101
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Adasme-Carreño F, Muñoz-Gutierrez C, Caballero J, Alzate-Morales JH. Performance of the MM/GBSA scoring using a binding site hydrogen bond network-based frame selection: the protein kinase case. Phys Chem Chem Phys 2014; 16:14047-58. [DOI: 10.1039/c4cp01378f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Conformational clustering using hydrogen bond network analysis improved the MM/GBSA scoring for some protein-kinase–ligand systems used as case studies.
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Affiliation(s)
- Francisco Adasme-Carreño
- Centro de Bioinformática y Simulación Molecular (CBSM)
- Escuela de Ingeniería en Bioinformática
- Facultad de Ingeniería
- Universidad de Talca
- Talca, Chile
| | - Camila Muñoz-Gutierrez
- Centro de Bioinformática y Simulación Molecular (CBSM)
- Escuela de Ingeniería en Bioinformática
- Facultad de Ingeniería
- Universidad de Talca
- Talca, Chile
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular (CBSM)
- Escuela de Ingeniería en Bioinformática
- Facultad de Ingeniería
- Universidad de Talca
- Talca, Chile
| | - Jans H. Alzate-Morales
- Centro de Bioinformática y Simulación Molecular (CBSM)
- Escuela de Ingeniería en Bioinformática
- Facultad de Ingeniería
- Universidad de Talca
- Talca, Chile
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102
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Handa K, Nakagome I, Yamaotsu N, Gouda H, Hirono S. In Silieo Study on the Inhibitory Interaction of Drugs with Wild-type CYP2D6.1 and the Natural Variant CYP2D6.17. Drug Metab Pharmacokinet 2014; 29:52-60. [DOI: 10.2133/dmpk.dmpk-13-rg-044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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103
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Kirubakaran P, Kothandan G, Cho SJ, Muthusamy K. Molecular insights on TNKS1/TNKS2 and inhibitor-IWR1 interactions. ACTA ACUST UNITED AC 2014; 10:281-93. [DOI: 10.1039/c3mb70305c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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104
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Could MM-GBSA be accurate enough for calculation of absolute protein/ligand binding free energies? J Mol Graph Model 2013; 46:41-51. [DOI: 10.1016/j.jmgm.2013.09.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 09/06/2013] [Accepted: 09/07/2013] [Indexed: 11/20/2022]
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105
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Topin J, Arnaud J, Sarkar A, Audfray A, Gillon E, Perez S, Jamet H, Varrot A, Imberty A, Thomas A. Deciphering the glycan preference of bacterial lectins by glycan array and molecular docking with validation by microcalorimetry and crystallography. PLoS One 2013; 8:e71149. [PMID: 23976992 PMCID: PMC3747263 DOI: 10.1371/journal.pone.0071149] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 06/26/2013] [Indexed: 11/18/2022] Open
Abstract
Recent advances in glycobiology revealed the essential role of lectins for deciphering the glycocode by specific recognition of carbohydrates. Integrated multiscale approaches are needed for characterizing lectin specificity: combining on one hand high-throughput analysis by glycan array experiments and systematic molecular docking of oligosaccharide libraries and on the other hand detailed analysis of the lectin/oligosaccharide interaction by x-ray crystallography, microcalorimetry and free energy calculations. The lectins LecB from Pseudomonas aeruginosa and BambL from Burkholderia ambifaria are part of the virulence factors used by the pathogenic bacteria to invade the targeted host. These two lectins are not related but both recognize fucosylated oligosaccharides such as the histo-blood group oligosaccharides of the ABH(O) and Lewis epitopes. The specificities were characterized using semi-quantitative data from glycan array and analyzed by molecular docking with the Glide software. Reliable prediction of protein/oligosaccharide structures could be obtained as validated by existing crystal structures of complexes. Additionally, the crystal structure of BambL/Lewis x was determined at 1.6 Å resolution, which confirms that Lewis x has to adopt a high-energy conformation so as to bind to this lectin. Free energies of binding were calculated using a procedure combining the Glide docking protocol followed by free energy rescoring with the Prime/Molecular Mechanics Generalized Born Surface Area (MM-GBSA) method. The calculated data were in reasonable agreement with experimental free energies of binding obtained by titration microcalorimetry. The established predictive protocol is proposed to rationalize large sets of data such as glycan arrays and to help in lead discovery projects based on such high throughput technology.
