1
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Azhagesan A, Rajendran D, Varghese RP, George Priya Doss C, Chandrasekaran N. Assessment of polystyrene nano plastics effect on human salivary α-amylase structural alteration: Insights from an in vitro and in silico study. Int J Biol Macromol 2024; 257:128650. [PMID: 38065455 DOI: 10.1016/j.ijbiomac.2023.128650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/19/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
The study found that the enzyme activity of human salivary α-amylase (α-AHS) was competitively inhibited by nanoplastic polystyrene (PS-NPs), with a half-inhibitory concentration (IC50) of 92 μg/mL, while the maximum reaction rate (Vmax) remained unchanged at 909 μg/mL•min. An increase in the concentration of PS-NPs led to a quenching of α-AHS fluorescence with a slight red shift, indicating a static mechanism. The binding constant (Ka) and quenching constant (Kq) were calculated to be 2.92 × 1011 M-1 and 1.078 × 1019 M-1• S-1 respectively, with a hill coefficient (n) close to one and an apparent binding equilibrium constant (KA) of 1.54 × 1011 M-1. Molecular docking results suggested that the interaction between α-AHS and PS-NPs involved π-anion interactions between the active site Asp197, Asp300 residues, and van der Waals force interactions affecting the Tyr, Trp, and other residues. Fourier transform infrared (FT-IR) and circular dichroism (CD) analyses revealed conformational changes in α-AHS, including a loss of secondary structure α-helix and β-sheet. The study concludes that the interaction between α-AHS and PS-NPs leads to structural and functional changes in α-AHS, potentially impacting human health. This research provides a foundation for further toxicological analysis of MPs/NPs in the human digestive system.
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Affiliation(s)
- Ananthaselvam Azhagesan
- Centre for Nanobiotechnology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632 014, India
| | - Durgalakshmi Rajendran
- Centre for Nanobiotechnology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632 014, India
| | - Rinku Polachirakkal Varghese
- Department of Integrative Biology, School of BioSciences & Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632 014, India
| | - C George Priya Doss
- Department of Integrative Biology, School of BioSciences & Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632 014, India
| | - Natarajan Chandrasekaran
- Centre for Nanobiotechnology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632 014, India.
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2
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Monteleone S, Fedorov DG, Townsend-Nicholson A, Southey M, Bodkin M, Heifetz A. Hotspot Identification and Drug Design of Protein-Protein Interaction Modulators Using the Fragment Molecular Orbital Method. J Chem Inf Model 2022; 62:3784-3799. [PMID: 35939049 DOI: 10.1021/acs.jcim.2c00457] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein-protein interactions (PPIs) are essential for the function of many proteins. Aberrant PPIs have the potential to lead to disease, making PPIs promising targets for drug discovery. There are over 64,000 PPIs in the human interactome reference database; however, to date, very few PPI modulators have been approved for clinical use. Further development of PPI-specific therapeutics is highly dependent on the availability of structural data and the existence of reliable computational tools to explore the interface between two interacting proteins. The fragment molecular orbital (FMO) quantum mechanics method offers comprehensive and computationally inexpensive means of identifying the strength (in kcal/mol) and the chemical nature (electrostatic or hydrophobic) of the molecular interactions taking place at the protein-protein interface. We have integrated FMO and PPI exploration (FMO-PPI) to identify the residues that are critical for protein-protein binding (hotspots). To validate this approach, we have applied FMO-PPI to a dataset of protein-protein complexes representing several different protein subfamilies and obtained FMO-PPI results that are in agreement with published mutagenesis data. We observed that critical PPIs can be divided into three major categories: interactions between residues of two proteins (intermolecular), interactions between residues within the same protein (intramolecular), and interactions between residues of two proteins that are mediated by water molecules (water bridges). We extended our findings by demonstrating how this information obtained by FMO-PPI can be utilized to support the structure-based drug design of PPI modulators (SBDD-PPI).
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Affiliation(s)
- Stefania Monteleone
- Evotec UK Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Andrea Townsend-Nicholson
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Michelle Southey
- Evotec UK Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Michael Bodkin
- Evotec UK Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Alexander Heifetz
- Evotec UK Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
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3
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Yasuo N, Ishida T, Sekijima M. Computer aided drug discovery review for infectious diseases with case study of anti-Chagas project. Parasitol Int 2021; 83:102366. [PMID: 33915269 DOI: 10.1016/j.parint.2021.102366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/23/2021] [Accepted: 04/07/2021] [Indexed: 01/09/2023]
Abstract
Neglected tropical diseases (NTDs) are parasitic and bacterial infections that are widespread, especially in the tropics, and cause health problems for about one billion people over 149 countries worldwide. However, in terms of therapeutic agents, for example, nifurtimox and benznidazole were developed in the 1960s to treat Chagas disease, but new drugs are desirable because of their side effects. Drug discovery takes 12 to 14 years and costs $2.6 billon dollars, and hence, computer aided drug discovery (CADD) technology is expected to reduce the time and cost. This paper describes our methods and results based on CADD, mainly for NTDs. An overview of databases, molecular simulation and pharmacophore modeling, contest-based drug discovery, and machine learning and their results are presented herein.
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Affiliation(s)
- Nobuaki Yasuo
- Academy for Convergence of Materials and Informatics (TAC-MI), Tokyo Institute of Technology, S6-23, 2-12-1, Ookayama, Meguro-ku, Tokyo, Japan.
| | - Takashi Ishida
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-85, 2-12-1, Ookayama, Meguro-ku, Tokyo, Japan.
| | - Masakazu Sekijima
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 4259-J3-23, Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan.
