1
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Kumar A, Zhang KYJ. A cross docking pipeline for improving pose prediction and virtual screening performance. J Comput Aided Mol Des 2017; 32:163-173. [PMID: 28836076 DOI: 10.1007/s10822-017-0048-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/18/2017] [Indexed: 02/02/2023]
Abstract
Pose prediction and virtual screening performance of a molecular docking method depend on the choice of protein structures used for docking. Multiple structures for a target protein are often used to take into account the receptor flexibility and problems associated with a single receptor structure. However, the use of multiple receptor structures is computationally expensive when docking a large library of small molecules. Here, we propose a new cross-docking pipeline suitable to dock a large library of molecules while taking advantage of multiple target protein structures. Our method involves the selection of a suitable receptor for each ligand in a screening library utilizing ligand 3D shape similarity with crystallographic ligands. We have prospectively evaluated our method in D3R Grand Challenge 2 and demonstrated that our cross-docking pipeline can achieve similar or better performance than using either single or multiple-receptor structures. Moreover, our method displayed not only decent pose prediction performance but also better virtual screening performance over several other methods.
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Affiliation(s)
- Ashutosh Kumar
- Structural Bioinformatics Team, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Kam Y J Zhang
- Structural Bioinformatics Team, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
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2
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Xia J, Hsieh JH, Hu H, Wu S, Wang XS. The Development of Target-Specific Pose Filter Ensembles To Boost Ligand Enrichment for Structure-Based Virtual Screening. J Chem Inf Model 2017; 57:1414-1425. [PMID: 28511009 DOI: 10.1021/acs.jcim.6b00749] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-based virtual screening (SBVS) has become an indispensable technique for hit identification at the early stage of drug discovery. However, the accuracy of current scoring functions is not high enough to confer success to every target and thus remains to be improved. Previously, we had developed binary pose filters (PFs) using knowledge derived from the protein-ligand interface of a single X-ray structure of a specific target. This novel approach had been validated as an effective way to improve ligand enrichment. Continuing from it, in the present work we attempted to incorporate knowledge collected from diverse protein-ligand interfaces of multiple crystal structures of the same target to build PF ensembles (PFEs). Toward this end, we first constructed a comprehensive data set to meet the requirements of ensemble modeling and validation. This set contains 10 diverse targets, 118 well-prepared X-ray structures of protein-ligand complexes, and large benchmarking actives/decoys sets. Notably, we designed a unique workflow of two-layer classifiers based on the concept of ensemble learning and applied it to the construction of PFEs for all of the targets. Through extensive benchmarking studies, we demonstrated that (1) coupling PFE with Chemgauss4 significantly improves the early enrichment of Chemgauss4 itself and (2) PFEs show greater consistency in boosting early enrichment and larger overall enrichment than our prior PFs. In addition, we analyzed the pairwise topological similarities among cognate ligands used to construct PFEs and found that it is the higher chemical diversity of the cognate ligands that leads to the improved performance of PFEs. Taken together, the results so far prove that the incorporation of knowledge from diverse protein-ligand interfaces by ensemble modeling is able to enhance the screening competence of SBVS scoring functions.
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Affiliation(s)
- Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, China
| | - Jui-Hua Hsieh
- Kelly Government Solutions , Research Triangle Park, North Carolina 27709, United States
| | - Huabin Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, China
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, China
| | - Xiang Simon Wang
- Molecular Modeling and Drug Discovery Core Laboratory for District of Columbia Center for AIDS Research (DC CFAR), Department of Pharmaceutical Sciences, College of Pharmacy, Howard University , Washington, D.C. 20059, United States
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3
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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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4
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Abstract
It is now plausible to dock libraries of 10 million molecules against targets over several days or weeks. When the molecules screened are commercially available, they may be rapidly tested to find new leads. Although docking retains important liabilities (it cannot calculate affinities accurately nor even reliably rank order high-scoring molecules), it can often can distinguish likely from unlikely ligands, often with hit rates above 10%. Here we summarize the improvements in libraries, target quality, and methods that have supported these advances, and the open access resources that make docking accessible. Recent docking screens for new ligands are sketched, as are the binding, crystallographic, and in vivo assays that support them. Like any technique, controls are crucial, and key experimental ones are reviewed. With such controls, docking campaigns can find ligands with new chemotypes, often revealing the new biology that may be docking's greatest impact over the next few years.
