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Gogal RA, Nessler AJ, Thiel AC, Bernabe HV, Corrigan Grove RA, Cousineau LM, Litman JM, Miller JM, Qi G, Speranza MJ, Tollefson MR, Fenn TD, Michaelson JJ, Okada O, Piquemal JP, Ponder JW, Shen J, Smith RJH, Yang W, Ren P, Schnieders MJ. Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment. J Chem Phys 2024; 161:012501. [PMID: 38958156 PMCID: PMC11223778 DOI: 10.1063/5.0214652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024] Open
Abstract
Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid-base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.
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Affiliation(s)
- Rose A. Gogal
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Aaron J. Nessler
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Andrew C. Thiel
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Hernan V. Bernabe
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Rae A. Corrigan Grove
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Leah M. Cousineau
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA
| | - Jacob M. Litman
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA
| | - Jacob M. Miller
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Guowei Qi
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA
| | - Matthew J. Speranza
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Mallory R. Tollefson
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Timothy D. Fenn
- Analytical Development, LEXEO Therapeutics, New York, New York 10010, USA
| | - Jacob J. Michaelson
- Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA
| | - Okimasa Okada
- Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | | | - Jay W. Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
| | - Richard J. H. Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA
| | | | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas, Austin, Texas 78712, USA
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2
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Herrera-González I, González-Cuesta M, Thépaut M, Laigre E, Goyard D, Rojo J, García Fernández JM, Fieschi F, Renaudet O, Nieto PM, Ortiz Mellet C. High-Mannose Oligosaccharide Hemimimetics that Recapitulate the Conformation and Binding Mode to Concanavalin A, DC-SIGN and Langerin. Chemistry 2024; 30:e202303041. [PMID: 37828571 DOI: 10.1002/chem.202303041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 10/14/2023]
Abstract
The "carbohydrate chemical mimicry" exhibited by sp2 -iminosugars has been utilized to develop practical syntheses for analogs of the branched high-mannose-type oligosaccharides (HMOs) Man3 and Man5 . In these compounds, the terminal nonreducing Man residues have been substituted with 5,6-oxomethylidenemannonojirimycin (OMJ) motifs. The resulting oligomannoside hemimimetic accurately reproduce the structure, configuration, and conformational behavior of the original mannooligosaccharides, as confirmed by NMR and computational techniques. Binding studies with mannose binding lectins, including concanavalin A, DC-SIGN, and langerin, by enzyme-linked lectin assay and surface plasmon resonance revealed significant variations in their ability to accommodate the OMJ unit in the mannose binding site. Intriguingly, OMJMan segments demonstrated "in line" heteromultivalent effects during binding to the three lectins. Similar to the mannobiose (Man2 ) branches in HMOs, the binding modes involving the external or internal monosaccharide unit at the carbohydrate binding-domain exist in equilibrium, facilitating sliding and recapture processes. This equilibrium, which influences the multivalent binding of HMOs, can be finely modulated upon incorporation of the OMJ sp2 -iminosugar caps. As a proof of concept, the affinity and selectivity towards DC-SIGN and langerin were adjustable by presenting the OMJMan epitope in platforms with diverse architectures and valencies.
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Affiliation(s)
- Irene Herrera-González
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, C/ Profesor García González 1, 41012, Sevilla, Spain
- Present address: DCM, UMR 5250, Université Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
| | - Manuel González-Cuesta
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, C/ Profesor García González 1, 41012, Sevilla, Spain
| | - Michel Thépaut
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, 38000, Grenoble, France
| | - Eugénie Laigre
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, 38000, Grenoble, France
- DCM, UMR 5250, Université Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
| | - David Goyard
- DCM, UMR 5250, Université Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
| | - Javier Rojo
- Instituto de Investigaciones Químicas (IIQ), CSIC - Universidad de Sevilla, Américo Vespucio 49, 41092, Sevilla, Spain
| | - José M García Fernández
- Instituto de Investigaciones Químicas (IIQ), CSIC - Universidad de Sevilla, Américo Vespucio 49, 41092, Sevilla, Spain
| | - Franck Fieschi
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, 38000, Grenoble, France
- Institut Universitaire de France (IUF), Paris, France
| | - Olivier Renaudet
- DCM, UMR 5250, Université Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
| | - Pedro M Nieto
- Instituto de Investigaciones Químicas (IIQ), CSIC - Universidad de Sevilla, Américo Vespucio 49, 41092, Sevilla, Spain
| | - Carmen Ortiz Mellet
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, C/ Profesor García González 1, 41012, Sevilla, Spain
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3
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Tvaroška I, Kozmon S, Kóňa J. Molecular Modeling Insights into the Structure and Behavior of Integrins: A Review. Cells 2023; 12:cells12020324. [PMID: 36672259 PMCID: PMC9856412 DOI: 10.3390/cells12020324] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Integrins are heterodimeric glycoproteins crucial to the physiology and pathology of many biological functions. As adhesion molecules, they mediate immune cell trafficking, migration, and immunological synapse formation during inflammation and cancer. The recognition of the vital roles of integrins in various diseases revealed their therapeutic potential. Despite the great effort in the last thirty years, up to now, only seven integrin-based drugs have entered the market. Recent progress in deciphering integrin functions, signaling, and interactions with ligands, along with advancement in rational drug design strategies, provide an opportunity to exploit their therapeutic potential and discover novel agents. This review will discuss the molecular modeling methods used in determining integrins' dynamic properties and in providing information toward understanding their properties and function at the atomic level. Then, we will survey the relevant contributions and the current understanding of integrin structure, activation, the binding of essential ligands, and the role of molecular modeling methods in the rational design of antagonists. We will emphasize the role played by molecular modeling methods in progress in these areas and the designing of integrin antagonists.
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Affiliation(s)
- Igor Tvaroška
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovakia
- Correspondence:
| | - Stanislav Kozmon
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovakia
- Medical Vision o. z., Záhradnícka 4837/55, 821 08 Bratislava, Slovakia
| | - Juraj Kóňa
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovakia
- Medical Vision o. z., Záhradnícka 4837/55, 821 08 Bratislava, Slovakia
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Murayama K, Kashida H, Asanuma H. Methyl group configuration on acyclic threoninol nucleic acids ( aTNAs) impacts supramolecular properties. Org Biomol Chem 2022; 20:4115-4122. [PMID: 35274662 DOI: 10.1039/d2ob00266c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have synthesized acyclic allo-threoninol nucleic acids (allo-aTNAs), artificial xeno-nucleic acids (XNAs) that are diastereomers of acyclic threoninol nucleic acids (aTNAs), and have investigated their supramolecular properties. The allo-aTNAs formed homo-duplexes in an antiparallel manner but with lower thermal stability than DNA, whereas aTNAs formed extremely stable homo-duplexes. The allo-aTNAs formed duplexes with complementary aTNAs and serinol nucleic acid (SNA). The affinities of L-allo-aTNA were the highest for L-aTNA and the lowest for D-aTNA, with SNA being intermediate. The affinities of D-allo-aTNA were the reverse. Circular dichroism measurements revealed that L- and D-allo-aTNAs had weak right-handed and left-handed helicities, respectively. The weak helicity of allo-aTNAs likely explains the poor chiral discrimination of these XNAs, which is in contrast to aTNAs that have strong helical orthogonality. Energy-minimized structures of L-allo-aTNA/RNA and L-allo-aTNA/L-allo-aTNA indicated that the methyl group on the allo-aTNA strand is unfavourable for duplex formation. In contrast, the methyl group on L-aTNA likely stabilizes the duplex structure via hydrophobic effects and van der Waals interactions. Thus, the configuration of the methyl group on the XNA scaffold had an unexpectedly large impact on the hybridization ability and structure.
