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Aminpour M, Montemagno C, Tuszynski JA. An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications. Molecules 2019; 24:E1693. [PMID: 31052253 PMCID: PMC6539951 DOI: 10.3390/molecules24091693] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/17/2019] [Accepted: 04/23/2019] [Indexed: 01/29/2023] Open
Abstract
In this paper we review the current status of high-performance computing applications in the general area of drug discovery. We provide an introduction to the methodologies applied at atomic and molecular scales, followed by three specific examples of implementation of these tools. The first example describes in silico modeling of the adsorption of small molecules to organic and inorganic surfaces, which may be applied to drug delivery issues. The second example involves DNA translocation through nanopores with major significance to DNA sequencing efforts. The final example offers an overview of computer-aided drug design, with some illustrative examples of its usefulness.
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Affiliation(s)
- Maral Aminpour
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada.
- Ingenuity Lab, Edmonton, AB T6G 2R3, Canada.
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
| | - Carlo Montemagno
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada.
- Ingenuity Lab, Edmonton, AB T6G 2R3, Canada.
- Southern Illinois University, Carbondale, IL 62901, USA.
| | - Jack A Tuszynski
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada.
- Department of Mechanical Engineering and Aerospace Engineering (DIMEAS), Politecnico di Torino, 10129 Turin, Italy.
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Ramakrishnan SK, Zhu J, Gergely C. Organic-inorganic interface simulation for new material discoveries. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1277] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sathish Kumar Ramakrishnan
- Nanobiology Institute; Yale University; West Haven CT USA
- Laboratoire Charles Coulomb (L2C); UMR 5221 CNRS-Université de Montpellier; Montpellier France
| | - Jie Zhu
- Nanobiology Institute; Yale University; West Haven CT USA
| | - Csilla Gergely
- Laboratoire Charles Coulomb (L2C); UMR 5221 CNRS-Université de Montpellier; Montpellier France
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Pápa Z, Ramakrishnan SK, Martin M, Cloitre T, Zimányi L, Márquez J, Budai J, Tóth Z, Gergely C. Interactions at the Peptide/Silicon Surfaces: Evidence of Peptide Multilayer Assembly. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:7250-7258. [PMID: 27315212 DOI: 10.1021/acs.langmuir.6b00916] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Selective deposition of peptides from liquid solutions to n- and p-doped silicon has been demonstrated. The selectivity is governed by peptide/silicon adhesion differences. A noninvasive, fast characterization of the obtained peptide layers is required to promote their application for interfacing silicon-based devices with biological material. In this study we show that spectroscopic ellipsometry-a method increasingly used for the investigation of biointerfaces-can provide essential information about the amount of adsorbed peptide material and the degree of coverage on silicon surfaces. We observed the formation of peptide multilayers for a strongly binding adhesion peptide on p-doped silicon. Application of the patterned layer ellipsometric evaluation method combined with Sellmeier dispersion led to physically consistent results, which describe well the optical properties of peptide layers in the visible spectral range. This evaluation allowed the estimation of surface coverage, which is an important indicator of adsorption quality. The ellipsometric findings were well supported by atomic force microscopy results.
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Affiliation(s)
- Zsuzsanna Pápa
- ELI-ALPS, ELI-Hu Nkft , Dugonics ter 13, Szeged 6720, Hungary
| | - Sathish Kumar Ramakrishnan
- Laboratoire Charles Coulomb (L2C), UMR 5221, CNRS-Université de Montpellier , Montpellier, France
- Nanobiology Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Marta Martin
- Laboratoire Charles Coulomb (L2C), UMR 5221, CNRS-Université de Montpellier , Montpellier, France
| | - Thierry Cloitre
- Laboratoire Charles Coulomb (L2C), UMR 5221, CNRS-Université de Montpellier , Montpellier, France
| | - László Zimányi
- Institute of Biophysics, Biological Research Centre of the Hungarian Academy of Sciences , Szeged, Hungary
| | - Jessica Márquez
- Institute of Biophysics, Biological Research Centre of the Hungarian Academy of Sciences , Szeged, Hungary
- Faculty of Chemical Sciences, Universidad Autónoma de San Luis Potosí , San Luis Potosí, Mexico
| | - Judit Budai
- ELI-ALPS, ELI-Hu Nkft , Dugonics ter 13, Szeged 6720, Hungary
| | | | - Csilla Gergely
- Laboratoire Charles Coulomb (L2C), UMR 5221, CNRS-Université de Montpellier , Montpellier, France
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Li Z, Kermode JR, De Vita A. Molecular dynamics with on-the-fly machine learning of quantum-mechanical forces. PHYSICAL REVIEW LETTERS 2015; 114:096405. [PMID: 25793835 DOI: 10.1103/physrevlett.114.096405] [Citation(s) in RCA: 249] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Indexed: 05/06/2023]
Abstract
We present a molecular dynamics scheme which combines first-principles and machine-learning (ML) techniques in a single information-efficient approach. Forces on atoms are either predicted by Bayesian inference or, if necessary, computed by on-the-fly quantum-mechanical (QM) calculations and added to a growing ML database, whose completeness is, thus, never required. As a result, the scheme is accurate and general, while progressively fewer QM calls are needed when a new chemical process is encountered for the second and subsequent times, as demonstrated by tests on crystalline and molten silicon.