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Affiliation(s)
- John J Irwin
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
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5
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Choi J, Choi KE, Park SJ, Kim SY, Jee JG. Ensemble-Based Virtual Screening Led to the Discovery of New Classes of Potent Tyrosinase Inhibitors. J Chem Inf Model 2016; 56:354-67. [DOI: 10.1021/acs.jcim.5b00484] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joonhyeok Choi
- Research
Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, Republic of Korea
| | - Kwang-Eun Choi
- Research
Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, Republic of Korea
| | - Sung Jean Park
- College
of Pharmacy, Gachon University, Incheon 406-799, Republic of Korea
| | - Sun Yeou Kim
- College
of Pharmacy, Gachon University, Incheon 406-799, Republic of Korea
| | - Jun-Goo Jee
- Research
Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, Republic of Korea
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6
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Bietz S, Rarey M. SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles. J Chem Inf Model 2016; 56:248-59. [PMID: 26759067 DOI: 10.1021/acs.jcim.5b00588] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Structural flexibility of proteins has an important influence on molecular recognition and enzymatic function. In modeling, structure ensembles are therefore often applied as a valuable source of alternative protein conformations. However, their usage is often complicated by structural artifacts and inconsistent data annotation. Here, we present SIENA, a new computational approach for the automated assembly and preprocessing of protein binding site ensembles. Starting with an arbitrarily defined binding site in a single protein structure, SIENA searches for alternative conformations of the same or sequentially closely related binding sites. The method is based on an indexed database for identifying perfect k-mer matches and a recently published algorithm for the alignment of protein binding site conformations. Furthermore, SIENA provides a new algorithm for the interaction-based selection of binding site conformations which aims at covering all known ligand-binding geometries. Various experiments highlight that SIENA is able to generate comprehensive and well selected binding site ensembles improving the compatibility to both known and unconsidered ligand molecules. Starting with the whole PDB as data source, the computation time of the whole ensemble generation takes only a few seconds. SIENA is available via a Web service at www.zbh.uni-hamburg.de/siena .
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Affiliation(s)
- Stefan Bietz
- Center for Bioinformatics, University of Hamburg , Bundesstrasse 43, 20146 Hamburg, Germany
| | - Matthias Rarey
- Center for Bioinformatics, University of Hamburg , Bundesstrasse 43, 20146 Hamburg, Germany
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7
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Huang Z, Wong CF. Inexpensive Method for Selecting Receptor Structures for Virtual Screening. J Chem Inf Model 2015; 56:21-34. [PMID: 26651874 DOI: 10.1021/acs.jcim.5b00299] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This article introduces a screening performance index (SPI) to help select from a number of experimental structures one or a few that are more likely to identify more actives among its top hits from virtual screening of a compound library. It achieved this by docking only known actives to the experimental structures without considering a large number of decoys to reduce computational costs. The SPI is calculated by using the docking energies of the actives to all the receptor structures. We evaluated the performance of the SPI by applying it to study eight protein systems: fatty acid binding protein adipocyte FABP4, serine/threonine-protein kinase BRAF, beta-1 adrenergic receptor ADRB1, TGF-beta receptor type I TGFR1, adenosylhomocysteinase SAHH, thyroid hormone receptor beta-1 THB, phospholipase A2 group IIA PA2GA, and cytochrome P450 3a4 CP3A4. We found that the SPI agreed with the results from other popular performance metrics such as Boltzmann-Enhanced Discrimination Receiver Operator Characteristics (BEDROC), Robust Initial Enhancement (RIE), Area Under Accumulation Curve (AUAC), and Enrichment Factor (EF) but is less expensive to calculate. SPI also performed better than the best docking energy, the molecular volume of the bound ligand, and the resolution of crystal structure in selecting good receptor structures for virtual screening. The implications of these findings were further discussed in the context of ensemble docking, in situations when no experimental structure for the targeted protein was available, or under circumstances when quick choices of receptor structures need to be made before quantitative indexes such as the SPI and BEDROC can be calculated.
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Affiliation(s)
- Zunnan Huang
- China-America Cancer Research Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University , Dongguan, Guangdong Province, P. R. China , 523808
| | - Chung F Wong
- Department of Chemistry and Biochemistry and Center for Nanoscience, University of Missouri-Saint Louis , One University Boulevard, St. Louis, Missouri 63121, United States
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8
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Li Y, Li X, Dong Z. Statistical analysis of EGFR structures' performance in virtual screening. J Comput Aided Mol Des 2015; 29:1045-55. [PMID: 26476847 DOI: 10.1007/s10822-015-9877-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/14/2015] [Indexed: 12/11/2022]
Abstract
In this work the ability of EGFR structures to distinguish true inhibitors from decoys in docking and MM-PBSA is assessed by statistical procedures. The docking performance depends critically on the receptor conformation and bound state. The enrichment of known inhibitors is well correlated with the difference between EGFR structures rather than the bound-ligand property. The optimal structures for virtual screening can be selected based purely on the complex information. And the mixed combination of distinct EGFR conformations is recommended for ensemble docking. In MM-PBSA, a variety of EGFR structures have identically good performance in the scoring and ranking of known inhibitors, indicating that the choice of the receptor structure has little effect on the screening.
