1
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Panda SK, Karmakar S, Sen Gupta PS, Rana MK. Can Duvelisib and Eganelisib work for both cancer and COVID-19? Molecular-level insights from MD simulations and enhanced samplings. Phys Chem Chem Phys 2024; 26:10961-10973. [PMID: 38526354 DOI: 10.1039/d3cp05934k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
SARS-CoV-2 has caused severe illness and anxiety worldwide, evolving into more dreadful variants capable of evading the host's immunity. Cytokine storms, led by PI3Kγ, are common in cancer and SARS-CoV-2. Naturally, there is a yearning to see whether any drugs could alleviate cytokine storms for both. Upon investigation, we identified two anticancer drugs, Duvelisib and Eganelisib, that could also work against SARS-CoV-2. This report is the first to decipher their synergic therapeutic effectiveness against COVID-19 and cancer with molecular insights from atomistic simulations. In addition to PI3Kγ, these drugs exhibit specificity for the main protease among all SARS-CoV-2 targets, with significant negative binding free energies and small time-dependent conformational changes of the complexes. Complexation makes active sites and secondary structures highly mechanically stiff, with barely any deformation. Replica simulations estimated large pulling forces in enhanced sampling to dissociate the drugs from Mpro's active site. Furthermore, the radial distribution function (RDF) demonstrated that the therapeutic molecules were closest to the His41 and Cys145 catalytic dyad residues. Finally, analyses implied Duvelisib and Eganelisib as promising dual-purposed anti-COVID and anticancer drugs, potentially targeting Mpro and PI3Kγ to stop virus replication and cytokine storms concomitantly. We also distinguished hotspot residues imparting significant interactions.
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Affiliation(s)
- Saroj Kumar Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha 760010, India.
| | - Shaswata Karmakar
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha 760010, India.
| | - Parth Sarthi Sen Gupta
- School of Biosciences and Bioengineering, D Y Patil International University, Akurdi, Pune, India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha 760010, India.
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2
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Bartocci A, Dumont E. Situating the phosphonated calixarene-cytochrome C association by molecular dynamics simulations. J Chem Phys 2024; 160:105101. [PMID: 38465686 DOI: 10.1063/5.0198522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/20/2024] [Indexed: 03/12/2024] Open
Abstract
Protein-calixarenes binding plays an increasingly central role in many applications, spanning from molecular recognition to drug delivery strategies and protein inhibition. These ligands obey a specific bio-supramolecular chemistry, which can be revealed by computational approaches, such as molecular dynamics simulations. In this paper, we rely on all-atom, explicit-solvent molecular dynamics simulations to capture the electrostatically driven association of a phosphonated calix-[4]-arene with cytochome-C, which critically relies on surface-exposed paired lysines. Beyond two binding sites identified in direct agreement with the x-ray structure, the association has a larger structural impact on the protein dynamics. Then, our simulations allow a direct comparison to analogous calixarenes, namely, sulfonato, similarly reported as "molecular glue." Our work can contribute to a robust in silico predictive tool to assess binding sites for any given protein of interest for crystallization, with the specificity of a macromolecular cage whose endo/exo orientation plays a role in the binding.
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Affiliation(s)
- Alessio Bartocci
- Department of Physics, University of Trento, Via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Via Sommarive 14, I-38123 Trento, Italy
- Institut de Chimie de Strasbourg, UMR 7177, CNRS, Université de Strasbourg, Strasbourg Cedex 67083, France
| | - Elise Dumont
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, 06108 Nice, France
- Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
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3
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Amonov A, Scheiner S. Relation between Halogen Bond Strength and IR and NMR Spectroscopic Markers. Molecules 2023; 28:7520. [PMID: 38005241 PMCID: PMC10673387 DOI: 10.3390/molecules28227520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/04/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
The relationship between the strength of a halogen bond (XB) and various IR and NMR spectroscopic quantities is assessed through DFT calculations. Three different Lewis acids place a Br or I atom on a phenyl ring; each is paired with a collection of N and O bases of varying electron donor power. The weakest of the XBs display a C-X bond contraction coupled with a blue shift in the associated frequency, whereas the reverse trends occur for the stronger bonds. The best correlations with the XB interaction energy are observed with the NMR shielding of the C atom directly bonded to X and the coupling constants involving the C-X bond and the C-H/F bond that lies ortho to the X substituent, but these correlations are not accurate enough for the quantitative assessment of energy. These correlations tend to improve as the Lewis acid becomes more potent, which makes for a wider range of XB strengths.
