-mean-square coordinate deviation (RMSD) from the initial structure, and temperature factors. Moreover, exploration of the conformational space of the systems during the MD simulation was carried out by a clustering data mining technique using the average-linkage algorithm. Recognizing the key residues in the binding site of the enzyme that are involved in the binding mode with the aforementioned inhibitors was investigated by using two techniques: free energy decomposition and computational alanine scanning. The results from these simulations highlight the important residues in the ATP binding site and can be useful in the design process of potential new inhibitors.
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113
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Yang B, Hamza A, Chen G, Wang Y, Zhan CG. Computational determination of binding structures and free energies of phosphodiesterase-2 with benzo[1,4]diazepin-2-one derivatives. J Phys Chem B 2010; 114:16020-8. [PMID: 21077589 PMCID: PMC3072033 DOI: 10.1021/jp1086416] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Phosphodiesterase-2 (PDE2) is a key enzyme catalyzing hydrolysis of both cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP) that serve as intracellular second messengers. PDE2 has been recognized as an attractive drug target, and selective inhibitors of PDE2 are expected to be promising candidates for the memory enhancer, antidepressant, and anxiolytic agent. In the present study, we examined the detailed binding structures and free energies for PDE2 interacting with a promising series of inhibitors, i.e., benzo[1,4]diazepin-2-one derivatives, by carrying out molecular docking, molecular dynamics (MD) simulations, binding free energy calculations, and binding energy decompositions. The computational results provide valuable insights into the detailed enzyme-inhibitor binding modes including important intermolecular interactions, e.g., the π-π stacking interactions with the common benzo[1,4]diazepin-2-one scaffold of the inhibitors, hydrogen bonding and hydrophobic interactions with the substituents on the benzo[1,4]diazepin-2-one scaffold. Future rational design of new, more potent inhibitors of PDE2 should carefully account for all of these favorable intermolecular interactions. By use of the MD-simulated binding structures, the calculated binding free energies are in good agreement with the experimental activity data for all of the examined benzo[1,4]diazepin-2-one derivatives. The enzyme-inhibitor binding modes determined and the agreement between the calculated and experimental results are expected to be valuable for future rational design of more potent inhibitors of PDE2.
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Affiliation(s)
- Bo Yang
- Department of Chemistry, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536
| | - Adel Hamza
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536
| | - Guangju Chen
- Department of Chemistry, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Yan Wang
- Department of Chemistry, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Chang-Guo Zhan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536
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114
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Yang Q, Fedida D, Xu H, Wang B, Du L, Wang X, Li M, You Q. Structure-based virtual screening and electrophysiological evaluation of new chemotypes of K(v)1.5 channel blockers. ChemMedChem 2010; 5:1353-8. [PMID: 20540065 DOI: 10.1002/cmdc.201000162] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Atrial fibrillation (AF) is the most prevalent nonfatal cardiac rhythm disorder associated with an increased risk of heart failure and stroke. Considering the ventricular side effects induced by anti-arrhythmic agents in current use, K(v)1.5 channel blockers have attracted a great deal of deliberation owing to their selective actions on atrial electrophysiology. Herein we report new chemotypes of K(v)1.5 channel blockers that were identified through a combination of structure-based virtual screening and in silico druglike property prediction including six scoring functions, as well as electrophysiological evaluation. Among them, five of the 18 compounds exhibited >50 % blockade ratio at 10 microM, and have structural features different from conventional K(v)1.5 channel blockers. These novel scaffolds could serve as hits for further optimization and SAR studies for the discovery of selective agents to treat AF.
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Affiliation(s)
- Qian Yang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, Jiangsu, China
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115
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Baldi P, Nasr R. When is chemical similarity significant? The statistical distribution of chemical similarity scores and its extreme values. J Chem Inf Model 2010; 50:1205-22. [PMID: 20540577 DOI: 10.1021/ci100010v] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
As repositories of chemical molecules continue to expand and become more open, it becomes increasingly important to develop tools to search them efficiently and assess the statistical significance of chemical similarity scores. Here, we develop a general framework for understanding, modeling, predicting, and approximating the distribution of chemical similarity scores and its extreme values in large databases. The framework can be applied to different chemical representations and similarity measures but is demonstrated here using the most common binary fingerprints with the Tanimoto similarity measure. After introducing several probabilistic models of fingerprints, including the Conditional Gaussian Uniform model, we show that the distribution of Tanimoto scores can be approximated by the distribution of the ratio of two correlated Normal random variables associated with the corresponding unions and intersections. This remains true also when the distribution of similarity scores is conditioned on the size of the query molecules to derive more fine-grained results and improve chemical retrieval. The corresponding extreme value distributions for the maximum scores are approximated by Weibull distributions. From these various distributions and their analytical forms, Z-scores, E-values, and p-values are derived to assess the significance of similarity scores. In addition, the framework also allows one to predict the value of standard chemical retrieval metrics, such as sensitivity and specificity at fixed thresholds, or receiver operating characteristic (ROC) curves at multiple thresholds, and to detect outliers in the form of atypical molecules. Numerous and diverse experiments that have been performed, in part with large sets of molecules from the ChemDB, show remarkable agreement between theory and empirical results.