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Affiliation(s)
- Yan Li
- The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA.
| | - Xiang Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA.
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9
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Antunes DA, Devaurs D, Kavraki LE. Understanding the challenges of protein flexibility in drug design. Expert Opin Drug Discov 2015; 10:1301-13. [DOI: 10.1517/17460441.2015.1094458] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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10
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Hou X, Li K, Yu X, Sun JP, Fang H. Protein Flexibility in Docking-Based Virtual Screening: Discovery of Novel Lymphoid-Specific Tyrosine Phosphatase Inhibitors Using Multiple Crystal Structures. J Chem Inf Model 2015; 55:1973-83. [DOI: 10.1021/acs.jcim.5b00344] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Xuben Hou
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology
of Natural Products (MOE), School of Pharmacy, ‡Department of Physiology, School
of Medicine, and §Key Laboratory Experimental Teratology of the Ministry of Education
and Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Kangshuai Li
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology
of Natural Products (MOE), School of Pharmacy, ‡Department of Physiology, School
of Medicine, and §Key Laboratory Experimental Teratology of the Ministry of Education
and Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Xiao Yu
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology
of Natural Products (MOE), School of Pharmacy, ‡Department of Physiology, School
of Medicine, and §Key Laboratory Experimental Teratology of the Ministry of Education
and Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Jin-peng Sun
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology
of Natural Products (MOE), School of Pharmacy, ‡Department of Physiology, School
of Medicine, and §Key Laboratory Experimental Teratology of the Ministry of Education
and Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Hao Fang
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology
of Natural Products (MOE), School of Pharmacy, ‡Department of Physiology, School
of Medicine, and §Key Laboratory Experimental Teratology of the Ministry of Education
and Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
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11
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Xu D, Wang B, Meroueh SO. Structure-based computational approaches for small-molecule modulation of protein-protein interactions. Methods Mol Biol 2015; 1278:77-92. [PMID: 25859944 DOI: 10.1007/978-1-4939-2425-7_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Three-dimensional structures of proteins offer an opportunity for the rational design of small molecules to modulate protein-protein interactions. The presence of a well-defined binding pocket on the surface of protein complexes, particularly at their interface, can be used for docking-based virtual screening of chemical libraries. Several approaches have been developed to identify binding pockets that are implemented in programs such as SiteMap, fpocket, and FTSite. These programs enable the scoring of these pockets to determine whether they are suitable to accommodate high-affinity small molecules. Virtual screening of commercial or combinatorial libraries can be carried out to enrich these libraries and select compounds for further experimental validation. In virtual screening, a compound library is docked to the target protein. The resulting structures are scored and ranked for the selection and experimental validation of top candidates. Molecular docking has been implemented in a number of computer programs such as AutoDock Vina. We select a set of protein-protein interactions that have been successfully inhibited with small molecules in the past. Several computer programs are applied to identify pockets on the surface, and molecular docking is conducted in an attempt to reproduce the binding pose of the inhibitors. The results highlight the strengths and limitations of computational methods for the design of PPI inhibitors.
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Affiliation(s)
- David Xu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 W. 10th Street, Indianapolis, IN, 46202, USA
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12
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Lv M, Ma S, Tian Y, Zhang X, Lv W, Zhai H. Computational studies on the binding mechanism between triazolone inhibitors and Chk1 by molecular docking and molecular dynamics. MOLECULAR BIOSYSTEMS 2014; 11:275-86. [PMID: 25372494 DOI: 10.1039/c4mb00449c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chk1, a serine/threonine protein kinase that participates in transducing DNA damage signals, is an attractive target due to its involvement in tumor initiation and progression. As a novel Chk1 inhibitor, the triazolone's bioactivity mechanism is not clear. In this study, we carried out an integrated computational study that combines molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations to identify the key factors necessary for the bioactivities. With the aim of discerning the structural features that affect the inhibitory activity of triazolones, MK-8776, a Chk1 inhibitor that reached the clinical stage, was also used as a reference for simulations. A comparative analysis of the triazolone inhibitors at the molecular level offers valuable insight into the structural and energetic properties. A general feature is that all the studied inhibitors bind in the pocket characterized by residues Leu14, Val22, Ala35, Glu84, Tyr85, Cys86, and Leu136 of Chk1. Moreover, introducing hydrophobic groups into triazolone inhibitors is favorable for binding to Chk1, which is corroborated by residue Leu136 with a relatively large difference in the contribution between MK-8776 and five triazolones to the total binding free energies. A hydrogen bond between the polar hydrogen atoms at R1 and Cys86 can facilitate proper placement of the inhibitor in the binding pocket of Chk1 that favors binding. However, the introduction of hydrophilic groups into the R2 position diminishes binding affinity. The information provided by this research is of benefit for further rational design of novel promising inhibitors of Chk1.