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Affiliation(s)
- Keiji Murayama
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
| | - Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
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5
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DFT studies on the physicochemical properties of a new potential drug carrier containing cellobiose units and its complex with paracetamol. Struct Chem 2022. [DOI: 10.1007/s11224-022-01950-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Cristófalo AE, Nieto PM, Thépaut M, Fieschi F, Di Chenna PH, Uhrig ML. Synthesis, self-assembly and Langerin recognition studies of a resorcinarene-based glycocluster exposing a hyaluronic acid thiodisaccharide mimetic. Org Biomol Chem 2021; 19:6455-6467. [PMID: 34236375 DOI: 10.1039/d1ob00895a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we report the synthesis of an octavalent glycocluster exposing a thiodisaccharide mimetic of the repetitive unit of hyaluronic acid, βSGlcA(1 → 3)βSGlcNAc, constructed on a calix[4]resorcinarene scaffold by CuAAC reaction of suitable precursors. This glycocluster showed a strong tendency toward self-aggregation. DOSY-NMR and DLS experiments demonstrated the formation of spherical micelles of d ≅ 6.2 nm, in good agreement. TEM micrographs showed the presence of particles of different sizes, depending on the pH of the starting solution, thus evidencing that the negative charge on the micelle surface due to ionization of the GlcA residues plays an important role in the aggregation process. STD-NMR and DLS experiments provided evidence of the interaction between the synthetic glycocluster and Langerin, a relevant C-type lectin. This interaction was not observed in the STD-NMR experiments performed with the basic disaccharide, providing evidence of a multivalent effect.
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Affiliation(s)
- Alejandro E Cristófalo
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EGA Buenos Aires, Argentina. and CONICET-Universidad de Buenos Aires, Centro de Investigaciones en Hidratos de Carbono (CIHIDECAR), C1428EGA Buenos Aires, Argentina
| | - Pedro M Nieto
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), cicCartuja, CSIC and Universidad de Sevilla, 41092 Sevilla, España.
| | - Michel Thépaut
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Franck Fieschi
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Pablo H Di Chenna
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EGA Buenos Aires, Argentina. and CONICET-Universidad de Buenos Aires, Unidad de Microanálisis y Métodos Físicos Aplicados a la Química Orgánica (UMYMFOR), C1428EGA Buenos Aires, Argentina
| | - María Laura Uhrig
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EGA Buenos Aires, Argentina. and CONICET-Universidad de Buenos Aires, Centro de Investigaciones en Hidratos de Carbono (CIHIDECAR), C1428EGA Buenos Aires, Argentina
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7
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Litman J, Thiel AC, Schnieders MJ. Scalable Indirect Free Energy Method Applied to Divalent Cation-Metalloprotein Binding. J Chem Theory Comput 2019; 15:4602-4614. [DOI: 10.1021/acs.jctc.9b00147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jacob Litman
- University of Iowa, Department of Biochemistry, 51 Newton Road, 4-403 Bowen Science Building, Iowa City, Iowa 52242, United States
| | - Andrew C. Thiel
- University of Iowa, Department of Biomedical Engineering, 103 South Capitol Street, 5601 Seamans Center for the Engineering Arts and Sciences, Iowa City, Iowa 52242, United States
| | - Michael J. Schnieders
- University of Iowa, Department of Biochemistry, 51 Newton Road, 4-403 Bowen Science Building, Iowa City, Iowa 52242, United States
- University of Iowa, Department of Biomedical Engineering, 103 South Capitol Street, 5601 Seamans Center for the Engineering Arts and Sciences, Iowa City, Iowa 52242, United States
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8
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Rackers JA, Wang Z, Lu C, Laury ML, Lagardère L, Schnieders MJ, Piquemal JP, Ren P, Ponder JW. Tinker 8: Software Tools for Molecular Design. J Chem Theory Comput 2018; 14:5273-5289. [PMID: 30176213 PMCID: PMC6335969 DOI: 10.1021/acs.jctc.8b00529] [Citation(s) in RCA: 286] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Tinker software, currently released as version 8, is a modular molecular mechanics and dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with OpenMP extensions. It supports a wide variety of force fields, including polarizable models such as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. The package runs on Linux, macOS, and Windows systems. In addition to canonical Tinker, there are branches, Tinker-HP and Tinker-OpenMM, designed for use on message passing interface (MPI) parallel distributed memory supercomputers and state-of-the-art graphical processing units (GPUs), respectively. The Tinker suite also includes a tightly integrated Java-based graphical user interface called Force Field Explorer (FFE), which provides molecular visualization capabilities as well as the ability to launch and control Tinker calculations.
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Affiliation(s)
- Joshua A. Rackers
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Zhi Wang
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Chao Lu
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Marie L. Laury
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Louis Lagardère
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Michael J. Schnieders
- Department of Biomedical Engineering, The University of Iowa, Iowa City, IA 52242, United States
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jay W. Ponder
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
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9
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Investigating the Interaction of Cyclic RGD Peptidomimetics with α Vβ₆ Integrin by Biochemical and Molecular Docking Studies. Cancers (Basel) 2017; 9:cancers9100128. [PMID: 28934103 PMCID: PMC5664067 DOI: 10.3390/cancers9100128] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/13/2017] [Accepted: 09/18/2017] [Indexed: 01/15/2023] Open
Abstract
The interaction of a small library of cyclic RGD (Arg-Gly-Asp) peptidomimetics with αVβ6 integrin has been investigated by means of competitive solid phase binding assays to the isolated receptor and docking calculations in the crystal structure of the αVβ6 binding site. To this aim, a rigid receptor-flexible ligand docking protocol has been set up and then applied to predict the binding mode of the cyclic RGD peptidomimetics to αVβ6 integrin. Although the RGD interaction with αVβ6 recapitulates the RGD binding mode observed in αVβ3, differences between the integrin binding pockets can strongly affect the ligand binding ability. In general, the peptidomimetics exhibited IC50 values for integrin αVβ6 (i.e., the concentration of compound required for 50% inhibition of biotinylated fibronectin binding to isolated αVβ6 integrin) in the nanomolar range (77–345 nM), about 10–100 times higher than those for the related αVβ3 receptor, with a single notable ligand displaying a low nanomolar IC50 value (2.3 nM). Insights from the properties of the binding pocket combined with the analysis of the docking poses provided a rationale for ligand recognition and selectivity.
