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Al-Ansi AY, Al-Shawesh GH, Ru X, Lin Z. Quantum Mechanics-Based Fast and Reliable Prediction of Binding Pose Structures. J Phys Chem B 2024; 128:6059-6070. [PMID: 38875526 DOI: 10.1021/acs.jpcb.4c02596] [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: 06/16/2024]
Abstract
Predicting the binding poses of docking with an accurate estimation of binding energies is highly important but very challenging in computational drug design. A quantum mechanics (QM) calculation-based docking approach considering multiple conformations and orientations of the ligand is introduced here to tackle the problem. This QM docking consists of three steps: generating an ensemble of binding poses with a conventional docking simulation, computing the binding energies with self-consistent charge density functional theory tightly binding with dispersion correction (DFTB-D) to selecting the 10 top binding modes, and optimizing the selected binding mode structures using the ONIOM(DFTB:PM7) technique to determine the binding poses. The ONIOM(DFTB-D:PM6) docking approach is tested on 121 ligand-receptor biocomplexes with the crystal structures obtained from the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB). The result shows that the new method is highly satisfactory for the accurate prediction of the binding poses. The new docking method should be beneficial to structure-based drug design.
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Affiliation(s)
- Amar Y Al-Ansi
- Department of Physics, University of Science and Technology of China, Hefei 230026, China
- Department of Physics, Sana'a University, Sana'a, Yemen
- Hangzhou Nain Biotech Co. Ltd., Hangzhou 310015, China
| | - Gamal H Al-Shawesh
- Department of Physics, University of Science and Technology of China, Hefei 230026, China
| | - Xiao Ru
- Department of Physics, University of Science and Technology of China, Hefei 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei 230088, China
| | - Zijing Lin
- Department of Physics, University of Science and Technology of China, Hefei 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei 230088, China
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2
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Rapacioli M, Buey MY, Spiegelman F. Addressing electronic and dynamical evolution of molecules and molecular clusters: DFTB simulations of energy relaxation in polycyclic aromatic hydrocarbons. Phys Chem Chem Phys 2024; 26:1499-1515. [PMID: 37933901 PMCID: PMC10793726 DOI: 10.1039/d3cp02852f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023]
Abstract
We present a review of the capabilities of the density functional based Tight Binding (DFTB) scheme to address the electronic relaxation and dynamical evolution of molecules and molecular clusters following energy deposition via either collision or photoabsorption. The basics and extensions of DFTB for addressing these systems and in particular their electronic states and their dynamical evolution are reviewed. Applications to PAH molecules and clusters, carbonaceous systems of major interest in astrochemical/astrophysical context, are reported. A variety of processes are examined and discussed such as collisional hydrogenation, fast collisional processes and induced electronic and charge dynamics, collision-induced fragmentation, photo-induced fragmentation, relaxation in high electronic states, electronic-to-vibrational energy conversion and statistical versus non-statistical fragmentation. This review illustrates how simulations may help to unravel different relaxation mechanisms depending on various factors such as the system size, specific electronic structure or excitation conditions, in close connection with experiments.
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Affiliation(s)
- Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantique (LCPQ/FERMI), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
| | - Maysa Yusef Buey
- Laboratoire de Chimie et Physique Quantique (LCPQ/FERMI), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
| | - Fernand Spiegelman
- Laboratoire de Chimie et Physique Quantique (LCPQ/FERMI), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
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3
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Castro-Amorim J, Oliveira A, Mukherjee AK, Ramos MJ, Fernandes PA. Unraveling the Reaction Mechanism of Russell's Viper Venom Factor X Activator: A Paradigm for the Reactivity of Zinc Metalloproteinases? J Chem Inf Model 2023. [PMID: 37092784 DOI: 10.1021/acs.jcim.2c01156] [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
Snake venom metalloproteinases (SVMPs) are important drug targets against snakebite envenoming, the neglected tropical disease with the highest mortality worldwide. Here, we focus on Russell's viper (Daboia russelii), one of the "big four" snakes of the Indian subcontinent that, together, are responsible for ca. 50,000 fatalities annually. The "Russell's viper venom factor X activator" (RVV-X), a highly toxic metalloproteinase, activates the blood coagulation factor X (FX), leading to the prey's abnormal blood clotting and death. Given its tremendous public health impact, the WHO recognized an urgent need to develop efficient, heat-stable, and affordable-for-all small-molecule inhibitors, for which a deep understanding of the mechanisms of action of snake's principal toxins is fundamental. In this study, we determine the catalytic mechanism of RVV-X by using a density functional theory/molecular mechanics (DFT:MM) methodology to calculate its free energy profile. The results showed that the catalytic process takes place via two steps. The first step involves a nucleophilic attack by an in situ generated hydroxide ion on the substrate carbonyl, yielding an activation barrier of 17.7 kcal·mol-1, while the second step corresponds to protonation of the peptide nitrogen and peptide bond cleavage with an energy barrier of 23.1 kcal·mol-1. Our study shows a unique role played by Zn2+ in catalysis by lowering the pKa of the Zn2+-bound water molecule, enough to permit the swift formation of the hydroxide nucleophile through barrierless deprotonation by the formally much less basic Glu140. Without the Zn2+ cofactor, this step would be rate-limiting.
