51
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Mortier J, Rakers C, Bermudez M, Murgueitio MS, Riniker S, Wolber G. The impact of molecular dynamics on drug design: applications for the characterization of ligand-macromolecule complexes. Drug Discov Today 2015; 20:686-702. [PMID: 25615716 DOI: 10.1016/j.drudis.2015.01.003] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Revised: 12/08/2014] [Accepted: 01/08/2015] [Indexed: 10/24/2022]
Abstract
Among all tools available to design new drugs, molecular dynamics (MD) simulations have become an essential technique. Initially developed to investigate molecular models with a limited number of atoms, computers now enable investigations of large macromolecular systems with a simulation time reaching the microsecond range. The reviewed articles cover four years of research to give an overview on the actual impact of MD on the current medicinal chemistry landscape with a particular emphasis on studies of ligand-protein interactions. With a special focus on studies combining computational approaches with data gained from other techniques, this review shows how deeply embedded MD simulations are in drug design strategies and articulates what the future of this technique could be.
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Affiliation(s)
- Jérémie Mortier
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany.
| | - Christin Rakers
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany
| | - Marcel Bermudez
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany
| | - Manuela S Murgueitio
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Gerhard Wolber
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany.
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52
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Bren U, Fuchs JE, Oostenbrink C. Cooperative binding of aflatoxin B1 by cytochrome P450 3A4: a computational study. Chem Res Toxicol 2014; 27:2136-47. [PMID: 25398138 DOI: 10.1021/tx5004062] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Aflatoxin B1 (AFB1)-the most potent natural carcinogen known to men-is metabolized by cytochrome P450 3A4 (CYP3A4), either to the genotoxic AFB1 exo-8,9-epoxide or to the detoxified 3α-hydroxy AFB1. The activation of the procarcinogen proceeds in a highly cooperative fashion, which differs from common allosteric regulation in the sense that it can be attributed to simultaneous occupancy of a single large and malleable active site by multiple ligand molecules. Unfortunately, unlike in the case of ketoconazole, there is currently no experimental structure available for the doubly ligated CYP3A4-AFB1 complex. Therefore, we employed a sequential molecular docking protocol to create various possible doubly ligated complexes and subsequently performed molecular dynamics simulations and free-energy calculations to check for their consistency with the available experimental data on regio- and stereoselectivity of both AFB1 oxidations as well as with available kinetic data. Only the system in which the first AFB1 molecule was bound in a face-on C8-C9 epoxidation mode and the second AFB1 molecule was bound in a side-on 3α-hydroxylation mode-a result of an unconstrained molecular docking protocol-has successfully fulfilled all the imposed criteria and is therefore proposed as the most likely structure of the doubly ligated complex of CYP3A4 with AFB1. The empirical Linear Interaction Energy method revealed that shape complementarity through nonpolar dispersion interactions between the two bound AFB1 molecules is the main source of the experimentally observed positive homotropic cooperativity. The reported study represents a nice example of how state-of-the-art molecular modeling techniques can be used to study complicated macromolecular complexes, whose structures have not yet been experimentally determined, and to validate these against the available experimental data. The proposed structure will facilitate future studies on the rational design of successful AFB1 modulators or on human subpopulations characterized by specific CYP3A4 polymorphisms that are especially sensitive to AFB1.
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Affiliation(s)
- Urban Bren
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Muthgasse 18, AT-1190 Vienna, Austria
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53
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Nair PC, Miners JO. Molecular dynamics simulations: from structure function relationships to drug discovery. In Silico Pharmacol 2014; 2:4. [PMID: 25516823 PMCID: PMC4244305 DOI: 10.1186/s40203-014-0004-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 11/04/2014] [Indexed: 01/29/2023] Open
Abstract
Molecular dynamics (MD) simulation is an emerging in silico technique with potential applications in diverse areas of pharmacology. Over the past three decades MD has evolved as an area of importance for understanding the atomic basis of complex phenomena such as molecular recognition, protein folding, and the transport of ions and small molecules across membranes. The application of MD simulations in isolation and in conjunction with experimental approaches have provided an increased understanding of protein structure-function relationships and demonstrated promise in drug discovery.