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Affiliation(s)
- Pierre Baldi
- School of Information and Computer Sciences, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California 92697-3435, USA
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116
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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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117
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Huang SY, Grinter SZ, Zou X. Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions. Phys Chem Chem Phys 2010; 12:12899-908. [PMID: 20730182 PMCID: PMC11103779 DOI: 10.1039/c0cp00151a] [Citation(s) in RCA: 294] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The scoring function is one of the most important components in structure-based drug design. Despite considerable success, accurate and rapid prediction of protein-ligand interactions is still a challenge in molecular docking. In this perspective, we have reviewed three basic types of scoring functions (force-field, empirical, and knowledge-based) and the consensus scoring technique that are used for protein-ligand docking. The commonly-used assessment criteria and publicly available protein-ligand databases for performance evaluation of the scoring functions have also been presented and discussed. We end with a discussion of the challenges faced by existing scoring functions and possible future directions for developing improved scoring functions.
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Affiliation(s)
- Sheng-You Huang
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute University of Missouri Columbia, MO 65211
| | - Sam Z. Grinter
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute University of Missouri Columbia, MO 65211
| | - Xiaoqin Zou
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute University of Missouri Columbia, MO 65211
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118
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Brooijmans N, Humblet C. Chemical Space Sampling in Virtual Screening by Different Crystal Structures. Chem Biol Drug Des 2010; 76:472-9. [DOI: 10.1111/j.1747-0285.2010.01041.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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119
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Simões CJV, Mukherjee T, Brito RMM, Jackson RM. Toward the Discovery of Functional Transthyretin Amyloid Inhibitors: Application of Virtual Screening Methods. J Chem Inf Model 2010; 50:1806-20. [DOI: 10.1021/ci100250z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Carlos J. V. Simões
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom and Center for Neuroscience and Cell Biology and Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Trishna Mukherjee
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom and Center for Neuroscience and Cell Biology and Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Rui M. M. Brito
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom and Center for Neuroscience and Cell Biology and Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Richard M. Jackson
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom and Center for Neuroscience and Cell Biology and Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
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120
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Experimental validation and docking studies of flavone derivatives on aldose reductase involved in diabetic retinopathy, neuropathy, and nephropathy. Med Chem Res 2010. [DOI: 10.1007/s00044-010-9412-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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121
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Huang SY, Zou X. Advances and challenges in protein-ligand docking. Int J Mol Sci 2010; 11:3016-34. [PMID: 21152288 PMCID: PMC2996748 DOI: 10.3390/ijms11083016] [Citation(s) in RCA: 297] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 08/09/2010] [Accepted: 08/10/2010] [Indexed: 02/04/2023] Open
Abstract
Molecular docking is a widely-used computational tool for the study of molecular recognition, which aims to predict the binding mode and binding affinity of a complex formed by two or more constituent molecules with known structures. An important type of molecular docking is protein-ligand docking because of its therapeutic applications in modern structure-based drug design. Here, we review the recent advances of protein flexibility, ligand sampling, and scoring functions—the three important aspects in protein-ligand docking. Challenges and possible future directions are discussed in the Conclusion.
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Affiliation(s)
- Sheng-You Huang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA;
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
- Informatics Institute, University of Missouri, Columbia, MO 65211, USA
| | - Xiaoqin Zou
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA;
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
- Informatics Institute, University of Missouri, Columbia, MO 65211, USA
- *Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-573-882-6045; Fax: +1-573-884-4232
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122
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Application of a novel in silico high-throughput screen to identify selective inhibitors for protein-protein interactions. Bioorg Med Chem Lett 2010; 20:5411-3. [PMID: 20709548 DOI: 10.1016/j.bmcl.2010.07.103] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 07/21/2010] [Accepted: 07/26/2010] [Indexed: 12/20/2022]
Abstract
Increasing numbers of target protein structures available for computational studies makes the structure-based screening paradigm more attractive for initial hit indentification. We have developed a novel in silico screening methodology incorporating Molecular Mechanics (MM)/implicit solvent methods to evaluate binding free energies and applied this technology to the identification of inhibitors of the TLR4/MD-2 interaction.