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Affiliation(s)
- Jeremie Topin
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
- Département de Chimie Moléculaire, UMR- Centre national de la recherche scientifique 5250 & ICMG FR 2607, Université Joseph Fourier, BP 53, 38041 Grenoble, France
| | - Julie Arnaud
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
| | - Anita Sarkar
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
| | - Aymeric Audfray
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
| | - Emilie Gillon
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
| | - Serge Perez
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
| | - Helene Jamet
- Département de Chimie Moléculaire, UMR- Centre national de la recherche scientifique 5250 & ICMG FR 2607, Université Joseph Fourier, BP 53, 38041 Grenoble, France
| | - Annabelle Varrot
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
| | - Anne Imberty
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
- * E-mail:
| | - Aline Thomas
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
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106
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In silico design: extended molecular dynamic simulations of a new series of dually acting inhibitors against EGFR and HER2. J Mol Graph Model 2013; 44:220-31. [PMID: 23911931 DOI: 10.1016/j.jmgm.2013.06.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 06/13/2013] [Accepted: 06/17/2013] [Indexed: 01/23/2023]
Abstract
Based on the hit structures that have been identified in our previous studies against EGFR and HER2, new potential inhibitors that share the same scaffold of the hit structures are designed and screened in silico. Insights into understanding the potential inhibitory effect of the new inhibitors against both EGFR and HER2 receptors is obtained using extended molecular dynamics (MD) simulations and different scoring techniques. The binding mechanisms and dynamics are detailed with respect to two approved inhibitors against EGFR (lapatinib) and HER2 (SYR127063). The best scoring inhibitor (T9) is chosen for additional in silico investigation against both the wild-type and T790M mutant strain of EGFR and the wild-type HER2. The results reveal that certain substitution patterns increase the stability and assure stronger binding and higher H-bond occupancy of the conserved water molecule that is commonly observed with kinase crystal structures. Furthermore, the new inhibitor (T9) forms stable interactions with the mutant strain as a direct consequence of the enhanced ability to form additional hydrogen bonding interactions with binding site residues.
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107
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Quantum polarized ligand docking investigation to understand the significance of protonation states in histone deacetylase inhibitors. J Mol Graph Model 2013; 44:44-53. [DOI: 10.1016/j.jmgm.2013.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 04/09/2013] [Accepted: 05/01/2013] [Indexed: 11/20/2022]
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108
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Priyadarshini V, Pradhan D, Munikumar M, Swargam S, Umamaheswari A, Rajasekhar D. Genome-based approaches to develop epitope-driven subunit vaccines against pathogens of infective endocarditis. J Biomol Struct Dyn 2013; 32:876-89. [PMID: 24404767 DOI: 10.1080/07391102.2013.795871] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Infective endocarditis (IE) has emerged as a public health problem due to changes in the etiologic spectrum and due to involvement of resistant bacterial strains with increased virulence. Developing potent vaccine is an important strategy to tackle IE. Complete genome sequences of eight selected pathogens of IE paved the way to design common T-cell driven subunit vaccines. Comparative genomics and subtractive genomic analysis were applied to identify adinosine tri phosphate (ATP)-binding cassette (ABC) transporter ATP-binding protein from Streptococcus mitis (reference organism) as common vaccine target. Reverse vaccinology technique was implemented using computational tools such as ProPred, SYFPEITHI, and Immune epitope database. Twenty-one T-cell epitopes were predicted from ABC transporter ATP-binding protein. Multiple sequence alignment of ABC transporter ATP-binding protein from eight selected IE pathogens was performed to identify six conserved T-cell epitopes. The six selected T-cell epitopes were further evaluated at structure level for HLA-DRB binding through homology modeling and molecular docking analysis using Maestro v9.2. The proposed six T-cell epitopes showed better binding affinity with the selected HLA-DRB alleles. Subsequently, the docking complexes of T-cell epitope and HLA-DRBs were ranked based on XP Gscore. The T-cell epitope (208-LNYITPDVV-216)-HLA-DRB1(∗)0101 (1T5 W) complex having the best XP Gscore (-13.25 kcal/mol) was assessed for conformational stability and interaction stability through molecular dynamic simulation for 10 ns using Desmond v3.2. The simulation results revealed that the HLA-DRB-epitope complex was stable throughout the simulation time. Thus, the epitope would be ideal candidate for T-cell driven subunit vaccine design against infective endocarditis.