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Affiliation(s)
- Pramod C Nair
- Department of Clinical Pharmacology, Flinders University School of Medicine, GPO Box 2100, Adelaide, SA 5001 Australia
| | - John O Miners
- Department of Clinical Pharmacology, Flinders University School of Medicine, GPO Box 2100, Adelaide, SA 5001 Australia
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54
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Jeřábek P, Florián J, Stiborová M, Martínek V. Flexible docking-based molecular dynamics/steered molecular dynamics calculations of protein-protein contacts in a complex of cytochrome P450 1A2 with cytochrome b5. Biochemistry 2014; 53:6695-705. [PMID: 25313797 DOI: 10.1021/bi500814t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Formation of transient complexes of cytochrome P450 (P450) with another protein of the endoplasmic reticulum membrane, cytochrome b5 (cyt b5), dictates the catalytic activities of several P450s. Therefore, we examined formation and binding modes of the complex of human P450 1A2 with cyt b5. Docking of soluble domains of these proteins was performed using an information-driven flexible docking approach implemented in HADDOCK. Stabilities of the five unique binding modes of the P450 1A2-cyt b5 complex yielded by HADDOCK were evaluated using explicit 10 ns molecular dynamics (MD) simulations in aqueous solution. Further, steered MD was used to compare the stability of the individual P450 1A2-cyt b5 binding modes. The best binding mode was characterized by a T-shaped mutual orientation of the porphyrin rings and a 10.7 Å distance between the two redox centers, thus satisfying the condition for a fast electron transfer. Mutagenesis studies and chemical cross-linking, which, in the absence of crystal structures, were previously used to deduce specific P450-cyt b5 interactions, indicated that the negatively charged convex surface of cyt b5 binds to the positively charged concave surface of P450. Our simulations further elaborate structural details of this interface, including nine ion pairs between R95, R100, R138, R362, K442, K455, and K465 side chains of P450 1A2 and E42, E43, E49, D65, D71, and heme propionates of cyt b5. The universal heme-centric system of internal coordinates was proposed to facilitate consistent classification of the orientation of the two porphyrins in any protein complex.
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Affiliation(s)
- Petr Jeřábek
- Department of Biochemistry, Faculty of Science, Charles University in Prague , Albertov 2030, 128 43 Prague 2, Czech Republic
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55
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Oostenbrink C. Structure‐Based Methods for Predicting the Sites and Products of Metabolism. ACTA ACUST UNITED AC 2014. [DOI: 10.1002/9783527673261.ch10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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56
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Lonsdale R, Rouse SL, Sansom MSP, Mulholland AJ. A multiscale approach to modelling drug metabolism by membrane-bound cytochrome P450 enzymes. PLoS Comput Biol 2014; 10:e1003714. [PMID: 25033460 PMCID: PMC4102395 DOI: 10.1371/journal.pcbi.1003714] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 05/28/2014] [Indexed: 01/30/2023] Open
Abstract
Cytochrome P450 enzymes are found in all life forms. P450s play an important role in drug metabolism, and have potential uses as biocatalysts. Human P450s are membrane-bound proteins. However, the interactions between P450s and their membrane environment are not well-understood. To date, all P450 crystal structures have been obtained from engineered proteins, from which the transmembrane helix was absent. A significant number of computational studies have been performed on P450s, but the majority of these have been performed on the solubilised forms of P450s. Here we present a multiscale approach for modelling P450s, spanning from coarse-grained and atomistic molecular dynamics simulations to reaction modelling using hybrid quantum mechanics/molecular mechanics (QM/MM) methods. To our knowledge, this is the first application of such an integrated multiscale approach to modelling of a membrane-bound enzyme. We have applied this protocol to a key human P450 involved in drug metabolism: CYP3A4. A biologically realistic model of CYP3A4, complete with its transmembrane helix and a membrane, has been constructed and characterised. The dynamics of this complex have been studied, and the oxidation of the anticoagulant R-warfarin has been modelled in the active site. Calculations have also been performed on the soluble form of the enzyme in aqueous solution. Important differences are observed between the membrane and solution systems, most notably for the gating residues and channels that control access to the active site. The protocol that we describe here is applicable to other membrane-bound enzymes.
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Affiliation(s)
- Richard Lonsdale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Sarah L. Rouse
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail: (MSPS); (AJM)
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
- * E-mail: (MSPS); (AJM)
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57
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Wang M, Baaden M, Wang J, Liang Z. A cooperative mechanism of clotrimazoles in P450 revealed by the dissociation picture of clotrimazole from P450. J Chem Inf Model 2014; 54:1218-25. [PMID: 24611729 DOI: 10.1021/ci400660e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dissociation processes of clotrimazole (CLT) in several models are comparatively investigated by molecular dynamics simulations to explore the cooperative mechanism of clotrimazoles in P450. Our results suggest that when P450 only accommodates the active CLT (CLT1), CLT1 continually diffuses away from heme, and the partial BC loop (residues 73-88) and the extended FG loop (residues 173-186) first close and then open. When the enzyme binds to two CLT molecules, CLT1 basically keeps close to heme, and the partial BC loop and the extended FG loop move close to each other. Clearly, the effector CLT (CLT2) plays a cooperative role in the inhibition of CLT1 on P450. CLT2 restrains the dissociation of CLT1 first through direct π-π stacking interactions and then through the rearranged binding site induced by CLT2. The presence of CLT1 can help to stabilize the protein structure around CLT2 by interacting with M86, Q173, and M174.