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4
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Abstract
The understanding of binding interactions between a protein and a small molecule plays a key role in the rationalization of potency and selectivity and in design of new ideas. However, even when a target of interest is structurally enabled, visual inspection and force field-based molecular mechanics calculations cannot always explain the full complexity of the molecular interactions that are critical in drug design. Quantum mechanical methods have the potential to address this shortcoming, but traditionally, computational expense has made the application of these calculations impractical. The fragment molecular orbital (FMO) method offers a solution that combines accuracy, speed, and the ability to characterize important interactions (i.e. its strength in kcal/mol and chemical nature: hydrophobic, electrostatic, etc) that would otherwise be hard to detect. In this chapter, we describe the FMO method and illustrate its application in the discovery of the benzothiazole (BZT) series as novel tyrosine kinase ITK inhibitors for treatment of allergic asthma.
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5
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Analyzing GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method. Methods Mol Biol 2021. [PMID: 32016893 DOI: 10.1007/978-1-0716-0282-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
G-protein-coupled receptors (GPCRs) have enormous physiological and biomedical importance, and therefore it is not surprising that they are the targets of many prescribed drugs. Further progress in GPCR drug discovery is highly dependent on the availability of protein structural information. However, the ability of X-ray crystallography to guide the drug discovery process for GPCR targets is limited by the availability of accurate tools to explore receptor-ligand interactions. Visual inspection and molecular mechanics approaches cannot explain the full complexity of molecular interactions. Quantum mechanics (QM) approaches are often too computationally expensive to be of practical use in time-sensitive situations, but the fragment molecular orbital (FMO) method offers an excellent solution that combines accuracy, speed, and the ability to reveal key interactions that would otherwise be hard to detect. Integration of GPCR crystallography or homology modelling with FMO reveals atomistic details of the individual contributions of each residue and water molecule toward ligand binding, including an analysis of their chemical nature. Such information is essential for an efficient structure-based drug design (SBDD) process. In this chapter, we describe how to use FMO in the characterization of GPCR-ligand interactions.
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6
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Hayakawa D, Sawada N, Watanabe Y, Gouda H. A molecular interaction field describing nonconventional intermolecular interactions and its application to protein–ligand interaction prediction. J Mol Graph Model 2020; 96:107515. [DOI: 10.1016/j.jmgm.2019.107515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 10/25/2022]
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7
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Heifetz A, Morao I, Babu MM, James T, Southey MWY, Fedorov DG, Aldeghi M, Bodkin MJ, Townsend-Nicholson A. Characterizing Interhelical Interactions of G-Protein Coupled Receptors with the Fragment Molecular Orbital Method. J Chem Theory Comput 2020; 16:2814-2824. [PMID: 32096994 PMCID: PMC7161079 DOI: 10.1021/acs.jctc.9b01136] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
G-protein coupled receptors (GPCRs) are the largest superfamily of membrane proteins, regulating almost every aspect of cellular activity and serving as key targets for drug discovery. We have identified an accurate and reliable computational method to characterize the strength and chemical nature of the interhelical interactions between the residues of transmembrane (TM) domains during different receptor activation states, something that cannot be characterized solely by visual inspection of structural information. Using the fragment molecular orbital (FMO) quantum mechanics method to analyze 35 crystal structures representing different branches of the class A GPCR family, we have identified 69 topologically equivalent TM residues that form a consensus network of 51 inter-TM interactions, providing novel results that are consistent with and help to rationalize experimental data. This discovery establishes a comprehensive picture of how defined molecular forces govern specific interhelical interactions which, in turn, support the structural stability, ligand binding, and activation of GPCRs.
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Affiliation(s)
- Alexander Heifetz
- Evotec
(U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
- Institute
of Structural & Molecular Biology, Research Department of Structural
& Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
- E-mail: (A.H.)
| | - Inaki Morao
- Evotec
(U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
- E-mail: (I.M.)
| | - M. Madan Babu
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Tim James
- Evotec
(U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | | | - Dmitri G. Fedorov
- CD-FMat,
National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Matteo Aldeghi
- Department
of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Michael J. Bodkin
- Evotec
(U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Andrea Townsend-Nicholson
- Institute
of Structural & Molecular Biology, Research Department of Structural
& Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
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8
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Bagheri S, Masoodi HR. The influence of CH … π interaction on coupling constants across N … H–F hydrogen bond in a substituted T-shaped configuration: a theoretical study. Mol Phys 2020. [DOI: 10.1080/00268976.2019.1580393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Sotoodeh Bagheri
- Department of Chemistry, Faculty of Science, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| | - Hamid Reza Masoodi
- Department of Chemistry, Faculty of Science, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
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9
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Morao I, Heifetz A, Fedorov DG. Accurate Scoring in Seconds with the Fragment Molecular Orbital and Density-Functional Tight-Binding Methods. Methods Mol Biol 2020; 2114:143-148. [PMID: 32016891 DOI: 10.1007/978-1-0716-0282-9_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The accurate evaluation of receptor-ligand interactions is an essential part of rational drug design. While quantum mechanical (QM) methods have been a promising means by which to achieve this, traditional QM is not applicable for large biological systems due to its high computational cost. Here, the fragment molecular orbital (FMO) method has been combined with the density-functional tight-binding (DFTB) method to compute energy calculations of biological systems in seconds. FMO-DFTB outperformed GBVI/WSA in identifying a set of 10 binders versus a background of 500 decoys applied to human k-opioid receptor. The significant increase in the speed and the high accuracy achieved with FMO-DFTB calculations allows FMO to be applied in areas of drug discovery that were not previously accessible to traditional QM methodologies. For the first time, it is now possible to perform FMO calculations in a high-throughput manner.
