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Listyarini R, Kriesche BM, Hofer TS. Characterization of the Coordination and Solvation Dynamics of Solvated Systems─Implications for the Analysis of Molecular Interactions in Solutions and Pure H 2O. J Chem Theory Comput 2024; 20:3028-3045. [PMID: 38595064 PMCID: PMC11044269 DOI: 10.1021/acs.jctc.4c00162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024]
Abstract
The characterization of solvation shells of atoms, ions, and molecules in solution is essential to relate solvation properties to chemical phenomena such as complex formation and reactivity. Different definitions of the first-shell coordination sphere from simulation data can lead to potentially conflicting data on the structural properties and associated ligand exchange dynamics. The definition of a solvation shell is typically based on a given threshold distance determined from the respective solute-solvent pair distribution function g(r) (i.e., GC). Alternatively, a nearest neighbor (NN) assignment based on geometric properties of the coordination complex without the need for a predetermined cutoff criterion, such as the relative angular distance (RAD) or the modified Voronoi (MV) tessellation, can be applied. In this study, the effect of different NN algorithms on the coordination number and ligand exchange dynamics evaluated for a series of monatomic ions in aqueous solution, carbon dioxide in aqueous and dichloromethane solutions, and pure liquid water has been investigated. In the case of the monatomic ions, the RAD approach is superior in achieving a well separated definition of the first solvation layer. In contrast, the MV algorithm provides a better separation of the NNs from a molecular point of view, leading to better results in the case of solvated CO2. When analyzing the coordination environment in pure water, the cutoff-based GC framework was found to be the most reliable approach. By comparison of the number of ligand exchange reactions and the associated mean ligand residence times (MRTs) with the properties of the coordination number autocorrelation functions, it is shown that although the average coordination numbers are sensitive to the different definitions of the first solvation shell, highly consistent estimates for the associated MRT of the solvated system are obtained in the majority of cases.
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Affiliation(s)
- Risnita
Vicky Listyarini
- Institute
of General, Inorganic and Theoretical Chemistry Center for Chemistry
and Biomedicine, University of Innsbruck Innrain 80-82, A-6020 Innsbruck, Austria
- Chemistry
Education Study Program Sanata Dharma University, Yogyakarta 55282, Indonesia
| | - Bernhard M. Kriesche
- Institute
of General, Inorganic and Theoretical Chemistry Center for Chemistry
and Biomedicine, University of Innsbruck Innrain 80-82, A-6020 Innsbruck, Austria
| | - Thomas S. Hofer
- Institute
of General, Inorganic and Theoretical Chemistry Center for Chemistry
and Biomedicine, University of Innsbruck Innrain 80-82, A-6020 Innsbruck, Austria
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Aloui M, Er-rajy M, Imtara H, Goudzal A, Zarougui S, El fadili M, Arthur DE, Mothana RA, Noman OM, Tarayrah M, Menana E. QSAR modelling, molecular docking, molecular dynamic and ADMET prediction of pyrrolopyrimidine derivatives as novel Bruton's tyrosine kinase (BTK) inhibitors. Saudi Pharm J 2024; 32:101911. [PMID: 38226346 PMCID: PMC10788635 DOI: 10.1016/j.jsps.2023.101911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/07/2023] [Indexed: 01/17/2024] Open
Abstract
In recent years, there has been a focus on developing and discovering novel Bruton's tyrosine kinase (BTK) inhibitors, as they offer an effective treatment strategy for B-cell malignancies. BTK plays a crucial role in B cell receptor (BCR)-mediated activation and proliferation by regulating downstream factors such as the NF-κB and MAP kinase pathways. To address this challenge and propose potential therapeutic options for B-cell lymphomas, researchers conducted 2D-QSAR and ADMET studies on pyrrolopyrimidine derivatives that act as inhibitors of the BCR site in cytochrome b. These studies aim to improve and identify new compounds that could serve as more potent potential BTK inhibitors, which would lead to the identification of new drug candidates in this field. In our study, we used 2D-QSAR (multiple linear regression, multiple nonlinear regression, and artificial neural networks), molecular docking, molecular dynamics, and ADMET properties to investigate the potential of 35 pyrrolopyrimidine derivatives as BTK inhibitors. A molecular docking study and molecular dynamics simulations of molecule 13 over 10 ns revealed that it establishes multiple hydrogen bonds with several residues and exhibits frequent stability throughout the simulation period. Based on the results obtained by molecular modeling, we proposed six new compounds (Pred1, Pred2, Pred3, Pred4, Pred5, and Pred6) with highly significant predicted activity by MLR models. A study based on the in silico evaluation of the predicted ADMET properties of the new candidate molecules is strongly recommended to classify these molecules as promising candidates for new anticancer agents specifically designed to target Bruton's tyrosine kinase (BTK) inhibition.