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Affiliation(s)
- Min Lv
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, Gansu Province, People's Republic of China.
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13
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Li Y, Li X, Dong Z. Concerted dynamic motions of an FABP4 model and its ligands revealed by microsecond molecular dynamics simulations. Biochemistry 2014; 53:6409-17. [PMID: 25231537 PMCID: PMC4196735 DOI: 10.1021/bi500374t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
In this work, we investigate the
dynamic motions of fatty acid
binding protein 4 (FABP4) in the absence and presence of a ligand
by explicitly solvated all-atom molecular dynamics simulations. The
dynamics of one ligand-free FABP4 and four ligand-bound FABP4s is
compared via multiple 1.2 μs simulations. In our simulations,
the protein interconverts between the open and closed states. Ligand-free
FABP4 prefers the closed state, whereas ligand binding induces a conformational
transition to the open state. Coupled with opening and closing of
FABP4, the ligand adopts distinct binding modes, which are identified
and compared with crystal structures. The concerted dynamics of protein
and ligand suggests that there may exist multiple FABP4–ligand
binding conformations. Thus, this work provides details about how
ligand binding affects the conformational preference of FABP4 and
how ligand binding is coupled with a conformational change of FABP4
at an atomic level.
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Affiliation(s)
- Yan Li
- The Hormel Institute, University of Minnesota , Austin, Minnesota 55912, United States
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14
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Kumar V, Krishna S, Siddiqi MI. Virtual screening strategies: recent advances in the identification and design of anti-cancer agents. Methods 2014; 71:64-70. [PMID: 25171960 DOI: 10.1016/j.ymeth.2014.08.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/31/2014] [Accepted: 08/19/2014] [Indexed: 01/29/2023] Open
Abstract
Virtual screening (VS) is a well-established technique, which is now routinely employed in computer aided drug designing process. VS can be broadly classified into two categories, i.e., ligand-based and structure-based approach. In recent years, VS has emerged as a time saving and cost effective technique, capable of screening millions of compounds in a user friendly manner. In the area of cancer drug design, VS methods have been widely used and helped in identifying novel molecules as potential anti-cancer agents. Both ligand-based VS (LBVS) structure-based VS (SBVS) methods have been highly useful in the identification of a number of potential anti-cancer agents exhibiting activities in nanomolar range. In tune with the rapid progress in the enhancement of computational power, VS has witnessed significant change in terms of speed and hit rate and in future it is expected that VS will be a preferential alternative to high throughput screening (HTS). This review, discusses recent trends and contribution of VS in the area of anti-cancer drug discovery.
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Affiliation(s)
- Vikash Kumar
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Shagun Krishna
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Mohammad Imran Siddiqi
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India; Academy of Scientific and Innovative Research, New Delhi, India.
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15
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An exhaustive yet simple virtual screening campaign against Sortase A from multiple drug resistant Staphylococcus aureus. Mol Biol Rep 2014; 41:5167-75. [PMID: 24797540 DOI: 10.1007/s11033-014-3384-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 04/22/2014] [Indexed: 10/25/2022]
Abstract
Methicillin resistant Staphylococcus aureus (MRSA) is one of the challenging bacterial pathogen due to its acquired resistance to the β lactam antibiotics. The Sortase A is an enzyme of Gram-positive bacteria including S. aureus to anchor surface proteins to the cell wall. Sortase A is well studied enzyme and considered as the drug target against MRSA. Sortase A plays active role in anchoring the virulence proteins on the cell wall of the Gram-positive bacteria. The inhibition of Sortase A activity results in the separation of S. aureus from the host cells and ultimately alleviation of the infection. Here, we adapted a structure-based virtual screening protocol which helped in identification of novel potential inhibitors of Sortase A. The protocol involved the docking of a chemical library of druglike compounds with the Sortase A binding site represented by multiple crystal structures. The compounds were ranked by multiple scoring functions and shortlisted for future experimental screening. The method resulted in shortlisting of three compounds as potential novel inhibitors of Sortase A out of a large chemical library. The high rankings of shortlisted compounds estimated by multiple scoring functions showed their binding potential with Sortase A. The results are proved to be a simple yet efficient choice of structure-based virtual screening. The identified compounds are druglike and show high rankings among all set protocols of the virtual screening. We hope that the study would eventually help to expedite the discovery of novel drug candidates against MRSA.
