Study of the structural features and solvent effects using ab initio molecular dynamics and energy decomposition analysis of atogepant in water and ammonia

Journal of Molecular Liquids - Tập 352 - Trang 118672 - 2022
T. Pooventhiran1, Bhavya S. Gangadharappa2, Ola A. Abu Ali3, Renjith Thomas1, Dalia I. Saleh3
1Department of Chemistry, St Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India
2Department of Biotechnology, MS Ramaiah Institute of Technology, Bangalore (Affiliated to VTU) 560054, Karnataka, India
3Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia

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Ashina, 2021, Migraine 3 Migraine: integrated approaches to clinical management and emerging treatments, Lancet, 397, 1506, 10.1016/S0140-6736(20)32342-4 Saunders, 2021, ll Endometriosis: Etiology, pathobiology, and therapeutic prospects, Cell, Lead. Edge, 184, 2807 Guo, 2021, Development and validation of a reporter gene assay for bioactivity determination of Anti-CGRP monoclonal antibodies, Anal. Biochem., 634, 114291, 10.1016/j.ab.2021.114291 Edvinsson, 2018, CGRP as the target of new migraine therapies — successful translation from bench to clinic, Nat. Rev. Neurol., 14, 338, 10.1038/s41582-018-0003-1 Gingell, 2019, New Insights into the Regulation of CGRP-Family Receptors, Trends Pharmacol. Sci., 40, 71, 10.1016/j.tips.2018.11.005 Charles, 2019, Therapeutics Targeting calcitonin gene-related peptide : a new era in migraine therapy, Lancet, 6736, 1 Luo, 2021, Bioorganic & Medicinal Chemistry Letters Calcitonin gene-related peptide (CGRP) receptor antagonists: Heterocyclic modification of a novel azepinone lead, Bioorg. Med. Chem. Lett., 43, 10.1016/j.bmcl.2021.128077 Raj, 2006, Keratinocyte Apoptosis in Epidermal Development and Disease Editor' s Note, J. Invest. Dermatol., 126, 243, 10.1038/sj.jid.5700008 Ashina, 2019, Personal View Migraine and the trigeminovascular system — 40 years and counting, Lancet, 18, 795, 10.1016/S1474-4422(19)30185-1 Goadsby, 2020, Articles Safety, tolerability, and efficacy of orally administered atogepant for the prevention of episodic migraine in adults: a double-blind, randomised phase 2b/3 trial, Lancet Neurol., 19, 727, 10.1016/S1474-4422(20)30234-9 Rosenbaum, 2020, Targeting receptor complexes: a new dimension in drug discovery, Nat. Rev., 19, 884 Reuter, 2019, Headache and pain CGRP antagonism and migraine: Where are we now?, J. Neurol. Sci., 10.1016/j.jns.2019.10.070 Chiang, 2020 Cui, 2020, The effect of solvents on crystal morphology of sucralose : Experiments and molecular dynamics simulation studies, J. Cryst. Growth., 532, 10.1016/j.jcrysgro.2019.125398 van Gunsteren, 1981, Effect of constraints, solvent and crystal environment on protein dynamics, Nature. 293, Nature, 293, 677, 10.1038/293677a0 Ma, 2019, Solubility Modeling and Solvent Effect for Flubendazole in 12 Neat Solvents, J. Chem. Eng. Data., 64, 1237, 10.1021/acs.jced.8b01126 Badger, 1995, Neutron diffraction analysis of the solvent accessible volume in cubic insulin crystals, Nat. Struct. Biol., 2, 77, 10.1038/nsb0195-77 Fadel, 2019, Role of solvent-anion charge transfer in oxidative degradation of battery electrolytes, Nat. Commun., 10, 1, 10.1038/s41467-019-11317-3 Makhatadze, 1995, Solvent isotope effect and protein stability, Nat. Struct. Biol., 2, 852, 10.1038/nsb1095-852 Cocinero, 2011, Sensing the anomeric effect in a solvent-free environment, Nat. Lett., 469, 76, 10.1038/nature09693 Bovey, 1960, Effect of Solvent Polarizability on the Ultra-Violet Spectral Shifts of Aromatic Compounds, Nature., 186, 1042, 10.1038/1861042a0 Yuan, 2019, Solvent-triggered reversible interconversion of all-nitrogen-donor-protected silver nanoclusters and their responsive optical properties, Nat. Commun., 10, 1, 10.1038/s41467-019-11988-y Vecera, 2016, Solvent-driven electron trapping and mass transport in reduced graphites to access perfect graphene, Nat. Commun., 7, 1, 