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123
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Feng Y, Li M, Wang B, Zheng YG. Discovery and Mechanistic Study of a Class of Protein Arginine Methylation Inhibitors. J Med Chem 2010; 53:6028-39. [DOI: 10.1021/jm100416n] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- You Feng
- Department of Chemistry, Center for Biotechnology and Drug Design, Georgia State University, P.O. Box 4098, Atlanta, Georgia 30302
| | - Mingyong Li
- Department of Chemistry, Center for Biotechnology and Drug Design, Georgia State University, P.O. Box 4098, Atlanta, Georgia 30302
| | - Binghe Wang
- Department of Chemistry, Center for Biotechnology and Drug Design, Georgia State University, P.O. Box 4098, Atlanta, Georgia 30302
| | - Yujun George Zheng
- Department of Chemistry, Center for Biotechnology and Drug Design, Georgia State University, P.O. Box 4098, Atlanta, Georgia 30302
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124
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Chen B, Mueller C, Willett P. Combination Rules for Group Fusion in Similarity-Based Virtual Screening. Mol Inform 2010; 29:533-41. [DOI: 10.1002/minf.201000050] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 06/14/2010] [Indexed: 11/10/2022]
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125
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Chemical validation of phosphodiesterase C as a chemotherapeutic target in Trypanosoma cruzi, the etiological agent of Chagas' disease. Antimicrob Agents Chemother 2010; 54:3738-45. [PMID: 20625148 DOI: 10.1128/aac.00313-10] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Trypanosoma cruzi phosphodiesterase (PDE) C (TcrPDEC), a novel and rather unusual PDE in which, unlike all other class I PDEs, the catalytic domain is localized in the middle of the polypeptide chain, is able to hydrolyze cyclic GMP (cGMP), although it prefers cyclic AMP (cAMP), and has a FYVE-type domain in its N-terminal region (S. Kunz et al., FEBS J. 272:6412-6422, 2005). TcrPDEC shows homology to the mammalian PDE4 family members. PDE4 inhibitors are currently under development for the treatment of inflammatory diseases, such as asthma, chronic pulmonary diseases, and psoriasis, and for treating depression and serving as cognitive enhancers. We therefore tested a number of compounds originally synthesized as potential PDE4 inhibitors on T. cruzi amastigote growth, and we obtained several useful hits. We then conducted homology modeling of T. cruzi PDEC and identified other compounds as potential inhibitors through virtual screening. Testing of these compounds against amastigote growth and recombinant TcrPDEC activity resulted in several potent inhibitors. The most-potent inhibitors were found to increase the cellular concentration of cAMP. Preincubation of cells in the presence of one of these compounds stimulated volume recovery after hyposmotic stress, in agreement with their TcrPDEC inhibitory activity in vitro, providing chemical validation of this target. The compounds found could be useful tools in the study of osmoregulation in T. cruzi. In addition, their further optimization could result in the development of new drugs against Chagas' disease and other trypanosomiases.
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126
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Ferreira RS, Simeonov A, Jadhav A, Eidam O, Mott BT, Keiser MJ, McKerrow JH, Maloney DJ, Irwin JJ, Shoichet BK. Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors. J Med Chem 2010; 53:4891-905. [PMID: 20540517 PMCID: PMC2895358 DOI: 10.1021/jm100488w] [Citation(s) in RCA: 162] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Indexed: 12/13/2022]
Abstract
Virtual and high-throughput screens (HTS) should have complementary strengths and weaknesses, but studies that prospectively and comprehensively compare them are rare. We undertook a parallel docking and HTS screen of 197861 compounds against cruzain, a thiol protease target for Chagas disease, looking for reversible, competitive inhibitors. On workup, 99% of the hits were eliminated as false positives, yielding 146 well-behaved, competitive ligands. These fell into five chemotypes: two were prioritized by scoring among the top 0.1% of the docking-ranked library, two were prioritized by behavior in the HTS and by clustering, and one chemotype was prioritized by both approaches. Determination of an inhibitor/cruzain crystal structure and comparison of the high-scoring docking hits to experiment illuminated the origins of docking false-negatives and false-positives. Prioritizing molecules that are both predicted by docking and are HTS-active yields well-behaved molecules, relatively unobscured by the false-positives to which both techniques are individually prone.
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Affiliation(s)
- Rafaela S. Ferreira
- Graduate Program in Chemistry and Chemical Biology
- Department of Pharmaceutical Chemistry
- Sandler Center for Basic Research in Parasitic Diseases
| | - Anton Simeonov
- NIH Chemical Genomics Center, Bethesda, Maryland 20892-3370
| | - Ajit Jadhav
- NIH Chemical Genomics Center, Bethesda, Maryland 20892-3370
| | | | - Bryan T. Mott
- NIH Chemical Genomics Center, Bethesda, Maryland 20892-3370
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127
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Kutchukian PS, Shakhnovich EI. De novo design: balancing novelty and confined chemical space. Expert Opin Drug Discov 2010; 5:789-812. [PMID: 22827800 DOI: 10.1517/17460441.2010.497534] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
IMPORTANCE OF THE FIELD De novo drug design serves as a tool for the discovery of new ligands for macromolecular targets as well as optimization of known ligands. Recently developed tools aim to address the multi-objective nature of drug design in an unprecedented manner. AREAS COVERED IN THIS REVIEW This article discusses recent advances in de novo drug design programs and accessory programs used to evaluate compounds post-generation. WHAT THE READER WILL GAIN The reader is introduced to the challenges inherent in de novo drug design and will become familiar with current trends in de novo design. Furthermore, the reader will be better prepared to assess the value of a tool, and be equipped to design more elegant tools in the future. TAKE HOME MESSAGE De novo drug design can assist in the efficient discovery of new compounds with a high affinity for a given target. The inclusion of existing chemoinformatic methods with current structure-based de novo design tools provides a means of enhancing the therapeutic value of these generated compounds.
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Affiliation(s)
- Peter S Kutchukian
- Harvard University, Chemistry and Chemical Biology Department, 12 Oxford Street, Cambridge, MA 02138, USA
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128
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Thilagavathi R, Mancera RL. Ligand-protein cross-docking with water molecules. J Chem Inf Model 2010; 50:415-21. [PMID: 20158272 DOI: 10.1021/ci900345h] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The accuracy of ligand-protein docking may be affected by the presence of water molecules on the surface of the protein. Cross-docking simulations have been performed on a number of ligand-protein complexes for various proteins whose crystal structures contain water molecules in their binding sites. Only common sets of water molecules found in the binding site of the proteins were considered. A statistically significant overall increase in accuracy was observed when water molecules were included in cross-docking simulations. These results confirm the importance of including water molecules whenever possible in ligand-protein docking simulations.