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10
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Pilkington-Miksa M, Araldi EMV, Arosio D, Belvisi L, Civera M, Manzoni L. New potent αvβ3 integrin ligands based on azabicycloalkane (γ,α)-dipeptide mimics. Org Biomol Chem 2016; 14:3221-33. [PMID: 26917057 DOI: 10.1039/c6ob00287k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We have designed a new synthetic strategy for the preparation of a new class of cyclic RGD integrin ligands in which the azabicycloalkane scaffold can be envisaged as a (γ,α) dipeptide mimic. The synthesis and in vitro biological evaluation of these RGD derivatives, as well as the computational study of their conformational properties and binding modes to αVβ3 integrin are described. Compound has shown to be a promising candidate as αVβ3 integrin antagonist able to interfere with both cell adhesion and movement on vitronectin with no evidence of cytotoxic effects.
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Affiliation(s)
- M Pilkington-Miksa
- Centro Interdisciplinare Studi Biomolecolari e Applicazioni Industriali, Università degli Studi di Milano, Via Fantoli 16/15, I-20138, Milano
| | - E M V Araldi
- Centro Interdisciplinare Studi Biomolecolari e Applicazioni Industriali, Università degli Studi di Milano, Via Fantoli 16/15, I-20138, Milano
| | - D Arosio
- Istituto di Scienze e Tecnologie Molecolari, Consiglio Nazionale delle Ricerche, Via C. Golgi 19, I-20133, Milano.
| | - L Belvisi
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, I-20133, Milano
| | - M Civera
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, I-20133, Milano
| | - L Manzoni
- Istituto di Scienze e Tecnologie Molecolari, Consiglio Nazionale delle Ricerche, Via C. Golgi 19, I-20133, Milano.
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11
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Leimkuhler B, Matthews C. Efficient molecular dynamics using geodesic integration and solvent-solute splitting. Proc Math Phys Eng Sci 2016; 472:20160138. [PMID: 27279779 PMCID: PMC4893190 DOI: 10.1098/rspa.2016.0138] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 04/08/2016] [Indexed: 12/03/2022] Open
Abstract
We present an approach to Langevin dynamics in the presence of holonomic constraints based on decomposition of the system into components representing geodesic flow, constrained impulse and constrained diffusion. We show that a particular ordering of the components results in an integrator that is an order of magnitude more accurate for configurational averages than existing alternatives. Moreover, by combining the geodesic integration method with a solvent-solute force splitting, we demonstrate that stepsizes of at least 8 fs can be used for solvated biomolecules with high sampling accuracy and without substantially altering diffusion rates, approximately increasing by a factor of two the efficiency of molecular dynamics sampling for such systems. The methods described in this article are easily implemented using the standard apparatus of modern simulation codes.
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Affiliation(s)
- Benedict Leimkuhler
- School of Mathematics and Maxwell Institute of Mathematical Sciences, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Charles Matthews
- Department of Statistics, University of Chicago, 5734 S. University Avenue, Chicago, IL 60637, USA
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12
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Tavousi P, Behandish M, Ilieş HT, Kazerounian K. Protofold II: Enhanced Model and Implementation for Kinetostatic Protein Folding1. J Nanotechnol Eng Med 2016. [DOI: 10.1115/1.4032759] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A reliable prediction of three-dimensional (3D) protein structures from sequence data remains a big challenge due to both theoretical and computational difficulties. We have previously shown that our kinetostatic compliance method (KCM) implemented into the Protofold package can overcome some of the key difficulties faced by other de novo structure prediction methods, such as the very small time steps required by the molecular dynamics (MD) approaches or the very large number of samples needed by the Monte Carlo (MC) sampling techniques. In this paper, we improve the free energy formulation used in Protofold by including the typically underrated entropic effects, imparted due to differences in hydrophobicity of the chemical groups, which dominate the folding of most water-soluble proteins. In addition to the model enhancement, we revisit the numerical implementation by redesigning the algorithms and introducing efficient data structures that reduce the expected complexity from quadratic to linear. Moreover, we develop and optimize parallel implementations of the algorithms on both central and graphics processing units (CPU/GPU) achieving speed-ups up to two orders of magnitude on the GPU. Our simulations are consistent with the general behavior observed in the folding process in aqueous solvent, confirming the effectiveness of model improvements. We report on the folding process at multiple levels, namely, the formation of secondary structural elements and tertiary interactions between secondary elements or across larger domains. We also observe significant enhancements in running times that make the folding simulation tractable for large molecules.
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Affiliation(s)
- Pouya Tavousi
- Kinematics Design Laboratory, Department of Mechanical Engineering, University of Connecticut, Storrs, CT 06269 e-mail:
| | - Morad Behandish
- Computational Design Laboratory, Department of Mechanical Engineering, University of Connecticut, Storrs, CT 06269 e-mail:
| | - Horea T. Ilieş
- Department of Mechanical Engineering, University of Connecticut, Storrs, CT 06269 e-mail:
| | - Kazem Kazerounian
- Department of Mechanical Engineering, University of Connecticut, Storrs, CT 06269 e-mail:
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13
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De Vivo M, Masetti M, Bottegoni G, Cavalli A. Role of Molecular Dynamics and Related Methods in Drug Discovery. J Med Chem 2016; 59:4035-61. [DOI: 10.1021/acs.jmedchem.5b01684] [Citation(s) in RCA: 538] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Marco De Vivo
- Laboratory
of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- IAS-5/INM-9 Computational
Biomedicine Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Matteo Masetti
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
6, I-40126 Bologna, Italy
| | - Giovanni Bottegoni
- CompuNet, Istituto
Italiano di Tecnologia, Via Morego
30, 16163 Genova, Italy
- BiKi Technologies
srl, Via XX Settembre 33/10, 16121 Genova, Italy
| | - Andrea Cavalli
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
6, I-40126 Bologna, Italy
- CompuNet, Istituto
Italiano di Tecnologia, Via Morego
30, 16163 Genova, Italy
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14
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Three-dimensional protein structure prediction: Methods and computational strategies. Comput Biol Chem 2014; 53PB:251-276. [DOI: 10.1016/j.compbiolchem.2014.10.001] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 10/03/2014] [Accepted: 10/07/2014] [Indexed: 01/01/2023]
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15
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Small MC, Lopes P, Andrade RB, MacKerell AD. Impact of ribosomal modification on the binding of the antibiotic telithromycin using a combined grand canonical monte carlo/molecular dynamics simulation approach. PLoS Comput Biol 2013; 9:e1003113. [PMID: 23785274 PMCID: PMC3681621 DOI: 10.1371/journal.pcbi.1003113] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 05/07/2013] [Indexed: 02/05/2023] Open
Abstract
Resistance to macrolide antibiotics is conferred by mutation of A2058 to G or methylation by Erm methyltransferases of the exocyclic N6 of A2058 (E. coli numbering) that forms the macrolide binding site in the 50S subunit of the ribosome. Ketolides such as telithromycin mitigate A2058G resistance yet remain susceptible to Erm-based resistance. Molecular details associated with macrolide resistance due to the A2058G mutation and methylation at N6 of A2058 by Erm methyltransferases were investigated using empirical force field-based simulations. To address the buried nature of the macrolide binding site, the number of waters within the pocket was allowed to fluctuate via the use of a Grand Canonical Monte Carlo (GCMC) methodology. The GCMC water insertion/deletion steps were alternated with Molecular Dynamics (MD) simulations to allow for relaxation of the entire system. From this GCMC/MD approach information on the interactions between telithromycin and the 50S ribosome was obtained. In the wild-type (WT) ribosome, the 2'-OH to A2058 N1 hydrogen bond samples short distances with a higher probability, while the effectiveness of telithromycin against the A2058G mutation is explained by a rearrangement of the hydrogen bonding pattern of the 2'-OH to 2058 that maintains the overall antibiotic-ribosome interactions. In both the WT and A2058G mutation there is significant flexibility in telithromycin's imidazole-pyridine side chain (ARM), indicating that entropic effects contribute to the binding affinity. Methylated ribosomes show lower sampling of short 2'-OH to 2058 distances and also demonstrate enhanced G2057-A2058 stacking leading to disrupted A752-U2609 Watson-Crick (WC) interactions as well as hydrogen bonding between telithromycin's ARM and U2609. This information will be of utility in the rational design of novel macrolide analogs with improved activity against methylated A2058 ribosomes.