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Affiliation(s)
- Akhtam Amonov
- Department of Optics and Spectroscopy, Engineering Physics Institute, Samarkand State University, University blv. 15, Samarkand 140104, Uzbekistan;
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
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4
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Guo C, Li Q, Xiao J, Ma F, Xia X, Shi M. Identification of defactinib derivatives targeting focal adhesion kinase using ensemble docking, molecular dynamics simulations and binding free energy calculations. J Biomol Struct Dyn 2023; 41:8654-8670. [PMID: 36281703 DOI: 10.1080/07391102.2022.2135601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/08/2022] [Indexed: 10/31/2022]
Abstract
Focal adhesion kinase (FAK) belongs to the nonreceptor tyrosine kinases, which selectively phosphorylate tyrosine residues on substrate proteins. FAK is associated with bladder, esophageal, gastric, neck, breast, ovarian and lung cancers. Thus, FAK has been considered as a potential target for tumor treatment. Currently, there are six adenosine triphosphate (ATP)-competitive FAK inhibitors tested in clinical trials but no approved inhibitors targeting FAK. Defactinib (VS-6063) is a second-generation FAK inhibitor with an IC50 of 0.6 nM. The binding model of VS-6063 with FAK may provide a reference model for developing new antitumor FAK-targeting drugs. In this study, the VS-6063/FAK binding model was constructed using ensemble docking and molecular dynamics simulations. Furthermore, the molecular mechanics/generalized Born (GB) surface area (MM/GBSA) method was employed to estimate the binding free energy between VS-6063 and FAK. The key residues involved in VS-6063/FAK binding were also determined using per-residue energy decomposition analysis. Based on the binding model, VS-6063 could be separated into seven regions to enhance its binding affinity with FAK. Meanwhile, 60 novel defactinib-based compounds were designed and verified using ensemble docking. Overall, the present study improves our understanding of the binding mechanism of human FAK with VS-6063 and provides new insights into future drug designs targeting FAK.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chuan Guo
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Qinxuan Li
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Jiujia Xiao
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Feng Ma
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Xun Xia
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Mingsong Shi
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
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5
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Adhav V, Saikrishnan K. The Realm of Unconventional Noncovalent Interactions in Proteins: Their Significance in Structure and Function. ACS OMEGA 2023; 8:22268-22284. [PMID: 37396257 PMCID: PMC10308531 DOI: 10.1021/acsomega.3c00205] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023]
Abstract
Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent interactions. It is critical to scrutinize these noncovalent interactions to understand their role in the energy landscape in folding, catalysis, and molecular recognition. This Review presents a comprehensive summary of unconventional noncovalent interactions, beyond conventional hydrogen bonds and hydrophobic interactions, which have gained prominence over the past decade. The noncovalent interactions discussed include low-barrier hydrogen bonds, C5 hydrogen bonds, C-H···π interactions, sulfur-mediated hydrogen bonds, n → π* interactions, London dispersion interactions, halogen bonds, chalcogen bonds, and tetrel bonds. This Review focuses on their chemical nature, interaction strength, and geometrical parameters obtained from X-ray crystallography, spectroscopy, bioinformatics, and computational chemistry. Also highlighted are their occurrence in proteins or their complexes and recent advances made toward understanding their role in biomolecular structure and function. Probing the chemical diversity of these interactions, we determined that the variable frequency of occurrence in proteins and the ability to synergize with one another are important not only for ab initio structure prediction but also to design proteins with new functionalities. A better understanding of these interactions will promote their utilization in designing and engineering ligands with potential therapeutic value.
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6
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Piña MDLN, Sahu AK, Frontera A, Biswal HS, Bauzá A. Tetrel bonds involving a CF 3 group participate in protein-drug recognition: a combined crystallographic and computational study. Phys Chem Chem Phys 2023; 25:12409-12419. [PMID: 37093130 DOI: 10.1039/d3cp00839h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
In this study, the ability of CF3 groups to bind to the electron-rich side chains and backbone groups of proteins has been investigated by combining a Protein Data Bank (PDB) survey and ab initio quantum mechanics calculations. More precisely, an inspection of the PDB involving organic ligands containing a CF3 group and electron-rich atoms (A = N, O and S) in the vicinity revealed 419 X-ray structures exhibiting CF3⋯A tetrel bonds (TtBs). In a posterior stage, those hits that exhibited the most relevant features in terms of directionality and intermolecular distance were selected for theoretical calculations at the RI-MP2/def2-TZVPD level of theory. Also, Hammett's regression plots of several TtB complexes involving meta- and para-substituted benzene derivatives were computed to shed light on the substituent effects. Moreover, the TtBs were characterized through several state-of-the-art computational techniques, such as the Quantum Theory of Atoms in Molecules (QTAIM) and Noncovalent Interactions plot (NCIplot) methodologies. We believe that the results gathered from our study will be useful for rational drug design and biological communities as well as for further expanding the role of this interaction to biomedical applications.