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Affiliation(s)
- Ramasamy Thilagavathi
- Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Pharmacy and Biomedical Sciences, Curtin University of Technology, Perth, WA 6845, Australia
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129
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Pencheva T, Soumana OS, Pajeva I, Miteva MA. Post-docking virtual screening of diverse binding pockets: Comparative study using DOCK, AMMOS, X-Score and FRED scoring functions. Eur J Med Chem 2010; 45:2622-8. [PMID: 20227800 DOI: 10.1016/j.ejmech.2009.12.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 12/08/2009] [Accepted: 12/10/2009] [Indexed: 10/20/2022]
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130
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Pierri CL, Parisi G, Porcelli V. Computational approaches for protein function prediction: a combined strategy from multiple sequence alignment to molecular docking-based virtual screening. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1695-712. [PMID: 20433957 DOI: 10.1016/j.bbapap.2010.04.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 03/04/2010] [Accepted: 04/14/2010] [Indexed: 12/12/2022]
Abstract
The functional characterization of proteins represents a daily challenge for biochemical, medical and computational sciences. Although finally proved on the bench, the function of a protein can be successfully predicted by computational approaches that drive the further experimental assays. Current methods for comparative modeling allow the construction of accurate 3D models for proteins of unknown structure, provided that a crystal structure of a homologous protein is available. Binding regions can be proposed by using binding site predictors, data inferred from homologous crystal structures, and data provided from a careful interpretation of the multiple sequence alignment of the investigated protein and its homologs. Once the location of a binding site has been proposed, chemical ligands that have a high likelihood of binding can be identified by using ligand docking and structure-based virtual screening of chemical libraries. Most docking algorithms allow building a list sorted by energy of the lowest energy docking configuration for each ligand of the library. In this review the state-of-the-art of computational approaches in 3D protein comparative modeling and in the study of protein-ligand interactions is provided. Furthermore a possible combined/concerted multistep strategy for protein function prediction, based on multiple sequence alignment, comparative modeling, binding region prediction, and structure-based virtual screening of chemical libraries, is described by using suitable examples. As practical examples, Abl-kinase molecular modeling studies, HPV-E6 protein multiple sequence alignment analysis, and some other model docking-based characterization reports are briefly described to highlight the importance of computational approaches in protein function prediction.
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Affiliation(s)
- Ciro Leonardo Pierri
- Department of Pharmaco-Biology, Laboratory of Biochemistry and Molecular Biology, University of Bari, Va E. Orabona, 4 - 70125 Bari, Italy.
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131
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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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132
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Krüger DM, Evers A. Comparison of structure- and ligand-based virtual screening protocols considering hit list complementarity and enrichment factors. ChemMedChem 2010; 5:148-58. [PMID: 19908272 DOI: 10.1002/cmdc.200900314] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Structure- and ligand-based virtual-screening methods (docking, 2D- and 3D-similarity searching) were analysed for their effectiveness in virtual screening against four different targets: angiotensin-converting enzyme (ACE), cyclooxygenase 2 (COX-2), thrombin and human immunodeficiency virus 1 (HIV-1) protease. The relative performance of the tools was compared by examining their ability to recognise known active compounds from a set of actives and nonactives. Furthermore, we investigated whether the application of different virtual-screening methods in parallel provides complementary or redundant hit lists. Docking was performed with GOLD, Glide, FlexX and Surflex. The obtained docking poses were rescored by using nine different scoring functions in addition to the scoring functions implemented as objective functions in the docking algorithms. Ligand-based virtual screening was done with ROCS (3D-similarity searching), Feature Trees and Scitegic Functional Fingerprints (2D-similarity searching). The results show that structure- and ligand-based virtual-screening methods provide comparable enrichments in detecting active compounds. Interestingly, the hit lists that are obtained from different virtual-screening methods are generally highly complementary. These results suggest that a parallel application of different structure- and ligand-based virtual-screening methods increases the chance of identifying more (and more diverse) active compounds from a virtual-screening campaign.
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Affiliation(s)
- Dennis M Krüger
- Institut für pharmazeutische und medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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133
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Guimarães CRW, Mathiowetz AM. Addressing Limitations with the MM-GB/SA Scoring Procedure using the WaterMap Method and Free Energy Perturbation Calculations. J Chem Inf Model 2010; 50:547-59. [DOI: 10.1021/ci900497d] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cristiano R. W. Guimarães
- CVMD Chemistry, PharmaTherapeutics Research and Development, Pfizer, Inc., 558 Eastern Point Road, Groton, Connecticut 06340
| | - Alan M. Mathiowetz
- CVMD Chemistry, PharmaTherapeutics Research and Development, Pfizer, Inc., 558 Eastern Point Road, Groton, Connecticut 06340
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134
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da Rocha Pita SS, Cirino JJV, de Alencastro RB, Castro HC, Rodrigues CR, Albuquerque MG. Molecular docking of a series of peptidomimetics in the trypanothione binding site of T. cruzi Trypanothione Reductase. J Mol Graph Model 2009; 28:330-5. [DOI: 10.1016/j.jmgm.2009.08.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 08/21/2009] [Accepted: 08/24/2009] [Indexed: 10/20/2022]
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135
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Fan H, Irwin JJ, Webb BM, Klebe G, Shoichet BK, Sali A. Molecular docking screens using comparative models of proteins. J Chem Inf Model 2009; 49:2512-27. [PMID: 19845314 PMCID: PMC2790034 DOI: 10.1021/ci9003706] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two orders of magnitude more protein sequences can be modeled by comparative modeling than have been determined by X-ray crystallography and NMR spectroscopy. Investigators have nevertheless been cautious about using comparative models for ligand discovery because of concerns about model errors. We suggest how to exploit comparative models for molecular screens, based on docking against a wide range of crystallographic structures and comparative models with known ligands. To account for the variation in the ligand-binding pocket as it binds different ligands, we calculate "consensus" enrichment by ranking each library compound by its best docking score against all available comparative models and/or modeling templates. For the majority of the targets, the consensus enrichment for multiple models was better than or comparable to that of the holo and apo X-ray structures. Even for single models, the models are significantly more enriching than the template structure if the template is paralogous and shares more than 25% sequence identity with the target.