10.1038/ncomms12411 Fan, 2021, Gold nanoparticles enhance antibody effect through direct cancer cell cytotoxicity by differential regulation of phagocytosis, Nat. Commun., 12, 1, 10.1038/s41467-021-26694-x Moon, 2021, Structure-controllable growth of nitrogenated graphene quantum dots via solvent catalysis for selective C-N bond activation, Nat. Commun., 12, 1, 10.1038/s41467-021-26122-0 Du, 2021, Evidence for ligand- and solvent-induced disproportionation of uranium(IV), Nat. Commun., 12, 1, 10.1038/s41467-021-25151-z Frisch, 2013, Gaussian09 Revision D.01 Frisch, 1984, Self-consistent molecular orbital methods 25. Supplementary functions for Gaussian basis sets, J. Chem. Phys., 80, 3265, 10.1063/1.447079 Longuet‐Higgins, 1957, Electronic Spectral Shifts of Nonpolar Molecules in Nonpolar Solvents, J. Chem. Phys., 27, 192, 10.1063/1.1743666 Krishnan, 1980, Self-consistent molecular orbital methods. XX. A basis set for correlated wave functions, J. Chem. Phys., 72, 650, 10.1063/1.438955 Rassolov, 2001, 6–31G* basis set for third-row atoms, J. Comput. Chem., 22, 976, 10.1002/jcc.1058 Ditchfield, 1971, Self-Consistent Molecular-Orbital Methods. IX. An Extended Gaussian-Type Basis for Molecular-Orbital Studies of Organic Molecules, J. Chem. Phys., 54, 724, 10.1063/1.1674902 Becke, 1993, Density-functional thermochemistry. III. The role of exact exchange, J. Chem. Phys., 98, 5648, 10.1063/1.464913 Schmider, 2000, Chemical content of the kinetic energy density, J. Mol. Struct. Theochem., 527, 51, 10.1016/S0166-1280(00)00477-2 Becke, 1988, Density-functional exchange-energy approximation with correct asymptotic behavior, Phys. Rev. A., 38, 3098, 10.1103/PhysRevA.38.3098 Becke, 2005, A density-functional model of the dispersion interaction, J. Chem. Phys., 123, 154101, 10.1063/1.2065267 Becke, 2014, Perspective: Fifty years of density-functional theory in chemical physics, J. Chem. Phys., 140, 18A301, 10.1063/1.4869598 Yanai, 2004, A new hybrid exchange–correlation functional using the Coulomb-attenuating method (CAM-B3LYP), Chem. Phys. Lett., 393, 51, 10.1016/j.cplett.2004.06.011 Okuno, 2012, Tuned CAM-B3LYP functional in the time-dependent density functional theory scheme for excitation energies and properties of diarylethene derivatives, J. Photochem. Photobiol. A Chem., 235, 29, 10.1016/j.jphotochem.2012.03.003 O'boyle, 2008, A library for package-independent computational chemistry algorithms, J. Comput. Chem., 29, 839, 10.1002/jcc.20823 Lu, 2012, Multiwfn: A multifunctional wavefunction analyzer, J. Comput. Chem., 33, 580, 10.1002/jcc.22885 Neese, 2012, The ORCA program system, WIREs Comput. Mol. Sci., 2, 73, 10.1002/wcms.81 Neese, 2018, Software update: the ORCA program system, version 4.0, Wiley Interdiscip, Rev. Comput. Mol. Sci., 8, 1 Boys, 1960, Construction of some molecular orbitals to be approximately invariant for changes from one molecule to another, Rev. Mod. Phys., 32, 296, 10.1103/RevModPhys.32.296 Riplinger, 2016, Sparse maps - A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory, J. Chem. Phys., 144, 024109, 10.1063/1.4939030 Liakos, 2015, Exploring the accuracy limits of local pair natural orbital coupled-cluster theory, J. Chem. Theory Comput., 11, 1525, 10.1021/ct501129s Pipek, 1989, A fast intrinsic localization procedure applicable for ab initio and semiempirical linear combination of atomic orbital wave functions, J. Chem. Phys., 90, 4916, 10.1063/1.456588 Schneider, 2016, Decomposition of Intermolecular Interaction Energies within the Local Pair Natural Orbital Coupled Cluster Framework, J. Chem. Theory Comput., 12, 4778, 10.1021/acs.jctc.6b00523 Altun, 2019, Local Energy Decomposition of Open-Shell Molecular Systems in the Domain-Based Local Pair Natural Orbital Coupled Cluster Framework, J. Chem. Theory Comput., 15, 1616, 10.1021/acs.jctc.8b01145 Bistoni, 2020, Finding chemical concepts in the Hilbert space : Coupled cluster analyses of non-covalent