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Affiliation(s)
- Zhenwei Li
- King's College London, Physics Department, Strand, London WC2R 2LS, United Kingdom
| | - James R Kermode
- King's College London, Physics Department, Strand, London WC2R 2LS, United Kingdom
- Warwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alessandro De Vita
- King's College London, Physics Department, Strand, London WC2R 2LS, United Kingdom
- CENMAT-UTS, Via Alfonso Valerio 2, 34127 Trieste, Italy
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Peguiron A, Colombi Ciacchi L, De Vita A, Kermode JR, Moras G. Accuracy of buffered-force QM/MM simulations of silica. J Chem Phys 2015; 142:064116. [DOI: 10.1063/1.4907786] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Anke Peguiron
- Fraunhofer IWM, Wöhlerstraße 11, 79108 Freiburg, Germany
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group, Faculty of Production Engineering and Bremen Center for Computational Materials Science, University of Bremen, Am Fallturm 1, 28359 Bremen, Germany
- Center for Environmental Research and Sustainable Technology (UFT), 28359 Bremen, Germany
| | - Alessandro De Vita
- Department of Physics, King’s College London, Strand, London WC2R 2LS, United Kingdom
- CENMAT-UTS, Via Alfonso Valerio 2, 34127 Trieste, Italy
| | - James R. Kermode
- Department of Physics, King’s College London, Strand, London WC2R 2LS, United Kingdom
- Warwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom
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Multiscale Modelling of Materials Chemomechanics: Brittle Fracture of Oxides and Semiconductors. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.mspro.2014.06.271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Sarsam J, Finnis MW, Tangney P. Atomistic force field for alumina fit to density functional theory. J Chem Phys 2013; 139:204704. [DOI: 10.1063/1.4832695] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Beck P, Brommer P, Roth J, Trebin HR. Influence of polarizability on metal oxide properties studied by molecular dynamics simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:485401. [PMID: 23139206 DOI: 10.1088/0953-8984/24/48/485401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We have studied the dependence of metal oxide properties in molecular dynamics (MD) simulations on the polarizability of oxygen ions. We present studies of both liquid and crystalline structures of silica (SiO(2)), magnesia (MgO) and alumina (Al(2)O(3)). For each of the three oxides, two separately optimized sets of force fields were used: (i) long-range Coulomb interactions between oxide and metal ions combined with a short-range pair potential; (ii) extension of force field (i) by adding polarizability to the oxygen ions. We show that while an effective potential of type (i) without polarizable oxygen ions can describe radial distributions and lattice constants reasonably well, potentials of type (ii) are required to obtain correct values for bond angles and the equation of state. The importance of polarizability for metal oxide properties decreases with increasing temperature.
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Affiliation(s)
- Philipp Beck
- Institut für Theoretische und Angewandte Physik (ITAP), Universität Stuttgart, Stuttgart, Germany.
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Izvekov S, Rice BM. Mechanism of densification in silica glass under pressure as revealed by a bottom-up pairwise effective interaction model. J Chem Phys 2012; 136:134508. [DOI: 10.1063/1.3696865] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Hocker S, Beck P, Schmauder S, Roth J, Trebin HR. Simulation of crack propagation in alumina with ab initio based polarizable force field. J Chem Phys 2012; 136:084707. [DOI: 10.1063/1.3685900] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Beck P, Brommer P, Roth J, Trebin HR. Ab initio based polarizable force field generation and application to liquid silica and magnesia. J Chem Phys 2011; 135:234512. [DOI: 10.1063/1.3668603] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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