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Affiliation(s)
- Mian Wang
- School of Chemistry and Chemical Engineering, Guangxi University , Nanning 530004, China
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58
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Liu T, Qian G, Wang W, Zhang Y. Molecular docking to understand the metabolic behavior of GNF-351 by CYP3A4 and its potential drug–drug interaction with ketoconazole. Eur J Drug Metab Pharmacokinet 2014; 40:235-8. [DOI: 10.1007/s13318-014-0201-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 04/15/2014] [Indexed: 01/03/2023]
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59
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Pimenta AC, Martins JM, Fernandes R, Moreira IS. Ligand-Induced Structural Changes in TEM-1 Probed by Molecular Dynamics and Relative Binding Free Energy Calculations. J Chem Inf Model 2013; 53:2648-58. [DOI: 10.1021/ci400269d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- A. C. Pimenta
- REQUIMTE/Departamento
de Química, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
- Centro
de Investigação em Saúde e Ambiente, da Escola
Superior de Tecnologia da Saúde do Porto, do Instituto Politécnico do Porto, Rua Valente Perfeito 322, 4400-330 Vila Nova de Gaia, Portugal
- Centro
de Farmacologia e Biopatologia Química (U38-FCT), Faculdade
de Medicina da Universidade do Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - J. M. Martins
- REQUIMTE/Departamento
de Química, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - R. Fernandes
- Centro
de Investigação em Saúde e Ambiente, da Escola
Superior de Tecnologia da Saúde do Porto, do Instituto Politécnico do Porto, Rua Valente Perfeito 322, 4400-330 Vila Nova de Gaia, Portugal
- Centro
de Farmacologia e Biopatologia Química (U38-FCT), Faculdade
de Medicina da Universidade do Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - I. S. Moreira
- REQUIMTE/Departamento
de Química, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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60
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Bortolato A, Tehan BG, Bodnarchuk MS, Essex JW, Mason JS. Water Network Perturbation in Ligand Binding: Adenosine A2A Antagonists as a Case Study. J Chem Inf Model 2013; 53:1700-13. [DOI: 10.1021/ci4001458] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrea Bortolato
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts,
AL7 3AX, U.K
| | - Ben G. Tehan
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts,
AL7 3AX, U.K
| | - Michael S. Bodnarchuk
- School of
Chemistry, University of Southampton, Highfield,
Southampton,
Hampshire, SO17 1BJ, U.K
| | - Jonathan W. Essex
- School of
Chemistry, University of Southampton, Highfield,
Southampton,
Hampshire, SO17 1BJ, U.K
| | - Jonathan S. Mason
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts,
AL7 3AX, U.K
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61
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Kaiyawet N, Rungrotmongkol T, Hannongbua S. Effect of halogen substitutions on dUMP to stability of thymidylate synthase/dUMP/mTHF ternary complex using molecular dynamics simulation. J Chem Inf Model 2013; 53:1315-23. [PMID: 23705822 DOI: 10.1021/ci400131y] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The stability of the thymidylate synthase (TS)/2-deoxyuridine-5-monophosphate (dUMP)/5,10-methylene-5,6,7,8-tetrahydrofolate (mTHF) ternary complex formation and Michael addition are considered as important steps that are involved in the inhibition mechanism of the anticancer prodrug 5-fluorouracil (5-FU). Here, the effect of three different halogen substitutions on the C-5 position of the dUMP (XdUMPs = FdUMP, CldUMP, and BrdUMP), the normal substrate, on the stability of the TS/dUMP and TS/dUMP/mTHF binary and ternary complexes, respectively, was investigated via molecular dynamics simulation. The simulated results revealed that the stability of all the systems was substantially increased by mTHF binding to the catalytic pocket. In the ternary complex, a much greater stabilization of the dUMP and XdUMPs through electrostatic interactions, including charge-charge and hydrogen bond interactions, was found compared to mTHF. An additional unique hydrogen bond between the substituted fluorine of FdUMP and the hydroxyl group of the TS Y94 residue was observed in both the binary and ternary complexes. The distance between the S(-) atom of the TS C146 residue and the C6 atom of dUMP, at <4 Å in all systems, suggested that a Michael addition with the formation of a S-C6 covalent bond potentially occurred, although the hydrogen atom on C6 of dUMP is substituted by a halogen atom. The MM/PBSA binding free energy revealed the significant role of the bridging waters around the ligands in the increased binding affinity (∼10 kcal/mol) of dUMP/XdUMP, either alone or together with mTHF, toward TS. The order of the averaged binding affinity in the ternary systems was found to be CldUMP ≈ FdUMP > dUMP > BrdUMP, suggesting that CldUMP could be a potent candidate TS inhibitor, the same as FdUMP (the metabolite form of 5-FU).