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Affiliation(s)
- Meagan C. Small
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland, United States of America
| | - Pedro Lopes
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland, United States of America
| | - Rodrigo B. Andrade
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland, United States of America
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16
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Mingozzi M, Dal Corso A, Marchini M, Guzzetti I, Civera M, Piarulli U, Arosio D, Belvisi L, Potenza D, Pignataro L, Gennari C. CyclicisoDGR Peptidomimetics as Low-Nanomolar αvβ3Integrin Ligands. Chemistry 2013; 19:3563-7. [DOI: 10.1002/chem.201204639] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Indexed: 02/04/2023]
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17
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A fragment-based approach to the SAMPL3 Challenge. J Comput Aided Mol Des 2012; 26:583-94. [PMID: 22290624 DOI: 10.1007/s10822-012-9546-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 01/19/2012] [Indexed: 01/09/2023]
Abstract
The success of molecular fragment-based design depends critically on the ability to make predictions of binding poses and of affinity ranking for compounds assembled by linking fragments. The SAMPL3 Challenge provides a unique opportunity to evaluate the performance of a state-of-the-art fragment-based design methodology with respect to these requirements. In this article, we present results derived from linking fragments to predict affinity and pose in the SAMPL3 Challenge. The goal is to demonstrate how incorporating different aspects of modeling protein-ligand interactions impact the accuracy of the predictions, including protein dielectric models, charged versus neutral ligands, ΔΔGs solvation energies, and induced conformational stress. The core method is based on annealing of chemical potential in a Grand Canonical Monte Carlo (GC/MC) simulation. By imposing an initially very high chemical potential and then automatically running a sequence of simulations at successively decreasing chemical potentials, the GC/MC simulation efficiently discovers statistical distributions of bound fragment locations and orientations not found reliably without the annealing. This method accounts for configurational entropy, the role of bound water molecules, and results in a prediction of all the locations on the protein that have any affinity for the fragment. Disregarding any of these factors in affinity-rank prediction leads to significantly worse correlation with experimentally-determined free energies of binding. We relate three important conclusions from this challenge as applied to GC/MC: (1) modeling neutral ligands--regardless of the charged state in the active site--produced better affinity ranking than using charged ligands, although, in both cases, the poses were almost exactly overlaid; (2) simulating explicit water molecules in the GC/MC gave better affinity and pose predictions; and (3) applying a ΔΔGs solvation correction further improved the ranking of the neutral ligands. Using the GC/MC method under a variety of parameters in the blinded SAMPL3 Challenge provided important insights to the relevant parameters and boundaries in predicting binding affinities using simulated annealing of chemical potential calculations.
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18
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Heterobivalent ligands target cell-surface receptor combinations in vivo. Proc Natl Acad Sci U S A 2012; 109:21295-300. [PMID: 23236171 DOI: 10.1073/pnas.1211762109] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A challenge in tumor targeting is to deliver payloads to cancers while sparing normal tissues. A limited number of antibodies appear to meet this challenge as therapeutics themselves or as drug-antibody conjugates. However, antibodies suffer from their large size, which can lead to unfavorable pharmacokinetics for some therapeutic payloads, and that they are targeted against only a single epitope, which can reduce their selectivity and specificity. Here, we propose an alternative targeting approach based on patterns of cell surface proteins to rationally develop small, synthetic heteromultivalent ligands (htMVLs) that target multiple receptors simultaneously. To gain insight into the multivalent ligand strategy in vivo, we have generated synthetic htMVLs that contain melanocortin (MSH) and cholecystokinin (CCK) pharmacophores that are connected via a fluorescent labeled, rationally designed synthetic linker. These ligands were tested in an experimental animal model containing tumors that expressed only one (control) or both (target) MSH and CCK receptors. After systemic injection of the htMVL in tumor-bearing mice, label was highly retained in tumors that expressed both, compared with one, target receptors. Selectivity was quantified by using ex vivo measurement of Europium-labeled htMVL, which had up to 12-fold higher specificity for dual compared with single receptor expressing cells. This proof-of-principle study provides in vivo evidence that small, rationally designed bivalent htMVLs can be used to selectively target cells that express both, compared with single complimentary cell surface targets. These data open the possibility that specific combinations of targets on tumors can be identified and selectively targeted using htMVLs.
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19
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Taha HA, Richards MR, Lowary TL. Conformational Analysis of Furanoside-Containing Mono- and Oligosaccharides. Chem Rev 2012; 113:1851-76. [DOI: 10.1021/cr300249c] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hashem A. Taha
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Michele R. Richards
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Todd L. Lowary
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
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20
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Marchini M, Mingozzi M, Colombo R, Guzzetti I, Belvisi L, Vasile F, Potenza D, Piarulli U, Arosio D, Gennari C. Cyclic RGD peptidomimetics containing bifunctional diketopiperazine scaffolds as new potent integrin ligands. Chemistry 2012; 18:6195-207. [PMID: 22517378 DOI: 10.1002/chem.201200457] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Indexed: 11/09/2022]
Abstract
The synthesis of eight bifunctional diketopiperazine (DKP) scaffolds is described; these were formally derived from 2,3-diaminopropionic acid and aspartic acid (DKP-1-DKP-7) or glutamic acid (DKP-8) and feature an amine and a carboxylic acid functional group. The scaffolds differ in the configuration at the two stereocenters and the substitution at the diketopiperazinic nitrogen atoms. The bifunctional diketopiperazines were introduced into eight cyclic peptidomimetics containing the Arg-Gly-Asp (RGD) sequence. The resulting RGD peptidomimetics were screened for their ability to inhibit biotinylated vitronectin binding to the purified integrins α(v)β(3) and α(v)β(5), which are involved in tumor angiogenesis. Nanomolar IC(50) values were obtained for the RGD peptidomimetics derived from trans DKP scaffolds (DKP-2-DKP-8). Conformational studies of the cyclic RGD peptidomimetics by (1)H NMR spectroscopy experiments (VT-NMR and NOESY spectroscopy) in aqueous solution and Monte Carlo/Stochastic Dynamics (MC/SD) simulations revealed that the highest affinity ligands display well-defined preferred conformations featuring intramolecular hydrogen-bonded turn motifs and an extended arrangement of the RGD sequence [Cβ(Arg)-Cβ(Asp) average distance ≥8.8 Å]. Docking studies were performed, starting from the representative conformations obtained from the MC/SD simulations and taking as a reference model the crystal structure of the extracellular segment of integrin α(v)β(3) complexed with the cyclic pentapeptide, Cilengitide. The highest affinity ligands produced top-ranked poses conserving all the important interactions of the X-ray complex.