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Affiliation(s)
- Inaki Morao
- Evotec (UK) Ltd., Abingdon, Oxfordshire, UK.
| | | | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
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10
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Heifetz A, Sladek V, Townsend-Nicholson A, Fedorov DG. Characterizing Protein-Protein Interactions with the Fragment Molecular Orbital Method. Methods Mol Biol 2020; 2114:187-205. [PMID: 32016895 DOI: 10.1007/978-1-0716-0282-9_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Proteins are vital components of living systems, serving as building blocks, molecular machines, enzymes, receptors, ion channels, sensors, and transporters. Protein-protein interactions (PPIs) are a key part of their function. There are more than 645,000 reported disease-relevant PPIs in the human interactome, but drugs have been developed for only 2% of these targets. The advances in PPI-focused drug discovery are highly dependent on the availability of structural data and accurate computational tools for analysis of this data. Quantum mechanical approaches are often too expensive computationally, but the fragment molecular orbital (FMO) method offers an excellent solution that combines accuracy, speed and the ability to reveal key interactions that would otherwise be hard to detect. FMO provides essential information for PPI drug discovery, namely, identification of key interactions formed between residues of two proteins, including their strength (in kcal/mol) and their chemical nature (electrostatic or hydrophobic). In this chapter, we have demonstrated how three different FMO-based approaches (pair interaction energy analysis (PIE analysis), subsystem analysis (SA) and analysis of protein residue networks (PRNs)) have been applied to study PPI in three protein-protein complexes.
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Affiliation(s)
| | - Vladimir Sladek
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Andrea Townsend-Nicholson
- Research Department of Structural & Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
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11
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Abstract
Estimating the range of three-dimensional structures (conformations) that are available to a molecule is a key component of computer-aided drug design. Quantum mechanical simulation offers improved accuracy over forcefield methods, but at a high computational cost. The question is whether this increased cost can be justified in a context in which high-throughput analysis of large numbers of molecules is often key. This chapter discusses the application of quantum mechanics to conformational searching, with a focus on three key challenges: (1) the generation of ensembles that include a good approximation to a molecule's bioactive conformation at as prominent a ranking as possible; (2) rational analysis and modification of a pre-established bioactive conformation in terms of its energetics; and (3) approximation of real solution-phase conformational ensembles in tandem with NMR data. The impact of QM on the high-throughput application (1) is debatable, meaning that for the moment its primary application is still lower-throughput applications such as (2) and (3). The optimal choice of QM method is also discussed. Rigorous benchmarking suggests that DFT methods are only acceptable when used with large basis sets, but a trickle of papers continue to obtain useful results with relatively low-cost methods, leading to a dilemma that the literature has yet to fully resolve.
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12
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González R, Mroginski MA. Fully Quantum Chemical Treatment of Chromophore–Protein Interactions in Phytochromes. J Phys Chem B 2019; 123:9819-9830. [DOI: 10.1021/acs.jpcb.9b08938] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ronald González
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Maria A. Mroginski
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
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13
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Heifetz A, James T, Southey M, Morao I, Aldeghi M, Sarrat L, Fedorov DG, Bodkin MJ, Townsend-Nicholson A. Characterising GPCR-ligand interactions using a fragment molecular orbital-based approach. Curr Opin Struct Biol 2019; 55:85-92. [PMID: 31022570 DOI: 10.1016/j.sbi.2019.03.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/19/2019] [Accepted: 03/14/2019] [Indexed: 10/27/2022]
Abstract
There has been fantastic progress in solving GPCR crystal structures. However, the ability of X-ray crystallography to guide the drug discovery process for GPCR targets is limited by the availability of accurate tools to explore receptor-ligand interactions. Visual inspection and molecular mechanics approaches cannot explain the full complexity of molecular interactions. Quantum mechanical approaches (QM) are often too computationally expensive, but the fragment molecular orbital (FMO) method offers an excellent solution that combines accuracy, speed and the ability to reveal key interactions that would otherwise be hard to detect. Integration of GPCR crystallography or homology modelling with FMO reveals atomistic details of the individual contributions of each residue and water molecule towards ligand binding, including an analysis of their chemical nature.
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Affiliation(s)
- Alexander Heifetz
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom.
| | - Tim James
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Michelle Southey
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Inaki Morao
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Matteo Aldeghi
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Laurie Sarrat
- Evotec (France) SAS, 195 Route d' Espagne, 31036 Toulouse, France
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Mike J Bodkin
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Andrea Townsend-Nicholson
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of Biosciences, University College London, London,WC1E 6BT, United Kingdom
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14
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Wu J, Zhu S, Wu Y, Jiang T, Wang L, Jiang J, Wen J, Deng Y. Multiple CH/π Interactions Maintain the Binding of Aflatoxin B₁ in the Active Cavity of Human Cytochrome P450 1A2. Toxins (Basel) 2019; 11:toxins11030158. [PMID: 30871064 PMCID: PMC6468651 DOI: 10.3390/toxins11030158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/03/2019] [Accepted: 03/08/2019] [Indexed: 11/26/2022] Open
Abstract
Human cytochrome P450 1A2 (CYP1A2) is one of the key CYPs that activate aflatoxin B1 (AFB1), a notorious mycotoxin, into carcinogenic exo-8,9-epoxides (AFBO) in the liver. Although the structure of CYP1A2 is available, the mechanism of CYP1A2-specific binding to AFB1 has not been fully clarified. In this study, we used calculation biology to predict a model of CYP1A2 with AFB1, where Thr-124, Phe-125, Phe-226, and Phe-260 possibly participate in the specific binding. Site-directed mutagenesis was performed to construct mutants T124A, F125A, F226A, and F260A. Escherichia coli-expressed recombinant proteins T124A, F226A, and F260A had active structures, while F125A did not. This was evidenced by Fe2+∙Carbon monoxide (CO)-reduced difference spectra and circular dichroism spectroscopy. Mutant F125A was expressed in HEK293T cells. Steady kinetic assays showed that T124A had enhanced activity towards AFB1, while F125A, F226A, and F260A were significantly reduced in their ability to activate AFB1, implying that hydrogen bonds between Thr-124 and AFB1 were not important for substrate-specific binding, whereas Phe-125, Phe-226, and Phe-260 were essential for the process. The computation simulation and experimental results showed that the three key CH/π interactions between Phe-125, Phe-226, or Phe-260 and AFB1 collectively maintained the stable binding of AFB1 in the active cavity of CYP1A2.