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Affiliation(s)
- Nopporn Kaiyawet
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Patumwan, Bangkok 10330, Thailand
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62
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Baylon JL, Lenov IL, Sligar SG, Tajkhorshid E. Characterizing the membrane-bound state of cytochrome P450 3A4: structure, depth of insertion, and orientation. J Am Chem Soc 2013; 135:8542-51. [PMID: 23697766 PMCID: PMC3682445 DOI: 10.1021/ja4003525] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Cytochrome P450 3A4 (CYP3A4) is the
most abundant membrane-associated
isoform of the P450 family in humans and is responsible for biotransformation
of more than 50% of drugs metabolized in the body. Despite the large
number of crystallographic structures available for CYP3A4, no structural
information for its membrane-bound state at an atomic level is available.
In order to characterize binding, depth of insertion, membrane orientation,
and lipid interactions of CYP3A4, we have employed a combined experimental
and simulation approach in this study. Taking advantage of a novel
membrane representation, highly mobile membrane mimetic (HMMM), with
enhanced lipid mobility and dynamics, we have been able to capture
spontaneous binding and insertion of the globular domain of the enzyme
into the membrane in multiple independent, unbiased simulations. Despite
different initial orientations and positions of the protein in solution,
all the simulations converged into the same membrane-bound configuration
with regard to both the depth of membrane insertion and the orientation
of the enzyme on the surface of the membrane. In tandem, linear dichroism
measurements performed on CYP3A4 bound to Nanodisc membranes were
used to characterize the orientation of the enzyme in its membrane-bound
form experimentally. The heme tilt angles measured experimentally
are in close agreement with those calculated for the membrane-bound
structures resulted from the simulations, thereby verifying the validity
of the developed model. Membrane binding of the globular domain in
CYP3A4, which appears to be independent of the presence of the transmembrane
helix of the full-length enzyme, significantly reshapes the protein
at the membrane interface, causing conformational changes relevant
to access tunnels leading to the active site of the enzyme.
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Affiliation(s)
- Javier L Baylon
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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63
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Liu J, He X, Zhang JZH. Improving the scoring of protein-ligand binding affinity by including the effects of structural water and electronic polarization. J Chem Inf Model 2013; 53:1306-14. [PMID: 23651068 DOI: 10.1021/ci400067c] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Docking programs that use scoring functions to estimate binding affinities of small molecules to biological targets are widely applied in drug design and drug screening with partial success. But accurate and efficient scoring functions for protein-ligand binding affinity still present a grand challenge to computational chemists. In this study, the polarized protein-specific charge model (PPC) is incorporated into the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method to rescore the binding poses of some protein-ligand complexes, for which docking programs, such as Autodock, could not predict their binding modes correctly. Different sampling techniques (single minimized conformation and multiple molecular dynamics (MD) snapshots) are used to test the performance of MM/PBSA combined with the PPC model. Our results show the availability and effectiveness of this approach in correctly ranking the binding poses. More importantly, the bridging water molecules are found to play an important role in correctly determining the protein-ligand binding modes. Explicitly including these bridging water molecules in MM/PBSA calculations improves the prediction accuracy significantly. Our study sheds light on the importance of both bridging water molecules and the electronic polarization in the development of more reliable scoring functions for predicting molecular docking and protein-ligand binding affinity.