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Affiliation(s)
- María de Las Nieves Piña
- Department of Chemistry, Universitat de les Illes Balears, Crts de Valldemossa km 7.6, 07122 Palma de Mallorca, Baleares, Spain.
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, Khurda, 752050, Bhubaneswar, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crts de Valldemossa km 7.6, 07122 Palma de Mallorca, Baleares, Spain.
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, Khurda, 752050, Bhubaneswar, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crts de Valldemossa km 7.6, 07122 Palma de Mallorca, Baleares, Spain.
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7
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Burguera S, Frontera A, Bauza A. Regium-π Bonds Involving Nucleobases: Theoretical Study and Biological Implications. Inorg Chem 2023; 62:6740-6750. [PMID: 37083254 PMCID: PMC10155183 DOI: 10.1021/acs.inorgchem.3c00369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
In this study, we provide crystallographic (Protein Data Bank (PDB) inspection) and theoretical (RI-MP2/def2-TZVP//PBE0-D3/def2-SVP level of theory) evidence of the involvement of nucleobases in Regium-π bonds (RgBs). This noncovalent interaction involves an electrophilic site located on an element of group 11 (Cu, Ag, and Au) and an electron-rich species (lone pair, LP donor, or π-system). Concretely, an initial PDB search revealed several examples where RgBs were undertaken involving DNA bases and Cu(II), Ag(I), and Au(I/III) ions. While coordination positions (mainly at the N atoms of the base) are well known, the noncovalent binding force between these counterparts has been scarcely studied in the literature. In this regard, computational models shed light on the strength and directionality properties of the interaction, which was also further characterized from a charge-density perspective using Bader's "atoms in molecules" (AIM) theory, noncovalent interaction plot (NCIplot) visual index, and natural bonding orbital (NBO) analyses. As far as our knowledge extends, this is the first time that RgBs in metal-DNA complexes are systematically analyzed, and we believe the results might be useful for scientists working in the field of nucleic acid engineering and chemical biology as well as to increase the visibility of the interaction among the biological community.
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Affiliation(s)
- Sergi Burguera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| | - Antonio Bauza
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
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8
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de Azevedo Santos L, Ramalho TC, Hamlin TA, Bickelhaupt FM. Intermolecular Covalent Interactions: Nature and Directionality. Chemistry 2023; 29:e202203791. [PMID: 36478415 DOI: 10.1002/chem.202203791] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 12/12/2022]
Abstract
Quantum chemical methods were employed to analyze the nature and the origin of the directionality of pnictogen (PnB), chalcogen (ChB), and halogen bonds (XB) in archetypal Fm Z⋅⋅⋅F- complexes (Z=Pn, Ch, X), using relativistic density functional theory (DFT) at ZORA-M06/QZ4P. Quantitative Kohn-Sham MO and energy decomposition analyses (EDA) show that all these intermolecular interactions have in common that covalence, that is, HOMO-LUMO interactions, provide a crucial contribution to the bond energy, besides electrostatic attraction. Strikingly, all these bonds are directional (i.e., F-Z⋅⋅⋅F- is approximately linear) despite, and not because of, the electrostatic interactions which, in fact, favor bending. This constitutes a breakdown of the σ-hole model. It was shown how the σ-hole model fails by neglecting both, the essential physics behind the electrostatic interaction and that behind the directionality of electron-rich intermolecular interactions. Our findings are general and extend to the neutral, weaker ClI⋅⋅⋅NH3 , HClTe⋅⋅⋅NH3 , and H2 ClSb⋅⋅⋅NH3 complexes.