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Affiliation(s)
- Jun Wu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China.
| | - Sisi Zhu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China.
| | - Yunbo Wu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China.
| | - Tianqing Jiang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China.
| | - Lingling Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China.
| | - Jun Jiang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China.
| | - Jikai Wen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China.
| | - Yiqun Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China.
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15
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Yamanaka M. <b>Random matrix theory for an inter-fragment interaction energy matrix in fragment molecular orbital method </b>. CHEM-BIO INFORMATICS JOURNAL 2018. [DOI: 10.1273/cbij.18.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Masanori Yamanaka
- Department of Physics, College of Science and Technology, Nihon University
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16
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Ishikawa T, Mizuta S, Kaneko O, Yahata K. Fragment Molecular Orbital Study of the Interaction between Sarco/Endoplasmic Reticulum Ca 2+-ATPase and its Inhibitor Thapsigargin toward Anti-Malarial Development. J Phys Chem B 2018; 122:7970-7977. [PMID: 30067362 DOI: 10.1021/acs.jpcb.8b04509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Plasmodium falciparum, the causative agent of malignant malaria, is insensitive to thapsigargin (TG), a well-known inhibitor of the human sarco/endoplasmic reticulum Ca2+-ATPase (SERCA). To understand the key factor causing the difference of the sensitivity, the molecular interaction of TG and each SERCA was analyzed by the fragment molecular orbital (FMO) method. While the major component of the interaction energy was the nonpolar interaction, the major difference in the molecular interaction arose from the polar interaction, namely, the hydrogen bonding interaction with a hydroxyl group of TG. Additionally, we successfully confirmed these FMO calculation results by measuring the inhibitory activity of a synthesized TG derivative. Our calculations and experiments indicated that, by replacing the hydroxyl group of TG with another functional group, the sensitivities of TG to human and P. falciparum SERCAs can be reversed. This study provides important information to develop antimalarial compounds targeting P. falciparum SERCA.
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Affiliation(s)
- Takeshi Ishikawa
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences , Nagasaki University , 1-12-4 Sakamoto , Nagasaki 852-8523 , Japan.,Leading Program, Graduate School of Biomedical Sciences , Nagasaki University , 1-12-4 Sakamoto , Nagasaki 852-8523 , Japan
| | - Satoshi Mizuta
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences , Nagasaki University , 1-12-4 Sakamoto , Nagasaki 852-8523 , Japan
| | - Osamu Kaneko
- Leading Program, Graduate School of Biomedical Sciences , Nagasaki University , 1-12-4 Sakamoto , Nagasaki 852-8523 , Japan.,Department of Protozoology, Institute of Tropical Medicine (NEKKEN) , Nagasaki University , 1-12-4 Sakamoto , Nagasaki 852-8523 , Japan
| | - Kazuhide Yahata
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN) , Nagasaki University , 1-12-4 Sakamoto , Nagasaki 852-8523 , Japan
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17
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Thapa B, Beckett D, Jovan Jose KV, Raghavachari K. Assessment of Fragmentation Strategies for Large Proteins Using the Multilayer Molecules-in-Molecules Approach. J Chem Theory Comput 2018; 14:1383-1394. [DOI: 10.1021/acs.jctc.7b01198] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Bishnu Thapa
- Department of Chemistry, Indiana University, Bloomington 47405, Indiana, United States
| | - Daniel Beckett
- Department of Chemistry, Indiana University, Bloomington 47405, Indiana, United States
| | - K. V. Jovan Jose
- Department of Chemistry, Indiana University, Bloomington 47405, Indiana, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington 47405, Indiana, United States
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18
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19
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Chudyk EI, Sarrat L, Aldeghi M, Fedorov DG, Bodkin MJ, James T, Southey M, Robinson R, Morao I, Heifetz A. Exploring GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method. Methods Mol Biol 2018; 1705:179-195. [PMID: 29188563 DOI: 10.1007/978-1-4939-7465-8_8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The understanding of binding interactions between any protein and a small molecule plays a key role in the rationalization of affinity and selectivity. It is essential for an efficient structure-based drug design (SBDD) process. FMO enables ab initio approaches to be applied to systems that conventional quantum-mechanical (QM) methods would find challenging. The key advantage of the Fragment Molecular Orbital Method (FMO) is that it can reveal atomistic details about the individual contributions and chemical nature of each residue and water molecule toward ligand binding which would otherwise be difficult to detect without using QM methods. In this chapter, we demonstrate the typical use of FMO to analyze 19 crystal structures of β1 and β2 adrenergic receptors with their corresponding agonists and antagonists.
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Affiliation(s)
- Ewa I Chudyk
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Laurie Sarrat
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Matteo Aldeghi
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Dmitri G Fedorov
- CD-FMat, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568, Japan
| | - Mike J Bodkin
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Tim James
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Michelle Southey
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Roger Robinson
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Inaki Morao
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Alexander Heifetz
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK.