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Affiliation(s)
- Juliana Castro-Amorim
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Ana Oliveira
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Ashis K Mukherjee
- Institute of Advanced Study in Science and Technology, Vigyan Path Garchuk, Paschim Boragaon, Guwahati 781035, Assam, India
| | - Maria J Ramos
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Pedro A Fernandes
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
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4
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Tong Q, Xia M, Sun H, Sun Y, Han S, Li Q. Theoretical investigation of the mechanism of ethanol to propene catalyzed by phosphorus-modified FAU zeolite. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02911-8] [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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5
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Combining classical molecular docking with self-consistent charge density-functional tight-binding computations for the efficient and quality prediction of ligand binding structure. JOURNAL OF CHEMICAL RESEARCH 2022. [DOI: 10.1177/17475198221101999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
To improve the successful prediction rate of the existing molecular docking methods, a new docking approach is proposed that consists of three steps: generating an ensemble of docked poses with a conventional docking method, performing clustering analysis of the ensemble to select the representative poses, and optimizing the representative structures with a low-cost quantum mechanics method. Three quantum mechanics methods, self-consistent charge density-functional tight-binding, ONIOM(DFT:PM6), and ONIOM(SCC-DFTB:PM6), are tested on 18 ligand-receptor bio-complexes. The rate of successful binding pose predictions by the proposed self-consistent charge density-functional tight-binding docking method is the highest, at 67%. The self-consistent charge density-functional tight-binding docking method should be useful for the structure-based drug design.
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Yusef Buey M, Mineva T, Rapacioli M. Coupling density functional based tight binding with class 1 force fields in a hybrid QM/MM scheme. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02878-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Synthesis, structure of 5,7-dimethyl-3-ferrocenyl-2,3-dihydro-1H-pyrazolo- [1,2-a]-pyrazol-4-ium tetrafluoroborate. DFTB calculations of interaction with DNA. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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Deng D, Suo B, Zou W. New Light on an Old Story: Breaking Kasha's Rule in Phosphorescence Mechanism of Organic Boron Compounds and Molecule Design. Int J Mol Sci 2022; 23:876. [PMID: 35055059 PMCID: PMC8776103 DOI: 10.3390/ijms23020876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/09/2022] [Accepted: 01/11/2022] [Indexed: 12/10/2022] Open
Abstract
In this work, the phosphorescence mechanism of (E)-3-(((4-nitrophenyl)imino)methyl)-2H-thiochroman-4-olate-BF2 compound (S-BF2) is investigated theoretically. The phosphorescence of S-BF2 has been reassigned to the second triplet state (T2) by the density matrix renormalization group (DMRG) method combined with the multi-configurational pair density functional theory (MCPDFT) to approach the limit of theoretical accuracy. The calculated radiative and non-radiative rate constants support the breakdown of Kasha's rule further. Our conclusion contradicts previous reports that phosphorescence comes from the first triplet state (T1). Based on the revised phosphorescence mechanism, we have purposefully designed some novel compounds in theory to enhance the phosphorescence efficiency from T2 by replacing substitute groups in S-BF2. Overall, both S-BF2 and newly designed high-efficiency molecules exhibit anti-Kasha T2 phosphorescence instead of the conventional T1 emission. This work provides a useful guidance for future design of high-efficiency green-emitting phosphors.