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Affiliation(s)
- Hao Fan
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, San Francisco, California 94158, USA
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136
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Genome wide analysis and comparative docking studies of new diaryl furan derivatives against human cyclooxygenase-2, lipoxygenase, thromboxane synthase and prostacyclin synthase enzymes involved in inflammatory pathway. J Mol Graph Model 2009; 28:313-29. [DOI: 10.1016/j.jmgm.2009.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 08/19/2009] [Accepted: 08/20/2009] [Indexed: 11/21/2022]
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137
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Muthenna P, Suryanarayana P, Gunda SK, Petrash JM, Reddy GB. Inhibition of aldose reductase by dietary antioxidant curcumin: Mechanism of inhibition, specificity and significance. FEBS Lett 2009; 583:3637-42. [DOI: 10.1016/j.febslet.2009.10.042] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 09/28/2009] [Accepted: 10/15/2009] [Indexed: 10/20/2022]
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138
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Musafia B, Senderowitz H. Bioactive Conformational Biasing: A New Method for Focusing Conformational Ensembles on Bioactive-Like Conformers. J Chem Inf Model 2009; 49:2469-80. [DOI: 10.1021/ci900163t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Boaz Musafia
- Epix Pharmaceuticals Ltd., 3 Hayetzira St., Ramat Gan 52521, Israel
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139
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Okimoto N, Futatsugi N, Fuji H, Suenaga A, Morimoto G, Yanai R, Ohno Y, Narumi T, Taiji M. High-performance drug discovery: computational screening by combining docking and molecular dynamics simulations. PLoS Comput Biol 2009; 5:e1000528. [PMID: 19816553 PMCID: PMC2746282 DOI: 10.1371/journal.pcbi.1000528] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Accepted: 09/03/2009] [Indexed: 11/29/2022] Open
Abstract
Virtual compound screening using molecular docking is widely used in the discovery of new lead compounds for drug design. However, this method is not completely reliable and therefore unsatisfactory. In this study, we used massive molecular dynamics simulations of protein-ligand conformations obtained by molecular docking in order to improve the enrichment performance of molecular docking. Our screening approach employed the molecular mechanics/Poisson-Boltzmann and surface area method to estimate the binding free energies. For the top-ranking 1,000 compounds obtained by docking to a target protein, approximately 6,000 molecular dynamics simulations were performed using multiple docking poses in about a week. As a result, the enrichment performance of the top 100 compounds by our approach was improved by 1.6–4.0 times that of the enrichment performance of molecular dockings. This result indicates that the application of molecular dynamics simulations to virtual screening for lead discovery is both effective and practical. However, further optimization of the computational protocols is required for screening various target proteins. Lead discovery is one of the most important processes in rational drug design. To improve the rate of the detection of lead compounds, various technologies such as high-throughput screening and combinatorial chemistry have been introduced into the pharmaceutical industry. However, since these technologies alone may not improve lead productivity, computational screening has become important. A central method for computational screening is molecular docking. This method generally docks many flexible ligands to a rigid protein and predicts the binding affinity for each ligand in a practical time. However, its ability to detect lead compounds is less reliable. In contrast, molecular dynamics simulations can treat both proteins and ligands in a flexible manner, directly estimate the effect of explicit water molecules, and provide more accurate binding affinity, although their computational costs and times are significantly greater than those of molecular docking. Therefore, we developed a special purpose computer “MDGRAPE-3” for molecular dynamics simulations and applied it to computational screening. In this paper, we report an effective method for computational screening; this method is a combination of molecular docking and massive-scale molecular dynamics simulations. The proposed method showed a higher and more stable enrichment performance than the molecular docking method used alone.
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Affiliation(s)
- Noriaki Okimoto
- High-performance Molecular Simulation Team, Computational Systems Biology Research Group, Advanced Computational Sciences Department, RIKEN Advanced Science Institute, Yokohama, Kanagawa, Japan.