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20
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Galabov B, Nikolova V, Cheshmedzhieva D, Hadjieva B, Schaefer HF. Hyperconjugative effects in π-hydrogen bonding: Theory and experiment. J Comput Chem 2017; 39:527-534. [DOI: 10.1002/jcc.25088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Boris Galabov
- Department of Chemistry and Pharmacy; University of Sofia; Sofia 1164 Bulgaria
- Center for Computational Quantum Chemistry, University of Georgia; Athens Georgia 30602
| | - Valia Nikolova
- Department of Chemistry and Pharmacy; University of Sofia; Sofia 1164 Bulgaria
| | | | - Boriana Hadjieva
- Department of Chemistry and Pharmacy; University of Sofia; Sofia 1164 Bulgaria
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia; Athens Georgia 30602
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21
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Yoshino R, Yasuo N, Hagiwara Y, Ishida T, Inaoka DK, Amano Y, Tateishi Y, Ohno K, Namatame I, Niimi T, Orita M, Kita K, Akiyama Y, Sekijima M. In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease. Sci Rep 2017; 7:6666. [PMID: 28751689 PMCID: PMC5532286 DOI: 10.1038/s41598-017-06411-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 06/14/2017] [Indexed: 01/23/2023] Open
Abstract
Chagas disease results from infection by Trypanosoma cruzi and is a neglected tropical disease (NTD). Although some treatment drugs are available, their use is associated with severe problems, including adverse effects and limited effectiveness during the chronic disease phase. To develop a novel anti-Chagas drug, we virtually screened 4.8 million small molecules against spermidine synthase (SpdSyn) as the target protein using our super computer “TSUBAME2.5” and conducted in vitro enzyme assays to determine the half-maximal inhibitory concentration values. We identified four hit compounds that inhibit T. cruzi SpdSyn (TcSpdSyn) by in silico and in vitro screening. We also determined the TcSpdSyn–hit compound complex structure using X-ray crystallography, which shows that the hit compound binds to the putrescine-binding site and interacts with Asp171 through a salt bridge.
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Affiliation(s)
- Ryunosuke Yoshino
- Advanced Computational Drug Discovery Unit, Institute of Innovative Research, Tokyo Institute of Technology, 4259-J3-23, Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan.,Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Yokohama, 226-8501, Japan.,Global Scientific Information and Computing Center, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.,Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Nobuaki Yasuo
- Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Yokohama, 226-8501, Japan.,Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Yohsuke Hagiwara
- Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Yokohama, 226-8501, Japan.,Medicinal Chemistry Research Labs, Drug Discovery Research, Astellas Pharma Inc, 21 Miyukigaoka, Tsukuba, Ibaraki, 305-8585, Japan
| | - Takashi Ishida
- Advanced Computational Drug Discovery Unit, Institute of Innovative Research, Tokyo Institute of Technology, 4259-J3-23, Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan.,Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Yokohama, 226-8501, Japan.,Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Daniel Ken Inaoka
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.,School of Tropical Medicine and Global Health, Nagasaki University, Sakamoto, Nagasaki, 852-8523, Japan
| | - Yasushi Amano
- Medicinal Chemistry Research Labs, Drug Discovery Research, Astellas Pharma Inc, 21 Miyukigaoka, Tsukuba, Ibaraki, 305-8585, Japan
| | - Yukihiro Tateishi
- Medicinal Chemistry Research Labs, Drug Discovery Research, Astellas Pharma Inc, 21 Miyukigaoka, Tsukuba, Ibaraki, 305-8585, Japan
| | - Kazuki Ohno
- Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Yokohama, 226-8501, Japan.,Medicinal Chemistry Research Labs, Drug Discovery Research, Astellas Pharma Inc, 21 Miyukigaoka, Tsukuba, Ibaraki, 305-8585, Japan.,Catalyst Inc., Risona Kudan Building 5F KS Floor, 1-5-6 Kudan Minami, Chiyoda-ku, Tokyo, 102-0074, Japan
| | - Ichiji Namatame
- Medicinal Chemistry Research Labs, Drug Discovery Research, Astellas Pharma Inc, 21 Miyukigaoka, Tsukuba, Ibaraki, 305-8585, Japan
| | - Tatsuya Niimi
- Medicinal Chemistry Research Labs, Drug Discovery Research, Astellas Pharma Inc, 21 Miyukigaoka, Tsukuba, Ibaraki, 305-8585, Japan
| | - Masaya Orita
- Medicinal Chemistry Research Labs, Drug Discovery Research, Astellas Pharma Inc, 21 Miyukigaoka, Tsukuba, Ibaraki, 305-8585, Japan
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.,School of Tropical Medicine and Global Health, Nagasaki University, Sakamoto, Nagasaki, 852-8523, Japan
| | - Yutaka Akiyama
- Advanced Computational Drug Discovery Unit, Institute of Innovative Research, Tokyo Institute of Technology, 4259-J3-23, Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan.,Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Yokohama, 226-8501, Japan.,Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Masakazu Sekijima
- Advanced Computational Drug Discovery Unit, Institute of Innovative Research, Tokyo Institute of Technology, 4259-J3-23, Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan. .,Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Yokohama, 226-8501, Japan. .,Global Scientific Information and Computing Center, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. .,Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan.