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Affiliation(s)
- Dan Deng
- Institute of Modern Physics, Northwest University, Xi’an 710127, China;
- Shaanxi Key Laboratory for Theoretical Physics Frontiers, Xi’an 710127, China
| | - Bingbing Suo
- Institute of Modern Physics, Northwest University, Xi’an 710127, China;
- Shaanxi Key Laboratory for Theoretical Physics Frontiers, Xi’an 710127, China
| | - Wenli Zou
- Institute of Modern Physics, Northwest University, Xi’an 710127, China;
- Shaanxi Key Laboratory for Theoretical Physics Frontiers, Xi’an 710127, China
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9
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Yan Z, Li X, Chung LW. Multiscale Quantum Refinement Approaches for Metalloproteins. J Chem Theory Comput 2021; 17:3783-3796. [PMID: 34032440 DOI: 10.1021/acs.jctc.1c00148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Biomolecules with metal ion(s) (e.g., metalloproteins) play many important biological roles. However, accurate structural determination of metalloproteins, particularly those containing transition metal ion(s), is challenging due to their complicated electronic structure, complex bonding of metal ions, and high number of conformations in biomolecules. Quantum refinement, which was proposed to combine crystallographic data with computational chemistry methods by several groups, can improve the local structures of some proteins. In this study, a quantum refinement method combining several multiscale computational schemes with experimental (X-ray diffraction) information was developed for metalloproteins. Various quantum refinement approaches using different ONIOM (our own N-layered integrated molecular orbital and molecular mechanics) combinations of quantum mechanics (QM), semiempirical (SE), and molecular mechanics (MM) methods were conducted to assess the performance and reliability on the refined local structure in two metalloproteins. The structures for two (Cu- or Zn-containing) metalloproteins were refined by combining two-layer ONIOM2(QM1/QM2) and ONIOM2(QM/MM) and three-layer ONIOM3(QM1/QM2/MM) schemes with experimental data. The accuracy of the quantum-refined metal binding sites was also examined and compared in these multiscale quantum refinement calculations. ONIOM3(QM/SE/MM) schemes were found to give good results with lower computational costs and were proposed to be a good choice for the multiscale computational scheme for quantum refinement calculations of metal binding site(s) in metalloproteins with high efficiency. Additionally, a two-center ONIOM approach was employed to speed up the quantum refinement calculations for the Zn metalloprotein with two remote active sites/ligands. Moreover, a recent quantum-embedding wavefunction-in-density functional theory (WF-in-DFT) method was also adopted as the high-level method in unprecedented ONIOM2(CCSD-in-B3LYP/MM) and ONIOM3(CCSD-in-B3LYP/SE/MM) calculations, which can be regarded as novel pseudo-three- and pseudo-four-layer ONIOM methods, respectively, to refine the key Zn binding site at the coupled-cluster singles and doubles (CCSD) level. These refined results indicate that multiscale quantum refinement schemes can be used to improve the structural accuracy obtained for local metal binding site(s) in metalloproteins with high efficiency.
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Affiliation(s)
- Zeyin Yan
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xin Li
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Lung Wa Chung
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
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10
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Ugbaja SC, Sanusi ZK, Appiah-Kubi P, Lawal MM, Kumalo HM. Computational modelling of potent β-secretase (BACE1) inhibitors towards Alzheimer's disease treatment. Biophys Chem 2020; 270:106536. [PMID: 33387910 DOI: 10.1016/j.bpc.2020.106536] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/28/2022]
Abstract
Researchers have identified the β-amyloid precursor protein cleaving enzyme 1 (BACE1) in the multifactorial pathway of Alzheimer's disease (AD) as a drug target. The design and development of molecules to inhibit BACE1 as a potential cure for AD thus remained significant. Herein, we simulated two potent BACE1 inhibitors (AM-6494 and CNP-520) to understand their binding affinity at the atomistic level. AM-6494 is a newly reported potent BACE1 inhibitor with an IC50 value of 0.4 nM in vivo and now picked for preclinical considerations. Umibecestat (CNP-520), which was discontinued at human trials lately, was considered to enable a reasonable evaluation of our results. Using density functional theory (DFT) and Our Own N-layered Integrated molecular Orbital and Molecular Mechanics (ONIOM), we achieved the aim of this investigation. These computational approaches enabled the prediction of the electronic properties of AM-6494 and CNP-520 plus their binding energies when complexed with BACE1. For AM-6494 and CNP-520 interaction with protonated BACE1, the ONIOM calculation gave binding free energy of -62.849 and -33.463 kcal/mol, respectively. In the unprotonated model, we observed binding free energy of -59.758 kcal/mol in AM-6494. Taken together thermochemistry of the process and molecular interaction plot, AM-6494 is more favourable than CNP-520 towards the inhibition of BACE1. The protonated model gave slightly better binding energy than the unprotonated form. However, both models could sufficiently describe ligand binding to BACE1 at the atomistic level. Understanding the detailed molecular interaction of these inhibitors could serve as a basis for pharmacophore exploration towards improved inhibitor design.