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140
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Rabinowitz JR, Little SB, Laws SC, Goldsmith MR. Molecular Modeling for Screening Environmental Chemicals for Estrogenicity: Use of the Toxicant-Target Approach. Chem Res Toxicol 2009; 22:1594-602. [DOI: 10.1021/tx900135x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- James R. Rabinowitz
- National Center for Computational Toxicology, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina
| | - Stephen B. Little
- National Center for Computational Toxicology, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina
| | - Susan C. Laws
- National Center for Computational Toxicology, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina
| | - Michael-Rock Goldsmith
- National Center for Computational Toxicology, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina
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141
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Cross JB, Thompson DC, Rai BK, Baber JC, Fan KY, Hu Y, Humblet C. Comparison of several molecular docking programs: pose prediction and virtual screening accuracy. J Chem Inf Model 2009; 49:1455-74. [PMID: 19476350 DOI: 10.1021/ci900056c] [Citation(s) in RCA: 316] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular docking programs are widely used modeling tools for predicting ligand binding modes and structure based virtual screening. In this study, six molecular docking programs (DOCK, FlexX, GLIDE, ICM, PhDOCK, and Surflex) were evaluated using metrics intended to assess docking pose and virtual screening accuracy. Cognate ligand docking to 68 diverse, high-resolution X-ray complexes revealed that ICM, GLIDE, and Surflex generated ligand poses close to the X-ray conformation more often than the other docking programs. GLIDE and Surflex also outperformed the other docking programs when used for virtual screening, based on mean ROC AUC and ROC enrichment values obtained for the 40 protein targets in the Directory of Useful Decoys (DUD). Further analysis uncovered general trends in accuracy that are specific for particular protein families. Modifying basic parameters in the software was shown to have a significant effect on docking and virtual screening results, suggesting that expert knowledge is critical for optimizing the accuracy of these methods.
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Affiliation(s)
- Jason B Cross
- Wyeth Research, Chemical Sciences, Collegeville, Pennsylvania 19426, USA.
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142
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O’Boyle NM, Liebeschuetz JW, Cole JC. Testing Assumptions and Hypotheses for Rescoring Success in Protein−Ligand Docking. J Chem Inf Model 2009; 49:1871-8. [DOI: 10.1021/ci900164f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Noel M. O’Boyle
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
| | | | - Jason C. Cole
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
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143
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Baber JC, Thompson DC, Cross JB, Humblet C. GARD: A Generally Applicable Replacement for RMSD. J Chem Inf Model 2009; 49:1889-900. [DOI: 10.1021/ci9001074] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. Christian Baber
- Chemical Sciences, Wyeth Research, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140 and 865 Ridge Road, Princeton, New Jersey 08543, and Chemical Sciences, Wyeth Pharmaceuticals and Research Headquarters, 500 Arcola Road, Collegeville, Pennsylvania 19426
| | - David C. Thompson
- Chemical Sciences, Wyeth Research, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140 and 865 Ridge Road, Princeton, New Jersey 08543, and Chemical Sciences, Wyeth Pharmaceuticals and Research Headquarters, 500 Arcola Road, Collegeville, Pennsylvania 19426
| | - Jason B. Cross
- Chemical Sciences, Wyeth Research, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140 and 865 Ridge Road, Princeton, New Jersey 08543, and Chemical Sciences, Wyeth Pharmaceuticals and Research Headquarters, 500 Arcola Road, Collegeville, Pennsylvania 19426
| | - Christine Humblet
- Chemical Sciences, Wyeth Research, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140 and 865 Ridge Road, Princeton, New Jersey 08543, and Chemical Sciences, Wyeth Pharmaceuticals and Research Headquarters, 500 Arcola Road, Collegeville, Pennsylvania 19426
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144
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Cheng T, Li X, Li Y, Liu Z, Wang R. Comparative assessment of scoring functions on a diverse test set. J Chem Inf Model 2009; 49:1079-93. [PMID: 19358517 DOI: 10.1021/ci9000053] [Citation(s) in RCA: 369] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Scoring functions are widely applied to the evaluation of protein-ligand binding in structure-based drug design. We have conducted a comparative assessment of 16 popular scoring functions implemented in main-stream commercial software or released by academic research groups. A set of 195 diverse protein-ligand complexes with high-resolution crystal structures and reliable binding constants were selected through a systematic nonredundant sampling of the PDBbind database and used as the primary test set in our study. All scoring functions were evaluated in three aspects, that is, "docking power", "ranking power", and "scoring power", and all evaluations were independent from the context of molecular docking or virtual screening. As for "docking power", six scoring functions, including GOLD::ASP, DS::PLP1, DrugScore(PDB), GlideScore-SP, DS::LigScore, and GOLD::ChemScore, achieved success rates over 70% when the acceptance cutoff was root-mean-square deviation < 2.0 A. Combining these scoring functions into consensus scoring schemes improved the success rates to 80% or even higher. As for "ranking power" and "scoring power", the top four scoring functions on the primary test set were X-Score, DrugScore(CSD), DS::PLP, and SYBYL::ChemScore. They were able to correctly rank the protein-ligand complexes containing the same type of protein with success rates around 50%. Correlation coefficients between the experimental binding constants and the binding scores computed by these scoring functions ranged from 0.545 to 0.644. Besides the primary test set, each scoring function was also tested on four additional test sets, each consisting of a certain number of protein-ligand complexes containing one particular type of protein. Our study serves as an updated benchmark for evaluating the general performance of today's scoring functions. Our results indicate that no single scoring function consistently outperforms others in all three aspects. Thus, it is important in practice to choose the appropriate scoring functions for different purposes.