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Affiliation(s)
- Mattia Marchini
- Università degli Studi di Milano, Dipartimento di Chimica Organica e Industriale, Via Venezian, 21, I-20133, Milan, Italy
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21
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Ribeiro AAST, de Alencastro RB. Mixed monte carlo/molecular dynamics simulations in explicit solvent. J Comput Chem 2012; 33:901-5. [DOI: 10.1002/jcc.22925] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 11/04/2011] [Accepted: 12/09/2011] [Indexed: 11/06/2022]
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22
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Marcelo F, Cañada FJ, André S, Colombo C, Doro F, Gabius HJ, Bernardi A, Jiménez-Barbero J. α-N-Linked glycopeptides: conformational analysis and bioactivity as lectin ligands. Org Biomol Chem 2012; 10:5916-23. [DOI: 10.1039/c2ob07135e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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23
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Motto I, Bordogna A, Soshilov AA, Denison MS, Bonati L. New aryl hydrocarbon receptor homology model targeted to improve docking reliability. J Chem Inf Model 2011; 51:2868-81. [PMID: 21981577 PMCID: PMC3263330 DOI: 10.1021/ci2001617] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-dependent, basic helix-loop-helix Per-ARNT-Sim (PAS) containing transcription factor that can bind and be activated by structurally diverse chemicals, including the toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). As no experimentally determined structures of the AhR ligand binding domain (LBD) are available and previous homology models were only derived from apo template structures, we developed a new model based on holo X-ray structures of the hypoxia-inducible factor 2α (HIF-2α) PAS B domain, targeted to improve the accuracy of the binding site for molecular docking applications. We experimentally confirmed the ability of two HIF-2α crystallographic ligands to bind to the mAhR with relatively high affinity and demonstrated that they are AhR agonists, thus justifying the use of the holo HIF-2α structures as templates. A specific modeling/docking approach was proposed to predict the binding modes of AhR ligands in the modeled LBD. It was validated by comparison of the calculated and the experimental binding affinities of active THS ligands and TCDD for the mAhR and by functional activity analysis using several mAhR mutants generated on the basis of the modeling results. Finally the ability of the proposed approach to reproduce the different affinities of TCDD for AhRs of different species was confirmed, and a first test of its reliability in virtual screening is carried out by analyzing the correlation between the calculated and experimental binding affinities of a set of 14 PCDDs.
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Affiliation(s)
- Ilaria Motto
- Dipartimento di Scienze dell’Ambiente e del Territorio, Università degli Studi di Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Annalisa Bordogna
- Dipartimento di Scienze dell’Ambiente e del Territorio, Università degli Studi di Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Anatoly A. Soshilov
- Department of Environmental Toxicology, Meyer Hall, University of California, Davis, California 95616
| | - Michael S. Denison
- Department of Environmental Toxicology, Meyer Hall, University of California, Davis, California 95616
| | - Laura Bonati
- Dipartimento di Scienze dell’Ambiente e del Territorio, Università degli Studi di Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
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24
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Bradbury MW, Stump D, Guarnieri F, Berk PD. Molecular modeling and functional confirmation of a predicted fatty acid binding site of mitochondrial aspartate aminotransferase. J Mol Biol 2011; 412:412-22. [PMID: 21803047 PMCID: PMC3167029 DOI: 10.1016/j.jmb.2011.07.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 07/14/2011] [Accepted: 07/18/2011] [Indexed: 10/18/2022]
Abstract
Molecular interactions are necessary for proteins to perform their functions. The identification of a putative plasma membrane fatty acid transporter as mitochondrial aspartate aminotransferase (mAsp-AT) indicated that the protein must have a fatty acid binding site. Molecular modeling suggests that such a site exists in the form of a 500-Å(3) hydrophobic cleft on the surface of the molecule and identifies specific amino acid residues that are likely to be important for binding. The modeling and comparison with the cytosolic isoform indicated that two residues (Arg201 and Ala219) were likely to be important to the structure and function of the binding site. These residues were mutated to determine if they were essential to that function. Expression constructs with wild-type or mutated cDNAs were produced for bacteria and eukaryotic cells. Proteins expressed in Escherichia coli were tested for oleate binding affinity, which was decreased in the mutant proteins. 3T3 fibroblasts were transfected with expression constructs for both normal and mutated forms. Plasma membrane expression was documented by indirect immunofluorescence before [(3)H]oleic acid uptake kinetics were assayed. The V(max) for uptake was significantly increased by overexpression of the wild-type protein but changed little after transfection with mutated proteins, despite their presence on the plasma membrane. The hydrophobic cleft in mAsp-AT can serve as a fatty acid binding site. Specific residues are essential for normal fatty acid binding, without which fatty acid uptake is compromised. These results confirm the function of this protein as a fatty acid binding protein.
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Affiliation(s)
- Michael W. Bradbury
- Department of Medicine, Mount Sinai School of Medicine, New York, NY 10029
- Department of Biochemistry, Lake Erie College of Osteopathic Medicine, Erie, PA 16509
| | - Decherd Stump
- Department of Medicine, Mount Sinai School of Medicine, New York, NY 10029
| | - Frank Guarnieri
- Department of Physiology & Biophysics, Virginia Commonwealth University, Richmond, VA 23298
- Department of Biomedical Engineering, Boston University, Boston, MA 02218
- Phase III Pharmaceuticals, Brooklyn, NY 11223
| | - Paul D. Berk
- Department of Medicine, Mount Sinai School of Medicine, New York, NY 10029
- Department of Medicine, Columbia University Medical Center, New York, NY 10032
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25
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Neratova IV, Komarov PV, Pavlov AS, Ivanov VA. Collapse of an AB copolymer single chain with alternating blocks of different stiffness. Russ Chem Bull 2011. [DOI: 10.1007/s11172-011-0038-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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26
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Lee SM, Lee OS, O'Halloran TV, Schatz GC, Nguyen ST. Triggered release of pharmacophores from [Ni(HAsO₃)]-loaded polymer-caged nanobin enhances pro-apoptotic activity: a combined experimental and theoretical study. ACS NANO 2011; 5:3961-9. [PMID: 21466214 PMCID: PMC3650135 DOI: 10.1021/nn200478m] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Nanoscale drug delivery platforms can provide an attractive therapeutic strategy for cancer treatments, as they can substantially reduce the adverse side effects associated with toxic small-molecule anticancer agents. For enhanced therapeutic efficacy to be achieved with such platforms, a tumor-specific drug-release trigger is a critical requirement. This article reports the use of a pH-sensitive polymer network that surrounds a nanoscale liposome core to trigger the release of both encapsulated hydrophilic, membrane-impermeable Ni(II) cations and amphipathic, membrane-permeable As(III) anticancer agents under acidic conditions commonly encountered in hypoxic tumor tissues and late endosomes. Computational modeling studies provide clear evidence that the acid-triggered drug-release mechanism for this polymer-caged nanobin (PCN) platform arises from a pH- and temperature-responsive conformation change of the cross-linked polymer cage. As a result, the simultaneous release of both of the active agents in this multicomponent therapeutic enhances the pro-apoptotic activity of As(III) while diminishing its acute toxicity, potentially reducing the undesirable side effects commonly associated with this free drug. The ability to engender acid-triggered release of drugs co-encapsulated inside a liposomal template makes drug delivery using PCN an attractive strategy for triggered drug release.