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Affiliation(s)
- Lucas de Azevedo Santos
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Teodorico C Ramalho
- Department of Chemistry, Institute of Natural Sciences, Federal University of Lavras CEP, 37200-900, Lavras, MG, Brazil.,Center for Basic and Applied Research, University Hradec Kralove, Hradec Kralove, Czech Republic
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.,Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.,Department of Chemical Sciences, University of Johannesburg Auckland Park, Johannesburg, 2006, South Africa
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9
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Deepa P, Thirumeignanam D. Understanding the impact of halogen functional group (Br, Cl, F, OH) in amprenavir ligand of the HIV protease. J Biomol Struct Dyn 2023; 41:12157-12170. [PMID: 36645135 DOI: 10.1080/07391102.2023.2166121] [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: 03/22/2022] [Accepted: 01/01/2023] [Indexed: 01/17/2023]
Abstract
We focused our attention towards the most dreadful disease that threatens the mankind of 20th century - Acquired immunodeficiency syndrome (AIDS), caused through the human immunodeficiency virus (HIV) and a sexually transmitted infection (STI). In this study, our foremost interest was to identify the potency and stability of HIV ligand- Amprenavir (APV) and its modelled functional group (Br, Cl, F, CF3, CH3, NH2) ligands through halogen and hydrogen bond contact, which will have a clear portrait on the structure activity of protein ligand interactions. This will assist chemist in synthesizing novel APV ligands, which are expected to inhibit the activity of HIV-1 protease enzyme. The binding strength of Amprenavir ligand with interacting hinge region amino acid side chains: Isoleucine (ILE 147, 150, 184), Valine (VAL 82), Alanine (ALA 28), Aspartic acid (25, 30, 125, 130) and Glycine (GLY 127, 149) were understood through interaction energy calculations at HF, B3LYP, M052X, MP2 level of theories for different basis set (6-311 G**, LANL2DZ). The present work will reveal an understandable picture about the halogen and hydrogen bond interaction that grip the contact of ligand and amino acids in the hinge region. Overall the Halogen atom (Br, Cl, F) functional groups improved the binding strength of APV in HIV protease; which provide a new novel path for the functional group preference on the ligand that enclose perfectly with the amino acid in the hinge region.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Palanisamy Deepa
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, India
| | - Duraisamy Thirumeignanam
- Department of Animal Nutrition, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Tirunelveli, India
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10
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Alghamdi S, Abbas F, Hussein R, Alhamzani A, El‐Shamy N. Spectroscopic characterization (IR, UV-Vis), and HOMO-LUMO, MEP, NLO, NBO Analysis and the Antifungal Activity for 4-Bromo-N-(2-nitrophenyl) benzamide; Using DFT Modeling and In silico Molecular Docking. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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11
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Inhibitors of Heptosyltransferase I to prevent heptose transfer against antibiotic resistance of E. coli: Energetics and stability analysis by DFT and molecular dynamics. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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12
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DFT reveals the support effects in Pd nanoclusters over defect-ridden graphene for the oxidative addition of bromobenzene. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Luo RS, Mao SN, Liu CJ, Zhou ZX, Huang ZY. SYNTHESIS, X-RAY STRUCTURE ANALYSIS, AND VIBRATIONAL SPECTRAL STUDIES OF 1-(3-((6-BROMOPYRIDO[2,3-d]PYRIMIDIN-4-YL) OXY)PHENYL)-3-CYCLOPENTYLUREA. J STRUCT CHEM+ 2022. [DOI: 10.1134/s002247662201005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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14
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Piña MDLN, Frontera A, Bauza A. Charge Assisted S/Se Chalcogen Bonds in SAM Riboswitches: A Combined PDB and ab Initio Study. ACS Chem Biol 2021; 16:1701-1708. [PMID: 34427431 PMCID: PMC8525861 DOI: 10.1021/acschembio.1c00417] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
In this study, we provide experimental
(Protein Data Bank (PDB)
inspection) and theoretical (RI-MP2/def2-TZVP level of theory) evidence
of the involvement of charge assisted chalcogen bonding (ChB) interactions
in the recognition and folding mechanisms of S-adenosylmethionine
(SAM) riboswitches. Concretely, an initial PDB search revealed several
examples where ChBs between S-adenosyl methionine (SAM)/adenosyl selenomethionine
(EEM) molecules and uracil (U) bases belonging to RNA take place.
While these interactions are usually described as a merely Coulombic
attraction between the positively charged S/Se group and RNA, theoretical
calculations indicated that the σ holes of S and Se are involved.
Moreover, computational models shed light on the strength and directionality
properties of the interaction, which was also further characterized
from a charge-density perspective using Bader’s “Atoms
in Molecules” (AIM) theory, Non-Covalent Interaction plot (NCIplot)
visual index, and Natural Bonding Orbital (NBO) analyses. As far as
our knowledge extends, this is the first time that ChBs in SAM–RNA
complexes have been systematically analyzed, and we believe the results
might be useful for scientists working in the field of RNA engineering
and chemical biology as well as to increase the visibility of the
interaction among the biological community.