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Affiliation(s)
- Tiejun Cheng
- State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, P. R. China
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145
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Nasr RJ, Swamidass SJ, Baldi PF. Large scale study of multiple-molecule queries. J Cheminform 2009; 1:7. [PMID: 20298525 PMCID: PMC3225883 DOI: 10.1186/1758-2946-1-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 06/04/2009] [Indexed: 12/04/2022] Open
Abstract
Background In ligand-based screening, as well as in other chemoinformatics applications, one seeks to effectively search large repositories of molecules in order to retrieve molecules that are similar typically to a single molecule lead. However, in some case, multiple molecules from the same family are available to seed the query and search for other members of the same family. Multiple-molecule query methods have been less studied than single-molecule query methods. Furthermore, the previous studies have relied on proprietary data and sometimes have not used proper cross-validation methods to assess the results. In contrast, here we develop and compare multiple-molecule query methods using several large publicly available data sets and background. We also create a framework based on a strict cross-validation protocol to allow unbiased benchmarking for direct comparison in future studies across several performance metrics. Results Fourteen different multiple-molecule query methods were defined and benchmarked using: (1) 41 publicly available data sets of related molecules with similar biological activity; and (2) publicly available background data sets consisting of up to 175,000 molecules randomly extracted from the ChemDB database and other sources. Eight of the fourteen methods were parameter free, and six of them fit one or two free parameters to the data using a careful cross-validation protocol. All the methods were assessed and compared for their ability to retrieve members of the same family against the background data set by using several performance metrics including the Area Under the Accumulation Curve (AUAC), Area Under the Curve (AUC), F1-measure, and BEDROC metrics. Consistent with the previous literature, the best parameter-free methods are the MAX-SIM and MIN-RANK methods, which score a molecule to a family by the maximum similarity, or minimum ranking, obtained across the family. One new parameterized method introduced in this study and two previously defined methods, the Exponential Tanimoto Discriminant (ETD), the Tanimoto Power Discriminant (TPD), and the Binary Kernel Discriminant (BKD), outperform most other methods but are more complex, requiring one or two parameters to be fit to the data. Conclusion Fourteen methods for multiple-molecule querying of chemical databases, including novel methods, (ETD) and (TPD), are validated using publicly available data sets, standard cross-validation protocols, and established metrics. The best results are obtained with ETD, TPD, BKD, MAX-SIM, and MIN-RANK. These results can be replicated and compared with the results of future studies using data freely downloadable from http://cdb.ics.uci.edu/.
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Affiliation(s)
- Ramzi J Nasr
- The Bren School of Information and Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697-3435, USA.
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146
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Rohrer SG, Baumann K. Maximum unbiased validation (MUV) data sets for virtual screening based on PubChem bioactivity data. J Chem Inf Model 2009; 49:169-84. [PMID: 19434821 DOI: 10.1021/ci8002649] [Citation(s) in RCA: 223] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Refined nearest neighbor analysis was recently introduced for the analysis of virtual screening benchmark data sets. It constitutes a technique from the field of spatial statistics and provides a mathematical framework for the nonparametric analysis of mapped point patterns. Here, refined nearest neighbor analysis is used to design benchmark data sets for virtual screening based on PubChem bioactivity data. A workflow is devised that purges data sets of compounds active against pharmaceutically relevant targets from unselective hits. Topological optimization using experimental design strategies monitored by refined nearest neighbor analysis functions is applied to generate corresponding data sets of actives and decoys that are unbiased with regard to analogue bias and artificial enrichment. These data sets provide a tool for Maximum Unbiased Validation (MUV) of virtual screening methods. The data sets and a software package implementing the MUV design workflow are freely available at http://www.pharmchem.tu-bs.de/lehre/baumann/MUV.html.
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Affiliation(s)
- Sebastian G Rohrer
- Institute of Pharmaceutical Chemistry, Beethovenstrasse 55, Braunschweig University of Technology, 38106 Braunschweig, Germany
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147
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Hevener KE, Zhao W, Ball DM, Babaoglu K, Qi J, White SW, Lee RE. Validation of molecular docking programs for virtual screening against dihydropteroate synthase. J Chem Inf Model 2009; 49:444-60. [PMID: 19434845 DOI: 10.1021/ci800293n] [Citation(s) in RCA: 324] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dihydropteroate synthase (DHPS) is the target of the sulfonamide class of antibiotics and has been a validated antibacterial drug target for nearly 70 years. The sulfonamides target the p-aminobenzoic acid (pABA) binding site of DHPS and interfere with folate biosynthesis and ultimately prevent bacterial replication. However, widespread bacterial resistance to these drugs has severely limited their effectiveness. This study explores the second and more highly conserved pterin binding site of DHPS as an alternative approach to developing novel antibiotics that avoid resistance. In this study, five commonly used docking programs, FlexX, Surflex, Glide, GOLD, and DOCK, and nine scoring functions, were evaluated for their ability to rank-order potential lead compounds for an extensive virtual screening study of the pterin binding site of B. anthracis DHPS. Their performance in ligand docking and scoring was judged by their ability to reproduce a known inhibitor conformation and to efficiently detect known active compounds seeded into three separate decoy sets. Two other metrics were used to assess performance; enrichment at 1% and 2% and Receiver Operating Characteristic (ROC) curves. The effectiveness of postdocking relaxation prior to rescoring and consensus scoring were also evaluated. Finally, we have developed a straightforward statistical method of including the inhibition constants of the known active compounds when analyzing enrichment results to more accurately assess scoring performance, which we call the 'sum of the sum of log rank' or SSLR. Of the docking and scoring functions evaluated, Surflex with Surflex-Score and Glide with GlideScore were the best overall performers for use in virtual screening against the DHPS target, with neither combination showing statistically significant superiority over the other in enrichment studies or pose selection. Postdocking ligand relaxation and consensus scoring did not improve overall enrichment.