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Affiliation(s)
| | | | - Thomas V. O'Halloran
- Corresponding Author Footnote. Address correspondence to: (T.V.O. for liposome synthesis, inorganic synthesis, and biology); (G.C.S. for molecular modeling); and (S.T.N. for polymer and PCN synthesis, characterization, and study)
| | - George C. Schatz
- Corresponding Author Footnote. Address correspondence to: (T.V.O. for liposome synthesis, inorganic synthesis, and biology); (G.C.S. for molecular modeling); and (S.T.N. for polymer and PCN synthesis, characterization, and study)
| | - SonBinh T. Nguyen
- Corresponding Author Footnote. Address correspondence to: (T.V.O. for liposome synthesis, inorganic synthesis, and biology); (G.C.S. for molecular modeling); and (S.T.N. for polymer and PCN synthesis, characterization, and study)
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27
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Guzzi C, Angulo J, Doro F, Reina JJ, Thépaut M, Fieschi F, Bernardi A, Rojo J, Nieto PM. Insights into molecular recognition of LewisX mimics by DC-SIGN using NMR and molecular modelling. Org Biomol Chem 2011; 9:7705-12. [DOI: 10.1039/c1ob05938f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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28
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Skovstrup S, Hansen SG, Skrydstrup T, Schiøtt B. Conformational Flexibility of Chitosan: A Molecular Modeling Study. Biomacromolecules 2010; 11:3196-207. [DOI: 10.1021/bm100736w] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Søren Skovstrup
- Centre for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Centre (iNANO), Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Signe Grann Hansen
- Centre for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Centre (iNANO), Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Troels Skrydstrup
- Centre for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Centre (iNANO), Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Birgit Schiøtt
- Centre for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Centre (iNANO), Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
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29
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Klenin K, Strodel B, Wales DJ, Wenzel W. Modelling proteins: conformational sampling and reconstruction of folding kinetics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:977-1000. [PMID: 20851219 DOI: 10.1016/j.bbapap.2010.09.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 09/03/2010] [Accepted: 09/05/2010] [Indexed: 01/08/2023]
Abstract
In the last decades biomolecular simulation has made tremendous inroads to help elucidate biomolecular processes in-silico. Despite enormous advances in molecular dynamics techniques and the available computational power, many problems involve long time scales and large-scale molecular rearrangements that are still difficult to sample adequately. In this review we therefore summarise recent efforts to fundamentally improve this situation by decoupling the sampling of the energy landscape from the description of the kinetics of the process. Recent years have seen the emergence of many advanced sampling techniques, which permit efficient characterisation of the relevant family of molecular conformations by dispensing with the details of the short-term kinetics of the process. Because these methods generate thermodynamic information at best, they must be complemented by techniques to reconstruct the kinetics of the process using the ensemble of relevant conformations. Here we review recent advances for both types of methods and discuss their perspectives to permit efficient and accurate modelling of large-scale conformational changes in biomolecules. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Konstantin Klenin
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology, P.O. Box 3640, D-76021 Karlsruhe, Germany
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30
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Maisuradze GG, Senet P, Czaplewski C, Liwo A, Scheraga HA. Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field. J Phys Chem A 2010; 114:4471-85. [PMID: 20166738 PMCID: PMC2849147 DOI: 10.1021/jp9117776] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Coarse-grained molecular dynamics simulations offer a dramatic extension of the time-scale of simulations compared to all-atom approaches. In this article, we describe the use of the physics-based united-residue (UNRES) force field, developed in our laboratory, in protein-structure simulations. We demonstrate that this force field offers about a 4000-times extension of the simulation time scale; this feature arises both from averaging out the fast-moving degrees of freedom and reduction of the cost of energy and force calculations compared to all-atom approaches with explicit solvent. With massively parallel computers, microsecond folding simulation times of proteins containing about 1000 residues can be obtained in days. A straightforward application of canonical UNRES/MD simulations, demonstrated with the example of the N-terminal part of the B-domain of staphylococcal protein A (PDB code: 1BDD, a three-alpha-helix bundle), discerns the folding mechanism and determines kinetic parameters by parallel simulations of several hundred or more trajectories. Use of generalized-ensemble techniques, of which the multiplexed replica exchange method proved to be the most effective, enables us to compute thermodynamics of folding and carry out fully physics-based prediction of protein structure, in which the predicted structure is determined as a mean over the most populated ensemble below the folding-transition temperature. By using principal component analysis of the UNRES folding trajectories of the formin-binding protein WW domain (PDB code: 1E0L; a three-stranded antiparallel beta-sheet) and 1BDD, we identified representative structures along the folding pathways and demonstrated that only a few (low-indexed) principal components can capture the main structural features of a protein-folding trajectory; the potentials of mean force calculated along these essential modes exhibit multiple minima, as opposed to those along the remaining modes that are unimodal. In addition, a comparison between the structures that are representative of the minima in the free-energy profile along the essential collective coordinates of protein folding (computed by principal component analysis) and the free-energy profile projected along the virtual-bond dihedral angles gamma of the backbone revealed the key residues involved in the transitions between the different basins of the folding free-energy profile, in agreement with existing experimental data for 1E0L .