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22
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Morao I, Fedorov DG, Robinson R, Southey M, Townsend‐Nicholson A, Bodkin MJ, Heifetz A. Rapid and accurate assessment of GPCR-ligand interactions Using the fragment molecular orbital-based density-functional tight-binding method. J Comput Chem 2017; 38:1987-1990. [PMID: 28675443 PMCID: PMC5600120 DOI: 10.1002/jcc.24850] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/07/2017] [Accepted: 05/16/2017] [Indexed: 01/17/2023]
Abstract
The reliable and precise evaluation of receptor–ligand interactions and pair‐interaction energy is an essential element of rational drug design. While quantum mechanical (QM) methods have been a promising means by which to achieve this, traditional QM is not applicable for large biological systems due to its high computational cost. Here, the fragment molecular orbital (FMO) method has been used to accelerate QM calculations, and by combining FMO with the density‐functional tight‐binding (DFTB) method we are able to decrease computational cost 1000 times, achieving results in seconds, instead of hours. We have applied FMO‐DFTB to three different GPCR–ligand systems. Our results correlate well with site directed mutagenesis data and findings presented in the published literature, demonstrating that FMO‐DFTB is a rapid and accurate means of GPCR–ligand interactions. © 2017 Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Inaki Morao
- Computational ChemistryEvotec (UK) Ltd114 Innovation Drive, Milton ParkAbingdonOxfordshireOX14 4RZUnited Kingdom
| | - Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat)National Institute of Advanced Industrial Science and Technology (AIST)1‐1‐1 UmezonoTsukubaIbaraki305‐8568Japan
| | - Roger Robinson
- Computational ChemistryEvotec (UK) Ltd114 Innovation Drive, Milton ParkAbingdonOxfordshireOX14 4RZUnited Kingdom
| | - Michelle Southey
- Computational ChemistryEvotec (UK) Ltd114 Innovation Drive, Milton ParkAbingdonOxfordshireOX14 4RZUnited Kingdom
| | - Andrea Townsend‐Nicholson
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of BiosciencesUniversity College LondonLondonWC1E 6BTUnited Kingdom
| | - Mike J. Bodkin
- Computational ChemistryEvotec (UK) Ltd114 Innovation Drive, Milton ParkAbingdonOxfordshireOX14 4RZUnited Kingdom
| | - Alexander Heifetz
- Computational ChemistryEvotec (UK) Ltd114 Innovation Drive, Milton ParkAbingdonOxfordshireOX14 4RZUnited Kingdom
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of BiosciencesUniversity College LondonLondonWC1E 6BTUnited Kingdom
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23
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Application of the fragment molecular orbital method analysis to fragment-based drug discovery of BET (bromodomain and extra-terminal proteins) inhibitors. J Mol Graph Model 2017; 74:73-82. [PMID: 28365532 DOI: 10.1016/j.jmgm.2017.02.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 02/01/2017] [Accepted: 02/21/2017] [Indexed: 11/23/2022]
Abstract
The molecular interactions of inhibitors of bromodomains (BRDs) were investigated. BRDs are protein interaction modules that recognizing ε-N-acetyl-lysine (εAc-Lys) motifs found in histone tails and are promising protein-protein interaction (PPI) targets. First, we analyzed a peptide ligand containing εAc-Lys to evaluate native PPIs. We then analyzed tetrahydroquinazoline-6-yl-benzensulfonamide derivatives found by fragment-based drug design (FBDD) and examined their interactions with the protein compared with the peptide ligand in terms of the inter-fragment interaction energy. In addition, we analyzed benzodiazepine derivatives that are high-affinity ligands for BRDs and examined differences in the CH/π interactions of the amino acid residues. We further surveyed changes in the charges of the amino acid residues among individual ligands, performed pair interaction energy decomposition analysis and estimated the water profile within the ligand binding site. Thus, useful insights for drug design were provided. Through these analyses and considerations, we show that the FMO method is a useful drug design tool to evaluate the process of FBDD and to explore PPI inhibitors.
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24
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Jarończyk M, Lipiński PFJ, Dobrowolski JC, Sadlej J. The FMO analysis of the molecular interaction of fentanyl derivatives with the μ-opioid receptor. CHEMICAL PAPERS 2017. [DOI: 10.1007/s11696-017-0136-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Using the fragment molecular orbital method to investigate agonist-orexin-2 receptor interactions. Biochem Soc Trans 2016; 44:574-81. [PMID: 27068972 PMCID: PMC5264495 DOI: 10.1042/bst20150250] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Indexed: 12/11/2022]
Abstract
The understanding of binding interactions between any protein and a small molecule plays a key role in the rationalization of affinity and selectivity and is essential for an efficient structure-based drug discovery (SBDD) process. Clearly, to begin SBDD, a structure is needed, and although there has been fantastic progress in solving G-protein-coupled receptor (GPCR) crystal structures, the process remains quite slow and is not currently feasible for every GPCR or GPCR-ligand complex. This situation significantly limits the ability of X-ray crystallography to impact the drug discovery process for GPCR targets in 'real-time' and hence there is still a need for other practical and cost-efficient alternatives. We present here an approach that integrates our previously described hierarchical GPCR modelling protocol (HGMP) and the fragment molecular orbital (FMO) quantum mechanics (QM) method to explore the interactions and selectivity of the human orexin-2 receptor (OX2R) and its recently discovered nonpeptidic agonists. HGMP generates a 3D model of GPCR structures and its complexes with small molecules by applying a set of computational methods. FMO allowsab initioapproaches to be applied to systems that conventional QM methods would find challenging. The key advantage of FMO is that it can reveal information on the individual contribution and chemical nature of each residue and water molecule to the ligand binding that normally would be difficult to detect without QM. We illustrate how the combination of both techniques provides a practical and efficient approach that can be used to analyse the existing structure-function relationships (SAR) and to drive forward SBDD in a real-world example for which there is no crystal structure of the complex available.
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26
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The influence of substituents on cooperativity between CH···π and N···H hydrogen bonds in a T-shaped configuration: X-benzene⊥(FH···pyrazine···HF) complexes as a working model. Struct Chem 2016. [DOI: 10.1007/s11224-016-0777-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Fedorov DG, Kitaura K. Subsystem Analysis for the Fragment Molecular Orbital Method and Its Application to Protein-Ligand Binding in Solution. J Phys Chem A 2016; 120:2218-31. [PMID: 26949816 DOI: 10.1021/acs.jpca.6b00163] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A subsystem analysis is derived incorporating interfragment interactions into the fragment properties, such as energies or charges. The relative stabilities of three alanine isomers, the α-helix, the β-turn, and the extended form are studied and the differences in fragment properties are elucidated. The analysis is further elaborated for studies of binding energies. The binding of the Trp-cage protein (PDB: 1L2Y ) to two ligands is studied in detail. Binding energies defined for each fragment can be used as a convenient descriptor for analyzing contributions to binding in solution.