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Affiliation(s)
- María de las Nieves Piña
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Antonio Bauza
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
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15
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Biswal HS, Kumar Sahu A, Frontera A, Bauzá A. Spodium Bonds in Biological Systems: Expanding the Role of Zn in Protein Structure and Function. J Chem Inf Model 2021; 61:3945-3954. [PMID: 34375103 PMCID: PMC8525862 DOI: 10.1021/acs.jcim.1c00594] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Understanding the structural and functional implications of metal ions is of pivotal significance to chemical biology. Herein, we report first time the evidence of spodium bonds (SpB's, an attractive noncovalent force involving elements from group 12 and electron-rich species) in tetrahedral Zn-binding sites. Through a combined crystallographic (PDB analysis) and computational (ab initio calculations) study, we demonstrate that Zn SpB's are abundant and might be involved in protein structure and enzyme inhibition.
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Affiliation(s)
- Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, 752050 Bhubaneswar, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, 400094 Mumbai, India
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, 752050 Bhubaneswar, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, 400094 Mumbai, India
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
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16
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Chen D, Chen Y, Yang D, Zheng Z, Zhou Z. Synthesis and
antitumor
activity of novel pyridino[2,3‐
d
]pyrimidine urea derivatives. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dongmei Chen
- School of Pharmaceutical Sciences Guizhou University Guiyang PR China
- Guizhou Engineering Laboratory for Synthetic Drugs Guiyang PR China
| | - Yumei Chen
- School of Pharmaceutical Sciences Guizhou University Guiyang PR China
- Guizhou Engineering Laboratory for Synthetic Drugs Guiyang PR China
| | - Di Yang
- School of Pharmaceutical Sciences Guizhou University Guiyang PR China
- Guizhou Engineering Laboratory for Synthetic Drugs Guiyang PR China
| | - Zhaopeng Zheng
- Department of Oncology Guizhou Provincial People's Hospital Guiyang PR China
| | - Zhixu Zhou
- School of Pharmaceutical Sciences Guizhou University Guiyang PR China
- Guizhou Engineering Laboratory for Synthetic Drugs Guiyang PR China
- Department of Dermatology Affiliated Hospital of Guizhou Medical University Guiyang PR China
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17
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Larrañaga O, Arrieta A, Fonseca Guerra C, Bickelhaupt FM, de Cózar A. Nature of Alkali- and Coinage-Metal Bonds versus Hydrogen Bonds. Chem Asian J 2021; 16:315-321. [PMID: 33372401 PMCID: PMC7898866 DOI: 10.1002/asia.202001201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/28/2020] [Indexed: 01/24/2023]
Abstract
We have quantum chemically studied the structure and nature of alkali- and coinage-metal bonds (M-bonds) versus that of hydrogen bonds between A-M and B- in archetypal [A-M⋅⋅⋅B]- model systems (A, B=F, Cl and M=H, Li, Na, Cu, Ag, Au), using relativistic density functional theory at ZORA-BP86-D3/TZ2P. We find that coinage-metal bonds are stronger than alkali-metal bonds which are stronger than the corresponding hydrogen bonds. Our main purpose is to understand how and why the structure, stability and nature of such bonds are affected if the monovalent central atom H of hydrogen bonds is replaced by an isoelectronic alkali- or coinage-metal atom. To this end, we have analyzed the bonds between A-M and B- using the activation strain model, quantitative Kohn-Sham molecular orbital (MO) theory, energy decomposition analysis (EDA), and Voronoi deformation density (VDD) analysis of the charge distribution.