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Affiliation(s)
- Kirk E Hevener
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
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148
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Nicolaou CA, Apostolakis J, Pattichis CS. De novo drug design using multiobjective evolutionary graphs. J Chem Inf Model 2009; 49:295-307. [PMID: 19434831 DOI: 10.1021/ci800308h] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Drug discovery and development is a complex, lengthy process, and failure of a candidate molecule can occur as a result of a combination of reasons, such as poor pharmacokinetics, lack of efficacy, or toxicity. Successful drug candidates necessarily represent a compromise between the numerous, sometimes competing objectives so that the benefits to patients outweigh potential drawbacks and risks. De novo drug design involves searching an immense space of feasible, druglike molecules to select those with the highest chances of becoming drugs using computational technology. Traditionally, de novo design has focused on designing molecules satisfying a single objective, such as similarity to a known ligand or an interaction score, and ignored the presence of the multiple objectives required for druglike behavior. Recently, methods have appeared in the literature that attempt to design molecules satisfying multiple predefined objectives and thereby produce candidate solutions with a higher chance of serving as viable drug leads. This paper describes the Multiobjective Evolutionary Graph Algorithm (MEGA), a new multiobjective optimization de novo design algorithmic framework that can be used to design structurally diverse molecules satisfying one or more objectives. The algorithm combines evolutionary techniques with graph-theory to directly manipulate graphs and perform an efficient global search for promising solutions. In the Experimental Section we present results from the application of MEGA for designing molecules that selectively bind to a known pharmaceutical target using the ChillScore interaction score family. The primary constraints applied to the design are based on the identified structure of the protein target and a known ligand currently marketed as a drug. A detailed explanation of the key elements of the specific implementation of the algorithm is given, including the methods for obtaining molecular building blocks, evolving the chemical graphs, and scoring the designed molecules. Our findings demonstrate that MEGA can produce structurally diverse candidate molecules representing a wide range of compromises of the supplied constraints and thus can be used as an "idea generator" to support expert chemists assigned with the task of molecular design.
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Affiliation(s)
- Christos A Nicolaou
- Computer Science Department, University of Cyprus, 75 Kallipoleos Street, CY-1678 Nicosia, Cyprus.
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149
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Vijayan RSK, Prabu M, Mascarenhas NM, Ghoshal N. Hybrid structure-based virtual screening protocol for the identification of novel BACE1 inhibitors. J Chem Inf Model 2009; 49:647-57. [PMID: 19434899 DOI: 10.1021/ci800386v] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACE1, also called beta-secretase or memapsin 2, is an extensively studied aspartic protease, involved in etiopathogenesis and progression of Alzheimer's disease (AD). We report herein a modified structure-based virtual screening protocol that augments the lead identification process against BACE1 during virtual screening endeavors. A hybrid structure-based virtual screening protocol that incorporates elements from both ligand-based and structure-based techniques was used for the identification of prospective small molecule inhibitors. Virtual screening, using an active-site-derived pharmacophore, followed by ROCS (rapid overlay of chemical structures)-based GOLD (genetic optimization in ligand docking) docking was used to identify a library of focused candidates. The efficacy of the ROCS-based GOLD docking method together with our customized weighted consensus scoring function was evaluated against conventional docking methods for its ability to discern true positives from a screening library. An in-depth structural analysis of the binding mode of the top-ranking molecules reveals that emulation of the curial interaction patterns deemed necessary for BACE1 inhibition. The results obtained from our validation study ensure the superiority of our docking methodology over conventional docking methods in yielding higher enrichment rates.
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Affiliation(s)
- R S K Vijayan
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology (A unit of CSIR), Kolkata 700032, India
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150
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Amadasi A, Mozzarelli A, Meda C, Maggi A, Cozzini P. Identification of xenoestrogens in food additives by an integrated in silico and in vitro approach. Chem Res Toxicol 2009; 22:52-63. [PMID: 19063592 DOI: 10.1021/tx800048m] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the search for xenoestrogens within food additives, we have analyzed the Joint FAO-WHO expert committee database, containing 1500 compounds, using an integrated in silico and in vitro approach. This analysis identified 31 potential estrogen receptor alpha ligands that were reduced to 13 upon applying a stringent filter based on ligand volume and binding mode. Among the 13 potential xenoestrogens, four were already known to exhibit an estrogenic activity, and the other nine were assayed in vitro, determining the binding affinity to the receptor and biological effects. Propyl gallate was found to act as an antagonist, and 4-hexylresorcinol was found to act as a potent transactivator; both ligands were active at nanomolar concentrations, as predicted by the in silico analysis. Some caution should be issued for the use of propyl gallate and 4-hexylresorcinol as food additives.
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Affiliation(s)
- Alessio Amadasi
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy
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