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Affiliation(s)
- Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST) , Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan
| | - Kazuo Kitaura
- Graduate School of System Informatics, Kobe University , 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
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28
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Heifetz A, Trani G, Aldeghi M, MacKinnon CH, McEwan PA, Brookfield FA, Chudyk EI, Bodkin M, Pei Z, Burch JD, Ortwine DF. Fragment Molecular Orbital Method Applied to Lead Optimization of Novel Interleukin-2 Inducible T-Cell Kinase (ITK) Inhibitors. J Med Chem 2016; 59:4352-63. [PMID: 26950250 DOI: 10.1021/acs.jmedchem.6b00045] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Inhibition of inducible T-cell kinase (ITK), a nonreceptor tyrosine kinase, may represent a novel treatment for allergic asthma. In our previous reports, we described the discovery of sulfonylpyridine (SAP), benzothiazole (BZT), indazole (IND), and tetrahydroindazole (THI) series as novel ITK inhibitors and how computational tools such as dihedral scans and docking were used to support this process. X-ray crystallography and modeling were applied to provide essential insight into ITK-ligand interactions. However, "visual inspection" traditionally used for the rationalization of protein-ligand affinity cannot always explain the full complexity of the molecular interactions. The fragment molecular orbital (FMO) quantum-mechanical (QM) method provides a complete list of the interactions formed between the ligand and protein that are often omitted from traditional structure-based descriptions. FMO methodology was successfully used as part of a rational structure-based drug design effort to improve the ITK potency of high-throughput screening hits, ultimately delivering ligands with potency in the subnanomolar range.
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Affiliation(s)
- Alexander Heifetz
- Evotec (U.K.) Ltd. , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Giancarlo Trani
- Evotec (U.K.) Ltd. , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Matteo Aldeghi
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Colin H MacKinnon
- Evotec (U.K.) Ltd. , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Paul A McEwan
- Evotec (U.K.) Ltd. , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Frederick A Brookfield
- Evotec (U.K.) Ltd. , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Ewa I Chudyk
- Evotec (U.K.) Ltd. , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Mike Bodkin
- Evotec (U.K.) Ltd. , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Zhonghua Pei
- Discovery Chemistry, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Jason D Burch
- Discovery Chemistry, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel F Ortwine
- Discovery Chemistry, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
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29
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Berg L, Mishra BK, Andersson CD, Ekström F, Linusson A. The Nature of Activated Non-classical Hydrogen Bonds: A Case Study on Acetylcholinesterase-Ligand Complexes. Chemistry 2016; 22:2672-81. [DOI: 10.1002/chem.201503973] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Lotta Berg
- Department of Chemistry; Umeå University; 901 87 Umeå Sweden
| | | | | | - Fredrik Ekström
- CBRN Defense and Security; Swedish Defense Research Agency; 906 21 Umeå Sweden
| | - Anna Linusson
- Department of Chemistry; Umeå University; 901 87 Umeå Sweden
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30
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Heifetz A, Chudyk EI, Gleave L, Aldeghi M, Cherezov V, Fedorov DG, Biggin PC, Bodkin MJ. The Fragment Molecular Orbital Method Reveals New Insight into the Chemical Nature of GPCR–Ligand Interactions. J Chem Inf Model 2015; 56:159-72. [PMID: 26642258 DOI: 10.1021/acs.jcim.5b00644] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Our interpretation of ligand-protein interactions is often informed by high-resolution structures, which represent the cornerstone of structure-based drug design. However, visual inspection and molecular mechanics approaches cannot explain the full complexity of molecular interactions. Quantum Mechanics approaches are often too computationally expensive, but one method, Fragment Molecular Orbital (FMO), offers an excellent compromise and has the potential to reveal key interactions that would otherwise be hard to detect. To illustrate this, we have applied the FMO method to 18 Class A GPCR-ligand crystal structures, representing different branches of the GPCR genome. Our work reveals key interactions that are often omitted from structure-based descriptions, including hydrophobic interactions, nonclassical hydrogen bonds, and the involvement of backbone atoms. This approach provides a more comprehensive picture of receptor-ligand interactions than is currently used and should prove useful for evaluation of the chemical nature of ligand binding and to support structure-based drug design.
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Affiliation(s)
- Alexander Heifetz
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Ewa I. Chudyk
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Laura Gleave
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Matteo Aldeghi
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Vadim Cherezov
- Department
of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, United States
- Laboratory
for Structural Biology of GPCRs, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Dmitri G. Fedorov
- NMRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Philip C. Biggin
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Mike J. Bodkin
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
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31
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Pharmacophore modeling for anti-Chagas drug design using the fragment molecular orbital method. PLoS One 2015; 10:e0125829. [PMID: 25961853 PMCID: PMC4427443 DOI: 10.1371/journal.pone.0125829] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 03/26/2015] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Chagas disease, caused by the parasite Trypanosoma cruzi, is a neglected tropical disease that causes severe human health problems. To develop a new chemotherapeutic agent for the treatment of Chagas disease, we predicted a pharmacophore model for T. cruzi dihydroorotate dehydrogenase (TcDHODH) by fragment molecular orbital (FMO) calculation for orotate, oxonate, and 43 orotate derivatives. METHODOLOGY/PRINCIPAL FINDINGS Intermolecular interactions in the complexes of TcDHODH with orotate, oxonate, and 43 orotate derivatives were analyzed by FMO calculation at the MP2/6-31G level. The results indicated that the orotate moiety, which is the base fragment of these compounds, interacts with the Lys43, Asn67, and Asn194 residues of TcDHODH and the cofactor flavin mononucleotide (FMN), whereas functional groups introduced at the orotate 5-position strongly interact with the Lys214 residue. CONCLUSIONS/SIGNIFICANCE FMO-based interaction energy analyses revealed a pharmacophore model for TcDHODH inhibitor. Hydrogen bond acceptor pharmacophores correspond to Lys43 and Lys214, hydrogen bond donor and acceptor pharmacophores correspond to Asn67 and Asn194, and the aromatic ring pharmacophore corresponds to FMN, which shows important characteristics of compounds that inhibit TcDHODH. In addition, the Lys214 residue is not conserved between TcDHODH and human DHODH. Our analysis suggests that these orotate derivatives should preferentially bind to TcDHODH, increasing their selectivity. Our results obtained by pharmacophore modeling provides insight into the structural requirements for the design of TcDHODH inhibitors and their development as new anti-Chagas drugs.