interactions, Wiley Interdiscip. Rev. Comput. Mol. Sci., 10, 10.1002/wcms.1442 Altun, 2019, Effect of Electron Correlation on Intermolecular Interactions: A Pair Natural Orbitals Coupled Cluster Based Local Energy Decomposition Study, J. Chem. Theory Comput., 15, 215, 10.1021/acs.jctc.8b00915 Altun, 2018, Local energy decomposition analysis of hydrogen-bonded dimers within a domain-based pair natural orbital coupled cluster study, Beilstein J. Org. Chem., 14, 919, 10.3762/bjoc.14.79 Altun, 2021, Local energy decomposition of coupled-cluster interaction energies: Interpretation, benchmarks, and comparison with symmetry-adapted perturbation theory, Int. J. Quantum Chem., 121, 10.1002/qua.26339 Woertink, 2010, Spectroscopic and Computational Studies of an End-on Bound Superoxo-Cu (II) Complex: Geometric and Electronic Factors That Determine the Ground State, Inorg. Chem., 96, 9450, 10.1021/ic101138u Gennari, 2010, Reversible Apical Coordination of Imidazole between the Ni (III) and Ni (II) Oxidation States of a Dithiolate Complex : A Process Related to the Ni Superoxide Dismutase, Inorg. Chem. Commun., 49, 6399, 10.1021/ic100945n Ye, 2010, Cryoreduction of the NO-Adduct of Taurine: r -Ketoglutarate Dioxygenase (TauD) Yields an Elusive {FeNO} 8 Species, J. Am. Chem. Soc., 132, 4739, 10.1021/ja909715g Bistoni, 2017, Understanding the role of dispersion in Frustrated Lewis Pairs and classical Lewis adducts : a Domain Based Local Pair Natural Orbital Coupled Cluster study, Chem. – A Eur. J., 23, 865, 10.1002/chem.201604127 De Souza, 2018, On the theoretical prediction of fluorescence rates from first principles using the path integral approach, J. Chem. Phys., 148, 10.1063/1.5010895 De Souza, 2019, Predicting phosphorescence rates of light organic molecules using TD-DFT and the path integral approach to dynamics, J. Chem. Theory Comput., 15, 1896, 10.1021/acs.jctc.8b00841 Pooventhiran, 2021, Structural aspects, conformational preference and other physico-chemical properties of Artesunate and the formation of self-assembly with graphene quantum dots : A fi rst principle analysis and surface enhancement of Raman activity investigation, J. Mol. Liq., 325, 10.1016/j.molliq.2020.114810 Al-Zaqri, 2020, First-Principle Studies of Istradefylline with Emphasis on the Stability, Reactivity, Interactions and Wavefunction-Dependent Properties, Polycycl. Aromat. Compd., 1 Pooventhiran, 2021, Aromat. Compd., 41, 1, 10.1080/10406638.2019.1567559 Al-Zaqri, 2021, Structure, conformational dynamics, quantum mechanical studies and potential biological activity analysis of multiple sclerosis medicine ozanimod, J. Mol. Struct., 1227, 10.1016/j.molstruc.2020.129685 Paul, 2021, Evidences for sulfur centered hydrogen bond with sulfur atoms as a donor in aromatic thiols and aliphatic thiols in aqueous solution, J. Mol. Liq. Bhattacharyya, 2021, Adsorption of the drug bempedoic acid over different 2D/3D nanosurfaces and enhancement of Raman activity enabling ultrasensitive detection: First principle analysis, Spectrochim. Acta Part A Mol. Biomol. Spectrosc., 254, 119630, 10.1016/j.saa.2021.119630 Bhattacharyya, 2021, The proton sponge 1,8-bis(dimethylamino)naphthalene : The quicker-picker-upper also for s-block metal cations?, Chem. Phys. Lett., 10.1016/j.cplett.2021.138735 Pooventhiran, 2021, Energy and Reactivity Profile and Proton Affinity Analysis of Rimegepant with Special Reference to its Potential Activity against SARS-Cov-2 Virus Proteins using Molecular Dynamics, J. Mol. Model., 27, 10.1007/s00894-021-04885-z Curutchet, 2017, Quantum chemical studies of light harvesting, Chem. Rev., 117, 294, 10.1021/acs.chemrev.5b00700 Chako, 1934, Absorption of Light in Organic Compounds, J. Chem. Phys., 2, 644, 10.1063/1.1749368 Rho, 2013, Improvement of light-harvesting efficiency in dye-sensitized solar cells using silica beads embedded in a TiO 2 nanoporous structure, J. Phys. D. Appl. Phys., 46, 024006, 10.1088/0022-3727/46/2/024006 