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Affiliation(s)
- Vani Priyadarshini
- a SVIMS Bioinformatics Centre, SVIMS University , Tirupati , Andhra Pradesh , 517507 , India
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109
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Ilatovskiy AV, Abagyan R, Kufareva I. Quantum Mechanics Approaches to Drug Research in the Era of Structural Chemogenomics. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2013; 113:1669-1675. [PMID: 25414519 PMCID: PMC4235788 DOI: 10.1002/qua.24400] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The rapid growth of the available crystallographic information about proteins and binding pockets creates remarkable opportunities for enriching the drug research pipelines with computational prediction of novel protein-ligand interactions. While ab initio quantum mechanical approaches are known to provide unprecedented accuracy in structure-based binding energy calculations, they are limited to only small systems of dozens of atoms. In the structural chemogenomics era, it is critical that new approaches are developed that enable application of QM methodologies to non-covalent interactions in systems as large as protein-ligand complexes and conformational ensembles. This perspective highlights recent advances towards bridging the gap between high accuracy and high volume computations in drug research.
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Affiliation(s)
- Andrey V. Ilatovskiy
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA, 92093
- Division of Molecular and Radiation Biophysics, Konstantinov Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia, 188300
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA, 92093
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA, 92093
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110
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Ahmed M, Sadek MM, Serrya RA, Kafafy AHN, Abouzid KA, Wang F. Assessment of new anti-HER2 ligands using combined docking, QM/MM scoring and MD simulation. J Mol Graph Model 2013; 40:91-8. [DOI: 10.1016/j.jmgm.2012.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 12/04/2012] [Accepted: 12/06/2012] [Indexed: 01/23/2023]
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111
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Sadek MM, Serrya RA, Kafafy AHN, Ahmed M, Wang F, Abouzid KAM. Discovery of new HER2/EGFR dual kinase inhibitors based on the anilinoquinazoline scaffold as potential anti-cancer agents. J Enzyme Inhib Med Chem 2013; 29:215-22. [PMID: 23402383 DOI: 10.3109/14756366.2013.765417] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Herein, we designed and synthesized certain anilinoquinazoline derivatives bearing bulky arylpyridinyl, arylpropenoyl and arylpyrazolyl moieties at the 4' position of the anilinoquinazoline, as potential dual HER2/EGFR kinase inhibitors. A detailed molecular modeling study was performed by docking the synthesized compounds in the active site of the epidermal growth factor receptor (EGFR). The synthesized compounds were further tested for their inhibitory activity on EGFR and HER2 tyrosine kinases. The aryl 2-imino-1,2-dihydropyridine derivatives 5d and 5e displayed the most potent inhibitory activity on EGFR with IC50 equal to 2.09 and 1.94 μM, respectively, and with IC50 equal to 3.98 and 1.04 μM on HER2, respectively. Furthermore, the anti-proliferative activity of these most active compounds on MDA-MB-231 breast cancer cell lines, known to overexpress EGFR, showed an IC50 range of 2.4 and 2.5 μM, respectively.
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Affiliation(s)
- Maiada M Sadek
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, MSA University , 6th October, Cairo , Egypt
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112
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Shen M, Zhou S, Li Y, Pan P, Zhang L, Hou T. Discovery and optimization of triazine derivatives as ROCK1 inhibitors: molecular docking, molecular dynamics simulations and free energy calculations. MOLECULAR BIOSYSTEMS 2013; 9:361-74. [DOI: 10.1039/c2mb25408e] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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113
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Kim M, Lee KW, Cho AE. Elucidation of allosteric inhibition mechanism of 2-Cys human peroxiredoxin by molecular modeling. J Chem Inf Model 2012. [PMID: 23194275 DOI: 10.1021/ci3004495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We used molecular dynamics (MD) simulations and protein docking to elucidate the mechanism of allosteric inhibition of the human form of peroxiredoxin (Prx), 2-Cys proliferation associated gene (PAG). Beginning by using the rat form of Prx, 2-Cys heme-binding protein as a template, we used homology modeling to find the structure of human 2-Cys PAG, which is in dimeric form. Molecular dynamics simulations showed that the structure of the reduced form of the 2-Cys PAG dimer fluctuates as the two monomers drift away and approach each other. We then used SiteMap to search for binding sites on the surface of this dimer. A binding site between the two monomers was found, and virtual screening with docking was performed to identify a ligand binding to this site. Subsequent MD simulation revealed that with this ligand in the binding site, the dimer structure of 2-Cys PAG becomes stabilized such that two cysteine residues from two monomers, which are partners of a disulfide bond of the oxidized form, remain separated. This mechanism can be used as an allosteric inhibition of Prx as a hydrogen peroxide reducer, the role of which has been studied as an anticancer drug target.
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Affiliation(s)
- Minsup Kim
- Department of Bioinformatics, Korea University, Sejong, Korea
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