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Affiliation(s)
- Jinfeng Liu
- State Key Laboratory of Precision Spectroscopy and Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
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64
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Cong S, Ma XT, Li YX, Wang JF. Structural Basis for the Mutation-Induced Dysfunction of Human CYP2J2: A Computational Study. J Chem Inf Model 2013; 53:1350-7. [DOI: 10.1021/ci400003p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shan Cong
- Key Laboratory of Systems Biomedicine
(Ministry of Education), Shanghai Center for Systems Biomedicine,
Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiao-Tu Ma
- Key Laboratory of Systems Biomedicine
(Ministry of Education), Shanghai Center for Systems Biomedicine,
Shanghai Jiao Tong University, Shanghai 200240, China
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65
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Molecular dynamics simulations give insight into D-glucose dioxidation at C2 and C3 by Agaricus meleagris pyranose dehydrogenase. J Comput Aided Mol Des 2013; 27:295-304. [PMID: 23591812 PMCID: PMC3657087 DOI: 10.1007/s10822-013-9645-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 04/04/2013] [Indexed: 11/11/2022]
Abstract
The flavin-dependent sugar oxidoreductase pyranose dehydrogenase (PDH) from the plant litter-degrading fungus Agaricus meleagris oxidizes d-glucose (GLC) efficiently at positions C2 and C3. The closely related pyranose 2-oxidase (P2O) from Trametes multicolor oxidizes GLC only at position C2. Consequently, the electron output per molecule GLC is twofold for PDH compared to P2O making it a promising catalyst for bioelectrochemistry or for introducing novel carbonyl functionalities into sugars. The aim of this study was to rationalize the mechanism of GLC dioxidation employing molecular dynamics simulations of GLC–PDH interactions. Shape complementarity through nonpolar van der Waals interactions was identified as the main driving force for GLC binding. Together with a very diverse hydrogen-bonding pattern, this has the potential to explain the experimentally observed promiscuity of PDH towards different sugars. Based on geometrical analysis, we propose a similar reaction mechanism as in P2O involving a general base proton abstraction, stabilization of the transition state, an alkoxide intermediate, through interaction with a protonated catalytic histidine followed by a hydride transfer to the flavin N5 atom. Our data suggest that the presence of the two potential catalytic bases His-512 and His-556 increases the versatility of the enzyme, by employing the most suitably oriented base depending on the substrate and its orientation in the active site. Our findings corroborate and rationalize the experimentally observed dioxidation of GLC by PDH and its promiscuity towards different sugars.
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66
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Leach AG. Tactics to Avoid Inhibition of Cytochrome P450s. TOPICS IN MEDICINAL CHEMISTRY 2013. [DOI: 10.1007/7355_2013_25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
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67
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Genheden S. Are homology models sufficiently good for free-energy simulations? J Chem Inf Model 2012; 52:3013-21. [PMID: 23113602 DOI: 10.1021/ci300349s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In this paper, I evaluate the usefulness of protein homology models in rigorous free-energy simulations to determine ligand affinities. Two templates were used to create models of the factor Xa protein and one template was used for dihydrofolate reductase from Plasmodium falciparum. Then, the relative free energies for several pairs of ligands were estimated using thermodynamic integration with the homology models as starting point of the simulation. These binding affinities were compared to affinities obtained when using published crystal structures as starting point of the simulations. Encouragingly, the differences between the affinities obtained when starting from either homology models or crystal structure were not statistical significant for a majority of the considered pairs of ligands. Differences between 1 and 2 kJ/mol were observed for the dihydrofolate reductase ligands and differences between 0 and 8 kJ/mol were observed for the factor Xa ligands. The largest difference for factor Xa was caused by an erroneous modeling of a loop region close to two of the ligands, and it was only observed when using one of the templates. Therefore, it is advisible to always use more than one template when creating homology models if they should be used in free-energy simulations.
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Affiliation(s)
- Samuel Genheden
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.