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Affiliation(s)
- Gia G Maisuradze
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA
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31
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da Ressurreição A, Vidu A, Civera M, Belvisi L, Potenza D, Manzoni L, Ongeri S, Gennari C, Piarulli U. Cyclic RGD-Peptidomimetics Containing Bifunctional Diketopiperazine Scaffolds as New Potent Integrin Ligands. Chemistry 2009; 15:12184-8. [DOI: 10.1002/chem.200902398] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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32
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Relative solvation free energies calculated using an ab initio QM/MM-based free energy perturbation method: dependence of results on simulation length. J Comput Aided Mol Des 2009; 23:837-43. [DOI: 10.1007/s10822-009-9300-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Accepted: 08/17/2009] [Indexed: 11/26/2022]
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33
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Manzoni L, Belvisi L, Arosio D, Civera M, Pilkington-Miksa M, Potenza D, Caprini A, Araldi EM, Monferini E, Mancino M, Podestà F, Scolastico C. Cyclic RGD-Containing Functionalized Azabicycloalkane Peptides as Potent Integrin Antagonists for Tumor Targeting. ChemMedChem 2009; 4:615-32. [DOI: 10.1002/cmdc.200800422] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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34
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Arosio D, Belvisi L, Colombo L, Colombo M, Invernizzi D, Manzoni L, Potenza D, Serra M, Castorina M, Pisano C, Scolastico C. A Potent Integrin Antagonist from a Small Library of Cyclic RGD Pentapeptide Mimics Including Benzyl-Substituted Azabicycloalkane Amino Acids. ChemMedChem 2008; 3:1589-603. [DOI: 10.1002/cmdc.200800143] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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35
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Potenza D, Belvisi L. Transferred-NOE NMR experiments on intact human platelets: receptor-bound conformation of RGD-peptide mimics. Org Biomol Chem 2008; 6:258-62. [DOI: 10.1039/b713036h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Pietra F. Why colchicine does not show mutarotation. With M05-2X density functional in the realm of tricky natural products. J PHYS ORG CHEM 2007. [DOI: 10.1002/poc.1263] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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37
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Rao S, Li X, Liang H. Developing coarse-grained force fields for polystyrene with different chain lengths from atomistic simulation. Macromol Res 2007. [DOI: 10.1007/bf03218940] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Hess S, Ovadia O, Shalev DE, Senderovich H, Qadri B, Yehezkel T, Salitra Y, Sheynis T, Jelinek R, Gilon C, Hoffman A. Effect of structural and conformation modifications, including backbone cyclization, of hydrophilic hexapeptides on their intestinal permeability and enzymatic stability. J Med Chem 2007; 50:6201-11. [PMID: 17983214 DOI: 10.1021/jm070836d] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A library of 18 hexapeptide analogs was synthesized, including sub-libraries of N- or C-methylation of the parent hexapeptide Phe-Gly-Gly-Gly-Gly-Phe, as well as backbone cyclized analogs of each linear analog with various ring sizes. N- or C-methylation as well as cyclization (but not backbone cyclization) have been suggested to improve intestinal permeability and metabolic stability of peptides in general. Here we aimed to assess their applicability to hydrophilic peptides. The intestinal permeability (Papp) of the 18-peptide library was in the range of 0.2-6.8 x 10-6 cm/sec. Based on several tests, we concluded that the absorption mechanism of all tested analogs is paracellular, regardless of the structural or conformational modifications. In all cases, backbone cyclization increased Papp (5-fold) in comparison to the linear analogs due to the smaller 3D size and also dramatically decreased peptide proteolysis by brush border enzymes. N- or C-methylation did not enhance the permeability of the linear analogs in this series.
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Affiliation(s)
- Shmuel Hess
- Departments of Pharmaceutics and Organic Chemistry, and the Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Safra Campus, Jerusalem 91904, Israel
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39
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Jiménez-Barbero J, Canales A, Northcote PT, Buey RM, Andreu JM, Díaz JF. NMR determination of the bioactive conformation of peloruside A bound to microtubules. J Am Chem Soc 2007; 128:8757-65. [PMID: 16819869 DOI: 10.1021/ja0580237] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report here on the determination of the conformation of Peloruside A bound to biochemically stabilized microtubules, by using TR-NOESY NMR experiments. As a previous step, the conformation of the free molecule in water solution has also been deduced. Despite the large size of the ring, Peloruside A mainly adopts two conformations in water solution. A conformational selection process takes place, and the microtubules-bound conformer is one of those present in the water solution, different than that existing in chloroform medium. A model of the binding mode to tubulin has also been proposed, by docking the bioactive conformation of peloruside, which involves the alpha-tubulin monomer, in contrast with taxol, which binds to the beta-monomer.
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Affiliation(s)
- Jesús Jiménez-Barbero
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
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40
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Mari S, Sánchez-Medina I, Mereghetti P, Belvisi L, Jiménez-Barbero J, Bernardi A. Synthesis and conformational analysis of an α-d-mannopyranosyl-(1→2)-α-d-mannopyranosyl-(1→6)-α-d-mannopyranose mimic. Carbohydr Res 2007; 342:1859-68. [PMID: 17420008 DOI: 10.1016/j.carres.2007.03.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2007] [Revised: 03/13/2007] [Accepted: 03/17/2007] [Indexed: 11/24/2022]
Abstract
A mimic of a (1-->2),(1-->6)-mannotrioside was synthesized by replacing the central mannose unit with an enantiomerically pure, conformationally stable trans-diaxial cyclohexanediol. The three-dimensional structure of the molecule was investigated by NMR spectroscopy supported by molecular modelling and was compared to the known features of the natural mannotrioside.
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Affiliation(s)
- Silvia Mari
- Centro de Investigaciones Biológicas, Departamento de Estructura y Functión de Proteínas, CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain
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41
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Li X, Kou D, Rao S, Liang H. Developing a coarse-grained force field for the diblock copolymer poly(styrene-b-butadiene) from atomistic simulation. J Chem Phys 2007; 124:204909. [PMID: 16774386 DOI: 10.1063/1.2200694] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We have developed a coarse-grained force field for the poly(styrene-b-butadiene) diblock copolymer. We describe the computational methods and discuss how they were applied to develop a coarse-grained force field for this diblock copolymer from the atomistic simulation. The new force field contains three different bonds, four angles, five dihedral angles, and three nonbonded terms. We successfully tested this coarse-grained model against the chain properties, including static and dynamic properties, derived from the atomistic simulation; the results suggest that the coarse-grained force field is an effective model.
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Affiliation(s)
- Xuejin Li
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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42
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Lwin TZ, Luo R. Overcoming entropic barrier with coupled sampling at dual resolutions. J Chem Phys 2007; 123:194904. [PMID: 16321110 DOI: 10.1063/1.2102871] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An enhanced sampling method is proposed for ab initio protein folding simulations. The new method couples a high-resolution model for accuracy and a low-resolution model for efficiency. It aims to overcome the entropic barrier found in the exponentially large protein conformational space when a high-resolution model, such as an all-atom molecular mechanics force field, is used. The proposed method is designed to satisfy the detailed balance condition so that the Boltzmann distribution can be generated in all sampling trajectories in both high and low resolutions. The method was tested on model analytical energy functions and ab initio folding simulations of a beta-hairpin peptide. It was found to be more efficient than replica-exchange method that is used as its building block. Analysis with the analytical energy functions shows that the number of energy calculations required to find global minima and to converge mean potential energies is much fewer with the new method. Ergodic measure shows that the new method explores the conformational space more rapidly. We also studied imperfect low-resolution energy models and found that the introduction of errors in low-resolution models does decrease its sampling efficiency. However, a reasonable increase in efficiency is still observed when the global minima of the low-resolution models are in the vicinity of the global minimum basin of the high-resolution model. Finally, our ab initio folding simulation of the tested peptide shows that the new method is able to fold the peptide in a very short simulation time. The structural distribution generated by the new method at the equilibrium portion of the trajectory resembles that in the equilibrium simulation starting from the crystal structure.