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Affiliation(s)
- Olatz Larrañaga
- Departamento de Química Orgánica I, Facultad de QuímicaUniversidad del País Vasco (UPV/EHU)Donostia International Physics Center (DIPC)P. K. 107220018San Sebastián-DonostiaSpain
| | - Ana Arrieta
- Departamento de Química Orgánica I, Facultad de QuímicaUniversidad del País Vasco (UPV/EHU)Donostia International Physics Center (DIPC)P. K. 107220018San Sebastián-DonostiaSpain
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081HV AmsterdamThe Netherlands
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081HV AmsterdamThe Netherlands
- Institute of Molecules and MaterialsRadboud UniversityHeyendaalseweg 135NL-6525AJ NijmegenThe Netherlands
| | - Abel de Cózar
- Departamento de Química Orgánica I, Facultad de QuímicaUniversidad del País Vasco (UPV/EHU)Donostia International Physics Center (DIPC)P. K. 107220018San Sebastián-DonostiaSpain
- IKERBASQUE, Basque Foundation for SciencePlaza Euskadi 548009BilbaoSpain
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Yu Y, Yu Q, Liu S, Wu C, Zhang X. Insight into the binding mode of HIF-2 agonists through molecular dynamic simulations and biological validation. Eur J Med Chem 2020; 211:112999. [PMID: 33189439 DOI: 10.1016/j.ejmech.2020.112999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/30/2020] [Accepted: 11/04/2020] [Indexed: 01/05/2023]
Abstract
Hypoxia-inducible factor-2 (HIF-2), a heterodimeric transcriptional protein consisting of HIF-2α and aryl hydrocarbon receptor nuclear translocator (ARNT) subunits, has a broad transcriptional profile that plays a vital role in human oxygen metabolism. M1001, a HIF-2 agonist identified by high-throughput screening (HTS), is capable of altering the conformation of Tyr281 of the HIF-2α PAS-B domain and enhancing the affinity of HIF-2α and ARNT for transcriptional activation. M1002, an analog of M1001, shows improved efficacy than M1001. However, the cocrystal structure of M1001 and HIF-2 has some defects in revealing the agonist binding mode due to the relatively low resolution, while the binding mode of M1002 remained unexplored. To in-depth understand agonist binding profiles, herein, the molecular dynamic (MD) simulations was applied to construct a stable agonist-protein model, and a possible binding mode was proposed through the analysis of the binding free energy and hydrogen bonding of the simulation results. Nine compounds were then synthesized and evaluated to verify the proposed binding mode. Among them, compound 10 manifested improved agonistic activity and reduced toxicity compared to M1002. This study provides deep insight into the binding mode of such HIF-2 agonists, which would be useful for designing novel agonists for HIF-2.
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Affiliation(s)
- Yancheng Yu
- Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Quanwei Yu
- Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Simeng Liu
- Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Chenyang Wu
- Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Xiaojin Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China.
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Yar M, Hashmi MA, Ayub K. The C2N surface as a highly selective sensor for the detection of nitrogen iodide from a mixture of NX3 (X = Cl, Br, I) explosives. RSC Adv 2020; 10:31997-32010. [PMID: 35518175 PMCID: PMC9056556 DOI: 10.1039/d0ra04930a] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/10/2020] [Indexed: 12/14/2022] Open
Abstract
Explosives are quite toxic and destructive; therefore, it is necessary to not only detect them but also remove them. The adsorption behavior of NX3 analytes (NCl3, NBr3 and NI3) over the microporous C2N surface was evaluated by DFT calculations. The nature of interactions between NX3 and C2N was characterized by adsorption energy, NCI, QTAIM, SAPT0, NBO, EDD and FMO analysis. The interaction energies of NX3 with C2N are in the range of −10.85 to −16.31 kcal mol−1 and follow the order of NCl3@C2N > NBr3@C2N > NI3@C2N, respectively. The 3D isosurfaces and 2D-RGD graph of NCI analysis qualitatively confirmed the existence of halogen bonding interactions among the studied systems. Halogen bonding was quantified by SAPT0 component energy analysis. The SAPT0 results revealed that ΔEdisp (56.75%) is the dominant contributor towards interaction energy, whereas contributions from ΔEelst and ΔEind are 29.41% and 14.34%, respectively. The QTAIM analysis also confirmed the presence of halogen bonding between atoms of NX3 and C2N surface. EDD analysis also validated NCI, QTAIM and NBO analysis. FMO analysis revealed that the adsorption of NI3 on the C2N surface caused the highest change in the EHOMO–LUMO gap (from 5.71 to 4.15 eV), and resulted in high sensitivity and selectivity of the C2N surface towards NI3, as compared to other analytes. It is worth mentioning that in all complexes, a significant difference in the EHOMO–LUMO gap was seen when electronic transitions occurred from the analyte to the C2N surface. Explosives are quite toxic and destructive; therefore, it is necessary to not only detect them but also remove them.![]()
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Affiliation(s)
- Muhammad Yar
- Department of Chemistry
- COMSATS University
- Abbottabad Campus
- Pakistan
| | | | - Khurshid Ayub
- Department of Chemistry
- COMSATS University
- Abbottabad Campus
- Pakistan
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