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68
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Berne S, Podobnik B, Zupanec N, Novak M, Kraševec N, Turk S, Korošec B, Lah L, Šuligoj E, Stojan J, Gobec S, Komel R. Virtual Screening Yields Inhibitors of Novel Antifungal Drug Target, Benzoate 4-Monooxygenase. J Chem Inf Model 2012; 52:3053-63. [DOI: 10.1021/ci3004418] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sabina Berne
- Faculty of Medicine, Institute
of Biochemistry, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
| | - Barbara Podobnik
- Lek Pharmaceuticals d.d., Verovškova 57, SI-1000 Ljubljana, Slovenia
| | - Neja Zupanec
- Laboratory for Molecular Biology
and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Metka Novak
- Laboratory for Molecular Biology
and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Nada Kraševec
- Laboratory for Molecular Biology
and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Samo Turk
- Faculty of Pharmacy, Chair of
Pharmaceutical Chemistry, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Branka Korošec
- Laboratory for Molecular Biology
and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Ljerka Lah
- Laboratory for Molecular Biology
and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Erika Šuligoj
- Laboratory for Molecular Biology
and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Jure Stojan
- Faculty of Medicine, Institute
of Biochemistry, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, Chair of
Pharmaceutical Chemistry, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Radovan Komel
- Faculty of Medicine, Institute
of Biochemistry, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
- Laboratory for Molecular Biology
and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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69
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Carl N, Hodošček M, Vehar B, Konc J, Brooks BR, Janežič D. Correlating protein hot spot surface analysis using ProBiS with simulated free energies of protein-protein interfacial residues. J Chem Inf Model 2012; 52:2541-9. [PMID: 23009716 DOI: 10.1021/ci3003254] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A protocol was developed for the computational determination of the contribution of interfacial amino acid residues to the free energy of protein-protein binding. Thermodynamic integration, based on molecular dynamics simulation in CHARMM, was used to determine the free energy associated with single point mutations to glycine in a protein-protein interface. The hot spot amino acids found in this way were then correlated to structural similarity scores detected by the ProBiS algorithm for local structural alignment. We find that amino acids with high structural similarity scores contribute on average -3.19 kcal/mol to the free energy of protein-protein binding and are thus correlated with hot spot residues, while residues with low similarity scores contribute on average only -0.43 kcal/mol. This suggests that the local structural alignment method provides a good approximation of the contribution of a residue to the free energy of binding and is particularly useful for detection of hot spots in proteins with known structures but undetermined protein-protein complexes.
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Affiliation(s)
- Nejc Carl
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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70
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Sevrioukova IF, Poulos TL. Understanding the mechanism of cytochrome P450 3A4: recent advances and remaining problems. Dalton Trans 2012; 42:3116-26. [PMID: 23018626 DOI: 10.1039/c2dt31833d] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cytochromes P450 (CYPs) represent a diverse group of heme-thiolate proteins found in almost all organisms. CYPs share a common protein fold but differ in substrate selectivity and catalyze a wide variety of monooxygenation reactions via activation of molecular oxygen. Among 57 human P450s, the 3A4 isoform (CYP3A4) is the most abundant and the most important because it metabolizes the majority of administered drugs. A remarkable feature of CYP3A4 is its extreme promiscuity in substrate specificity and cooperative substrate binding, which often leads to undesirable drug-drug interactions and toxic side effects. Owing to its importance in drug development and therapy, CYP3A4 has been the most extensively studied mammalian P450. In this review we provide an overview on recent progress and remaining problems in the CYP3A4 research.
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Affiliation(s)
- Irina F Sevrioukova
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.
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71
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Soares ROS, Caliri A. Stereochemical features of the envelope protein Domain III of dengue virus reveals putative antigenic site in the five-fold symmetry axis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:221-30. [PMID: 23009809 DOI: 10.1016/j.bbapap.2012.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 09/07/2012] [Accepted: 09/11/2012] [Indexed: 11/18/2022]
Abstract
We bring to attention a characteristic parasitic pattern present in the dengue virus: it undergoes several intensive thermodynamic variations due to host environmental changes, from a vector's digestive tract, through the human bloodstream and intracellular medium. Comparatively, among the known dengue serotypes, we evaluate the effects that these medium variations may induce to the overall structural characteristics of the Domain III of the envelope (E) protein, checking for stereochemical congruences that could lead to the identification of immunologic relevant regions. We used molecular dynamics and principal component analysis to study the protein in solution, for all four dengue serotypes, under distinct pH and temperature. We stated that, while the core of Domain III is remarkably rigid and effectively unaffected by most of the mentioned intensive variations, the loops account for major and distinguishable flexibilities. Therefore, the rigidity of the Domain III core provides a foothold that projects specifically two of these high flexible loop regions towards the inner face of the envelope pores, which are found at every five-fold symmetry axis of the icosahedron-shaped mature virus. These loops bear a remarkable low identity though with high occurrence of ionizable residues, including histidines. Such stereochemical properties can provide very particular serotype-specific electrostatic surface patterns, suggesting a viral fingerprint region, on which other specific molecules and ions can establish chemical interactions in an induced fit mechanism. We assert that the proposed regions share enough relevant features to qualify for further immunologic and pharmacologic essays, such as target peptide synthesis and phage display using dengue patients' sera.
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Affiliation(s)
- R O S Soares
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café, S/N. 14040-903, Ribeirão Preto, São Paulo, Brazil.
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