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32
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Nishio M, Umezawa Y, Fantini J, Weiss MS, Chakrabarti P. CH-π hydrogen bonds in biological macromolecules. Phys Chem Chem Phys 2015; 16:12648-83. [PMID: 24836323 DOI: 10.1039/c4cp00099d] [Citation(s) in RCA: 335] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP themed issue on "Weak Hydrogen Bonds - Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.
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Affiliation(s)
- Motohiro Nishio
- The CHPI Institute, 705-6-338, Minamioya, Machida-shi, Tokyo 194-0031, Japan.
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Nikolova V, Ilieva S, Galabov B, Schaefer HF. Experimental measurement and theory of substituent effects in π-hydrogen bonding: complexes of substituted phenols with benzene. J Org Chem 2014; 79:6823-31. [PMID: 25004256 DOI: 10.1021/jo500732m] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
IR spectroscopic experiments and theoretical DFT computations reveal the effects of aromatic substituents on π-hydrogen bonding between monosubstituted phenol derivatives and benzene. Simultaneous formation of two π-hydrogen bonds (red-shifting O-H···π and blue-shifting ortho-C-H···π) contribute to the stability of these complexes. The interaction of the acidic phenol O-H proton-donating group with the benzene π-system dominates the complex formation. The experimental shifts of O-H stretching frequencies for the different phenol complexes vary in the range 45-74 cm(-1). Strong effects on hydrogen-bonding energies and frequency shifts of electron-withdrawing aromatic substituents and very weak influence of electron-donating groups have been established. Experimental quantities and theoretical parameters are employed in rationalizing the properties of these complexes. The acidities of the proton-donating phenols describe quantitatively the hydrogen-bonding process. The results obtained provide clear evidence that, when the structural variations are in the proton-donating species, the substituent effects on π-hydrogen bonding follow classic mechanisms, comprising both resonance and direct through-space influences. The performance of three alternative DFT functionals (B3LYP, B97-D, and PBE0 combined with the 6-311++G(2df,2p) basis set) in predicting the O-H frequency shifts upon complexation is examined. For comparison, O-H frequency shifts for several complexes were also determined at MP2/6-31++G(d,p).
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Affiliation(s)
- Valia Nikolova
- Department of Chemistry, University of Sofia , 1 James Bourchier Avenue, Sofia 1164, Bulgaria
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Three- and four-body corrected fragment molecular orbital calculations with a novel subdividing fragmentation method applicable to structure-based drug design. J Mol Graph Model 2013; 41:31-42. [PMID: 23467020 DOI: 10.1016/j.jmgm.2013.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 01/25/2013] [Accepted: 01/25/2013] [Indexed: 12/30/2022]
Abstract
We develop an inter-fragment interaction energy (IFIE) analysis based on the three- and four-body corrected fragment molecular orbital (FMO3 and FMO4) method to evaluate the interactions of functional group units in structure-based drug design context. The novel subdividing fragmentation method for a ligand (in units of their functional groups) and amino acid residues (in units of their main and side chains) enables us to understand the ligand-binding mechanism in more detail without sacrificing chemical accuracy of the total energy and IFIEs by using the FMO4 method. We perform FMO4 calculations with the second order Møller-Plesset perturbation theory for an estrogen receptor (ER) and the 17β-estradiol (EST) complex using the proposed fragmentation method and assess the interaction for each ligand-binding site by the FMO4-IFIE analysis. When the steroidal EST is divided into two functional units including "A ring" and "D ring", respectively, the FMO4-IFIE analysis reveals their binding affinity with surrounding fragments of the amino acid residues; the "A ring" of EST has polarization interaction with the main chain of Thr347 and two hydrogen bonds with the side chains of Glu353 and Arg394; the "D ring" of EST has a hydrogen bond with the side chain of His524. In particular, the CH/π interactions of the "A ring" of EST with the side chains of Leu387 and Phe404 are easily identified in cooperation with the CHPI program. The FMO4-IFIE analysis using our novel subdividing fragmentation method, which provides higher resolution than the conventional IFIE analysis in units of ligand and each amino acid reside in the framework of two-body approximation, is a useful tool for revealing ligand-binding mechanism and would be applicable to rational drug design such as structure-based drug design and fragment-based drug design.
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Zhao C, Parrish RM, Smith MD, Pellechia PJ, Sherrill CD, Shimizu KD. Do Deuteriums Form Stronger CH−π Interactions? J Am Chem Soc 2012; 134:14306-9. [DOI: 10.1021/ja305788p] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chen Zhao
- Department of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Robert M. Parrish
- School of Chemistry and Biochemistry
and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
| | - Mark D. Smith
- Department of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Perry J. Pellechia
- Department of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - C. David Sherrill
- School of Chemistry and Biochemistry
and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
| | - Ken D. Shimizu
- Department of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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Wang K, Zhang J, Liu Y. Assignment of photoelectron spectra of the 2-allylphenol with the help of electron propagator theory. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2011.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Fedorov DG, Nagata T, Kitaura K. Exploring chemistry with the fragment molecular orbital method. Phys Chem Chem Phys 2012; 14:7562-77. [DOI: 10.1039/c2cp23784a] [Citation(s) in RCA: 290] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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