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Affiliation(s)
- Thur Zar Lwin
- Chemical and Material Physics Graduate Program, University of California, Irvine, CA 92697-3900, USA
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43
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Handl HL, Sankaranarayanan R, Josan JS, Vagner J, Mash EA, Gillies RJ, Hruby VJ. Synthesis and evaluation of bivalent NDP-alpha-MSH(7) peptide ligands for binding to the human melanocortin receptor 4 (hMC4R). Bioconjug Chem 2007; 18:1101-9. [PMID: 17591746 PMCID: PMC3538036 DOI: 10.1021/bc0603642] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate the potential utility of multivalent ligands as targeting agents for cancer imaging or therapy by determining the binding of homobivalent ligands to their corresponding receptors. This manuscript details the synthesis and evaluation of a series of bivalent ligands containing two copies of the truncated heptapeptide version of [Nle4-D-Phe7]-alpha-melanocyte stimulating hormone (NDP-alpha-MSH), referred to as MSH(7). These were connected with various semirigid linkers containing Pro-Gly repeats, with or without flexible poly(ethylene glycol) (PEGO) moieties at their termini. Modeling data suggest a distance of 20-50 A between the ligand binding sites of two adjacent G-protein coupled receptors, GPCRs. These bivalent ligands were observed to bind with higher affinity compared to their monovalent counterparts. Data suggest these ligands may be capable of cross-linking adjacent receptors. An optimal linker length of 25 +/- 10 A, inferred from these ligands, correlated well with the inter-receptor distance estimated through modeling. Although there was no difference in maximal binding affinities between the ligands constructed with the Pro-Gly repeats versus those constructed with the PEGO inserts, the PEGO-containing ligands bound with high affinities over a greater range of linker lengths.
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Affiliation(s)
- Heather L. Handl
- Departments of Radiology, Biochemistry, and Molecular Biophysics, Arizona Cancer Center, Tucson, Arizona 85724
| | | | - Jatinder S. Josan
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721
| | - Josef Vagner
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721
| | - Eugene A. Mash
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721
| | - Robert J. Gillies
- Departments of Radiology, Biochemistry, and Molecular Biophysics, Arizona Cancer Center, Tucson, Arizona 85724
| | - Victor J. Hruby
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721
- Address correspondence to Prof. Victor J. Hruby, Regents Professor of Chemistry, Department of Chemistry, 1306, E. University, P.O. Box 210041, Department of Chemistry, University of Arizona, Tucson, Arizona 85721 USA; Phone (520) 621-6332; FAX (520) 621-8407.
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Danieli E, Trabocchi A, Menchi G, Guarna A. Synthesis and Conformational Analysis of Constrained β-Turn Mimetics Incorporating a Bicyclic Turn Inducer by Use of the Petasis Three-Component Reaction on Solid Phase. European J Org Chem 2007. [DOI: 10.1002/ejoc.200600650] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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45
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Ragusa A, Hayes JM, Light ME, Kilburn JD. A Combined Computational and Experimental Approach for the Analysis of the Enantioselective Potential of a New Macrocyclic Receptor for N-Protected α-Amino Acids. Chemistry 2007; 13:2717-28. [PMID: 17200922 DOI: 10.1002/chem.200601289] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A new macrocyclic receptor incorporating a thiourea moiety has been synthesised. Crystal structures of the macrocycle showed that the receptor has a rigid backbone but the thiourea moiety can orientate itself to bind to a DMSO solvent molecule. Force-field (MMFFs) calculations were performed to model the macrocycle and its binding properties with respect to N-protected amino acids, which were measured experimentally by NMR titration. Binding free energies were calculated by using the mode integration algorithm (MINTA) or free-energy perturbation (FEP). Excellent qualitative agreement with experiment was obtained. To further exploit the accuracy of the free-energy predictions for this system, the faster free-energy algorithm MINTA was used as a prediction tool to test the binding affinity of the macrocycle towards a series of several other amino acid derivatives, which speeded up considerably the screening process and reduced laboratory costs.
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Affiliation(s)
- Andrea Ragusa
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
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46
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Terraneo G, Potenza D, Canales A, Jiménez-Barbero J, Baldridge KK, Bernardi A. A Simple Model System for the Study of Carbohydrate−Aromatic Interactions. J Am Chem Soc 2007; 129:2890-900. [PMID: 17309255 DOI: 10.1021/ja066633g] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A molecular scaffold was identified which enables the establishment of intramolecular interactions between a monosaccharide and a nearby phenyl ring. A group of molecules containing four different monosaccharides (glucose, galactose, N-acetyl-glucosamine, and N-acetyl-galactosamine) was synthesized and used to investigate the extent and nature of this carbohydrate-arene interaction, as well as the effect on the overall 3D structure of the molecules involved. The sugar-aromatic distance was evaluated by rigorous NMR studies supported by molecular modeling and found to be constant throughout the series, independent of the nature of the sugar and of the conformational behavior of the fragment connecting the two elements. Ab initio calculations at the B3LYP/DZV(2d,p) level of theory enable the analysis of the electronic nature of the interaction. The study shows that, given the opportunity, persistent intramolecular aromatic-sugar interactions can be established and can significantly influence overall molecular shape and energetics. These results have important implications in the design of structural mimics of oligosaccharides.
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Affiliation(s)
- Giancarlo Terraneo
- Universita' di Milano, Dipartimento di Chimica Organica e Industriale e Centro di Eccellenza CISI, via Venezian 21, 20133 Milano, Italy
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47
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48
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Free Energy Calculations: Use and Limitations in Predicting Ligand Binding Affinities. REVIEWS IN COMPUTATIONAL CHEMISTRY 2007. [DOI: 10.1002/9780470125939.ch4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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49
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Lee OS, Hwang S, Chung DS. Free Energy Peturbation and Molecular Dynamics Simulation Studies on the Enantiomeric Discrimination of Amines by Dimethyldiketopyridino-18-Crown-6. Supramol Chem 2006. [DOI: 10.1080/10610270008029448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- One-Sun Lee
- a Department of Chemistry , Seoul National University , Seoul, 151-742, Korea
| | - Sungu Hwang
- a Department of Chemistry , Seoul National University , Seoul, 151-742, Korea
| | - Doo Soo Chung
- a Department of Chemistry , Seoul National University , Seoul, 151-742, Korea
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50
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Mari S, Cañada FJ, Jiménez-Barbero J, Bernardi A, Marcou G, Motto I, Velter I, Nicotra F, La Ferla B. Synthesis and Conformational Analysis of Galactose-Derived Bicyclic Scaffolds. European J Org Chem 2006. [DOI: 10.1002/ejoc.200501012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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