Kumar, 2020, Synthesis, spectral properties, chemical descriptors and light harvesting studies of a new bioactive azo imidazole compound, J. Mol. Struct., 1199, 127035, 10.1016/j.molstruc.2019.127035 Afzal, 2019, Anti-Cancerous Brucine and Colchicine: Experimental and Theoretical Characterization, ChemistrySelect, 4, 11441, 10.1002/slct.201902698 Mary, 2020, Spectroscopic, quantum mechanical studies, ligand protein interactions and photovoltaic efficiency modeling of some bioactive benzothiazolinone acetamide analogs, Chem. Pap., 74, 1957, 10.1007/s11696-019-01047-7 Priya, 2020, Intricate spectroscopic profiling, light harvesting studies and other quantum mechanical properties of 3-phenyl-5-isooxazolone using experimental and computational strategies, J. Mol. Struct., 1203, 127461, 10.1016/j.molstruc.2019.127461 Thomas, 2019, Two neoteric pyrazole compounds as potential anti-cancer agents: Synthesis, electronic structure, physico-chemical properties and docking analysis, J. Mol. Struct., 1181, 455, 10.1016/j.molstruc.2019.01.003 Al-Otaibi, 2020, Hybrid and bioactive cocrystals of pyrazinamide with hydroxybenzoic acids: Detailed study of structure, spectroscopic characteristics, other potential applications and non-covalent interactions using SAPT, J. Mol. Struct., 1202, 127316, 10.1016/j.molstruc.2019.127316 Sun, 2016, An experimental and theoretical investigation of the electronic structures and photoelectrical properties of ethyl red and carminic acid for DSSC application, Materials (Basel), 9, 1, 10.3390/ma9100813 dos Santos, 2019, Designing new quinoline-based organic photosensitizers for dye-sensitized solar cells (DSSC): a theoretical investigation, J. Mol. Model., 25, 10.1007/s00894-019-3958-y Surendar, 2021, Quasi liquid Schiff bases from trans -2-hexenal and cytosine and l -leucine with potential antieczematic and antiarthritic activities : Synthesis, structure and quantum mechanical studies, J. Mol. Liq., 334, 10.1016/j.molliq.2021.116448 Surendar, 2021, Synthesis of three quasi liquid Schiff bases between hexanal and adenine, cytosine, and l-leucine, structural interpretation, quantum mechanical studies and biological activity prediction, J. Mol. Liq. Yedu, 2022, Vibrational Spectral Studies, Quantum Mechanical Properties, and Biological Activity Prediction and Inclusion Molecular Self-Assembly Formation of N-N' - Dimethylethylene Urea, Biointerface Res. Appl. Chem., 12, 3996 Pooventhiran, 2020, Detailed spectra, electronic properties, qualitative non-covalent interaction analysis, solvatochromism, docking and molecular dynamics simulations in different solvent atmosphere of cenobamate, Struct. Chem., 31, 2475, 10.1007/s11224-020-01607-8 Alsalme, 2021, Structural, physico-chemical landscapes, ground state and excited state properties in different solvent atmosphere of Avapritinib and its ultrasensitive detection using SERS/GERS on self-assembly formation with graphene quantum dots, J. Mol. Liq., 322, 10.1016/j.molliq.2020.114555 Alsalme, 2020, Modelling the structural and reactivity landscapes of tucatinib with special reference to its wavefunction-dependent properties and screening for potential antiviral activity, J. Mol. Model., 26, 341, 10.1007/s00894-020-04603-1 Alharthi, 2021, Excited-state electronic properties, structural studies, non-covalent interactions, and inhibition of the novel severe acute respiratory syndrome coronavirus 2 proteins in Ripretinib by first-principle simulations, J. Mol. Liq., 324, 10.1016/j.molliq.2020.115134 Al-Zaqri, 2020, Structural and physico-chemical evaluation of melatonin and its solution-state excited properties, with emphasis on its binding with novel coronavirus proteins, J. Mol. Liq., 318, 10.1016/j.molliq.2020.114082 Al-Zaqri, 2021, Structural investigations, quantum mechanical studies on proton and metal affinity and biological activity predictions of selpercatinib, J. Mol. Liq., 325, 10.1016/j.molliq.2020.114765