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16
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Abstract
Docking methodology aims to predict the experimental binding modes and affinities of small molecules within the binding site of particular receptor targets and is currently used as a standard computational tool in drug design for lead compound optimisation and in virtual screening studies to find novel biologically active molecules. The basic tools of a docking methodology include a search algorithm and an energy scoring function for generating and evaluating ligand poses. In this review, we present the search algorithms and scoring functions most commonly used in current molecular docking methods that focus on protein-ligand applications. We summarise the main topics and recent computational and methodological advances in protein-ligand docking. Protein flexibility, multiple ligand binding modes and the free-energy landscape profile for binding affinity prediction are important and interconnected challenges to be overcome by further methodological developments in the docking field.
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17
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Coleman RG, Carchia M, Sterling T, Irwin JJ, Shoichet BK. Ligand pose and orientational sampling in molecular docking. PLoS One 2013; 8:e75992. [PMID: 24098414 PMCID: PMC3787967 DOI: 10.1371/journal.pone.0075992] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 08/13/2013] [Indexed: 12/19/2022] Open
Abstract
Molecular docking remains an important tool for structure-based screening to find new ligands and chemical probes. As docking ambitions grow to include new scoring function terms, and to address ever more targets, the reliability and extendability of the orientation sampling, and the throughput of the method, become pressing. Here we explore sampling techniques that eliminate stochastic behavior in DOCK3.6, allowing us to optimize the method for regularly variable sampling of orientations. This also enabled a focused effort to optimize the code for efficiency, with a three-fold increase in the speed of the program. This, in turn, facilitated extensive testing of the method on the 102 targets, 22,805 ligands and 1,411,214 decoys of the Directory of Useful Decoys - Enhanced (DUD-E) benchmarking set, at multiple levels of sampling. Encouragingly, we observe that as sampling increases from 50 to 500 to 2000 to 5000 to 20000 molecular orientations in the binding site (and so from about 1×1010 to 4×1010 to 1×1011 to 2×1011 to 5×1011 mean atoms scored per target, since multiple conformations are sampled per orientation), the enrichment of ligands over decoys monotonically increases for most DUD-E targets. Meanwhile, including internal electrostatics in the evaluation ligand conformational energies, and restricting aromatic hydroxyls to low energy rotamers, further improved enrichment values. Several of the strategies used here to improve the efficiency of the code are broadly applicable in the field.
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Affiliation(s)
- Ryan G. Coleman
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Michael Carchia
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Teague Sterling
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - John J. Irwin
- Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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18
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Yuriev E, Ramsland PA. Latest developments in molecular docking: 2010-2011 in review. J Mol Recognit 2013; 26:215-39. [PMID: 23526775 DOI: 10.1002/jmr.2266] [Citation(s) in RCA: 201] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 01/16/2013] [Accepted: 01/19/2013] [Indexed: 12/28/2022]
Affiliation(s)
- Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences; Monash University; Parkville; VIC; 3052; Australia
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Rueda M, Totrov M, Abagyan R. ALiBERO: evolving a team of complementary pocket conformations rather than a single leader. J Chem Inf Model 2012; 52:2705-14. [PMID: 22947092 PMCID: PMC3478405 DOI: 10.1021/ci3001088] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Docking and virtual screening (VS) reach maximum potential when the receptor displays the structural changes needed for accurate ligand binding. Unfortunately, these conformational changes are often poorly represented in experimental structures or homology models, debilitating their docking performance. Recently, we have shown that receptors optimized with our LiBERO method (Ligand-guided Backbone Ensemble Receptor Optimization) were able to better discriminate active ligands from inactives in flexible-ligand VS docking experiments. The LiBERO method relies on the use of ligand information for selecting the best performing individual pockets from ensembles derived from normal-mode analysis or Monte Carlo. Here we present ALiBERO, a new computational tool that has expanded the pocket selection from single to multiple, allowing for automatic iteration of the sampling-selection procedure. The selection of pockets is performed by a dual method that uses exhaustive combinatorial search plus individual addition of pockets, selecting only those that maximize the discrimination of known actives compounds from decoys. The resulting optimized pockets showed increased VS performance when later used in much larger unrelated test sets consisting of biologically active and inactive ligands. In this paper we will describe the design and implementation of the algorithm, using as a reference the human estrogen receptor alpha.
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Affiliation(s)
- Manuel Rueda
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, USA
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