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Affiliation(s)
- Samuel C Ugbaja
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Zainab K Sanusi
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Patrick Appiah-Kubi
- Molecular Bio-computational and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Monsurat M Lawal
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4001, South Africa.
| | - Hezekiel M Kumalo
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4001, South Africa.
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11
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Inamori M, Yoshikawa T, Ikabata Y, Nishimura Y, Nakai H. Spin‐flip approach within time‐dependent density functional tight‐binding method: Theory and applications. J Comput Chem 2020; 41:1538-1548. [DOI: 10.1002/jcc.26197] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 03/07/2020] [Accepted: 03/10/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Mayu Inamori
- Department of Chemistry and Biochemistry, School of Advanced Science and EngineeringWaseda University Tokyo Japan
| | - Takeshi Yoshikawa
- Waseda Research Institute for Science and EngineeringWaseda University Tokyo Japan
| | - Yasuhiro Ikabata
- Waseda Research Institute for Science and EngineeringWaseda University Tokyo Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and EngineeringWaseda University Tokyo Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and EngineeringWaseda University Tokyo Japan
- Waseda Research Institute for Science and EngineeringWaseda University Tokyo Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB)Kyoto University Kyoto Japan
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12
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Komoto N, Yoshikawa T, Nishimura Y, Nakai H. Large-Scale Molecular Dynamics Simulation for Ground and Excited States Based on Divide-and-Conquer Long-Range Corrected Density-Functional Tight-Binding Method. J Chem Theory Comput 2020; 16:2369-2378. [DOI: 10.1021/acs.jctc.9b01268] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Nana Komoto
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Takeshi Yoshikawa
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8520, Japan
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13
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Spiegelman F, Tarrat N, Cuny J, Dontot L, Posenitskiy E, Martí C, Simon A, Rapacioli M. Density-functional tight-binding: basic concepts and applications to molecules and clusters. ADVANCES IN PHYSICS: X 2020; 5:1710252. [PMID: 33154977 PMCID: PMC7116320 DOI: 10.1080/23746149.2019.1710252] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023] Open
Abstract
The scope of this article is to present an overview of the Density Functional based Tight Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and its standard formulation up to second order. It also addresses methodological developments such as third order expansion, inclusion of non-covalent interactions, schemes to solve the self-interaction error, implementation of long-range short-range separation, treatment of excited states via the time-dependent DFTB scheme, inclusion of DFTB in hybrid high-level/low level schemes (DFT/DFTB or DFTB/MM), fragment decomposition of large systems, large scale potential energy landscape exploration with molecular dynamics in ground or excited states, non-adiabatic dynamics. A number of applications are reviewed, focusing on -(i)- the variety of systems that have been studied such as small molecules, large molecules and biomolecules, bare orfunctionalized clusters, supported or embedded systems, and -(ii)- properties and processes, such as vibrational spectroscopy, collisions, fragmentation, thermodynamics or non-adiabatic dynamics. Finally outlines and perspectives are given.
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Affiliation(s)
- Fernand Spiegelman
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Nathalie Tarrat
- CEMES, Université de Toulouse (UPS), CNRS, UPR8011, Toulouse, Toulouse, France
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Leo Dontot
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Evgeny Posenitskiy
- Laboratoire Collisions Agrégats et Réactivité LCAR/IRSAMC, UMR5589, Université de Toulouse (UPS) and CNRS, Toulouse, France
| | - Carles Martí
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
- Laboratoire de Chimie, UMR5182, Ecole Normale Supérieure de Lyon, Université de Lyon and CNRS, Lyon, France
| | - Aude Simon
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
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14
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Zhu H, Gao C, Filatov M, Zou W. Mössbauer isomer shifts and effective contact densities obtained by the exact two-component (X2C) relativistic method and its local variants. Phys Chem Chem Phys 2020; 22:26776-26786. [DOI: 10.1039/d0cp04549g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A standalone program to calculate scalar relativistic effective contact densities.