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Affiliation(s)
- Mourad Aloui
- LIMAS Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohammed Er-rajy
- LIMAS Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Hamada Imtara
- Faculty of Sciences, Arab American University Palestine, Jenin 44862, Palestine
| | - Amina Goudzal
- Engineering Laboratory of Organometallic, Molecular Materials and Environment, Sidi Mohamed Ben Abdellah University, Faculty of Sciences, Fez, Morocco
| | - Sara Zarougui
- LIMAS Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohamed El fadili
- LIMAS Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - David E. Arthur
- Department of Pure and Applied Chemistry, University of Maiduguri, Nigeria
| | - Ramzi A. Mothana
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Omar M. Noman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mahmoud Tarayrah
- Groupe Hospitalier Cochin-Port Royal, Faculty of Medicine, Institut Cochin, Paris University, CNRS, IN-SERM, 75000, Paris, France
| | - Elhalaoui Menana
- LIMAS Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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Kalayan J, Chakravorty A, Warwicker J, Henchman RH. Total free energy analysis of fully hydrated proteins. Proteins 2023; 91:74-90. [PMID: 35964252 PMCID: PMC10087023 DOI: 10.1002/prot.26411] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
The total free energy of a hydrated biomolecule and its corresponding decomposition of energy and entropy provides detailed information about regions of thermodynamic stability or instability. The free energies of four hydrated globular proteins with different net charges are calculated from a molecular dynamics simulation, with the energy coming from the system Hamiltonian and entropy using multiscale cell correlation. Water is found to be most stable around anionic residues, intermediate around cationic and polar residues, and least stable near hydrophobic residues, especially when more buried, with stability displaying moderate entropy-enthalpy compensation. Conversely, anionic residues in the proteins are energetically destabilized relative to singly solvated amino acids, while trends for other residues are less clear-cut. Almost all residues lose intraresidue entropy when in the protein, enthalpy changes are negative on average but may be positive or negative, and the resulting overall stability is moderate for some proteins and negligible for others. The free energy of water around single amino acids is found to closely match existing hydrophobicity scales. Regarding the effect of secondary structure, water is slightly more stable around loops, of intermediate stability around β strands and turns, and least stable around helices. An interesting asymmetry observed is that cationic residues stabilize a residue when bonded to its N-terminal side but destabilize it when on the C-terminal side, with a weaker reversed trend for anionic residues.
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Affiliation(s)
- Jas Kalayan
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Arghya Chakravorty
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | - Jim Warwicker
- Manchester Institute of Biotechnology and School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Richard H Henchman
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
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Kumar A, Craig VS, Page AJ, Webber GB, Wanless EJ, Andersson G. Ion Specificity in the Measured Concentration Depth Profile of Ions at the Vapor-Glycerol Interface. J Colloid Interface Sci 2022; 626:687-699. [DOI: 10.1016/j.jcis.2022.06.104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/04/2022] [Accepted: 06/21/2022] [Indexed: 10/31/2022]
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Abstract
As a fundamental property of all fluids, diffusion plays myriad roles in both science and our daily lives. Diffusive properties of many liquids including water have been extensively studied both experimentally and theoretically, while for transition metal ions, there exist significant experimental data that have not been extensively studied theoretically. Hence, high-confidence predictions for challenging systems like radioactive ions that are biohazardous cannot be reliably generated. In this work, a workflow named ISAIAH (Ion Simulation using AMBER for dIffusion Action when Hydrated) was designed to accurately simulate the diffusion coefficients of 15 monoatomic ions with charges varying from -1 to +3 in four water models. As the results indicate, good agreement with experimental values was achieved, leading us to select 239Pu4+ (for which no experimental data are available) as a candidate ion to make a theoretical prediction of its diffusion coefficient in water. Among all the force field parameter sets, the ones parametrized using an augmented 12-6-4 Lennard-Jones (LJ) potential showed lower average unsigned errors (AUE) for ions of various radii and electron configurations relative to some 12-6 LJ parameters. This observation agrees well with the fact that diffusion is affected by both the hydration free energy (HFE) and the ion-oxygen distance (IOD) between solute and solvent molecules, both of which are handled well by the 12-6-4 model.
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Affiliation(s)
- Zhen Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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