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Affiliation(s)
- Hong Zhu
- Institute of Modern Physics
- Northwest University, and Shaanxi Key Laboratory for Theoretical Physics Frontiers
- Xi'an
- P. R. China
| | - Chun Gao
- Institute of Modern Physics
- Northwest University, and Shaanxi Key Laboratory for Theoretical Physics Frontiers
- Xi'an
- P. R. China
| | - Michael Filatov
- Department of Chemistry
- Kyungpook National University
- Daegu 702-701
- South Korea
| | - Wenli Zou
- Institute of Modern Physics
- Northwest University, and Shaanxi Key Laboratory for Theoretical Physics Frontiers
- Xi'an
- P. R. China
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15
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Sanusi ZK, Govender T, Maguire GEM, Maseko SB, Lin J, Kruger HG, Honarparvar B. An insight to the molecular interactions of the FDA approved HIV PR drugs against L38L↑N↑L PR mutant. J Comput Aided Mol Des 2018; 32:459-471. [PMID: 29397520 DOI: 10.1007/s10822-018-0099-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 01/16/2018] [Indexed: 01/12/2023]
Abstract
The aspartate protease of the human immune deficiency type-1 virus (HIV-1) has become a crucial antiviral target in which many useful antiretroviral inhibitors have been developed. However, it seems the emergence of new HIV-1 PR mutations enhances drug resistance, hence, the available FDA approved drugs show less activity towards the protease. A mutation and insertion designated L38L↑N↑L PR was recently reported from subtype of C-SA HIV-1. An integrated two-layered ONIOM (QM:MM) method was employed in this study to examine the binding affinities of the nine HIV PR inhibitors against this mutant. The computed binding free energies as well as experimental data revealed a reduced inhibitory activity towards the L38L↑N↑L PR in comparison with subtype C-SA HIV-1 PR. This observation suggests that the insertion and mutations significantly affect the binding affinities or characteristics of the HIV PIs and/or parent PR. The same trend for the computational binding free energies was observed for eight of the nine inhibitors with respect to the experimental binding free energies. The outcome of this study shows that ONIOM method can be used as a reliable computational approach to rationalize lead compounds against specific targets. The nature of the intermolecular interactions in terms of the host-guest hydrogen bond interactions is discussed using the atoms in molecules (AIM) analysis. Natural bond orbital analysis was also used to determine the extent of charge transfer between the QM region of the L38L↑N↑L PR enzyme and FDA approved drugs. AIM analysis showed that the interaction between the QM region of the L38L↑N↑L PR and FDA approved drugs are electrostatic dominant, the bond stability computed from the NBO analysis supports the results from the AIM application. Future studies will focus on the improvement of the computational model by considering explicit water molecules in the active pocket. We believe that this approach has the potential to provide information that will aid in the design of much improved HIV-1 PR antiviral drugs.
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Affiliation(s)
- Zainab K Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.,School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Sibusiso B Maseko
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Johnson Lin
- School of Life Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
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16
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Sanusi ZK, Govender T, Maguire GEM, Maseko SB, Lin J, Kruger HG, Honarparvar B. Investigation of the binding free energies of FDA approved drugs against subtype B and C-SA HIV PR: ONIOM approach. J Mol Graph Model 2017; 76:77-85. [PMID: 28711760 DOI: 10.1016/j.jmgm.2017.06.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 06/08/2017] [Accepted: 06/09/2017] [Indexed: 01/15/2023]
Abstract
Human immune virus subtype C is the most widely spread HIV subtype in Sub-Sahara Africa and South Africa. A profound structural insight on finding potential lead compounds is therefore necessary for drug discovery. The focus of this study is to rationalize the nine Food and Drugs Administration (FDA) HIV antiviral drugs complexed to subtype B and C-SA PR using ONIOM approach. To achieve this, an integrated two-layered ONIOM model was used to optimize the geometrics of the FDA approved HIV-1 PR inhibitors for subtype B. In our hybrid ONIOM model, the HIV-1 PR inhibitors as well as the ASP 25/25' catalytic active residues were treated at high level quantum mechanics (QM) theory using B3LYP/6-31G(d), and the remaining HIV PR residues were considered using the AMBER force field. The experimental binding energies of the PR inhibitors were compared to the ONIOM calculated results. The theoretical binding free energies (?Gbind) for subtype B follow a similar trend to the experimental results, with one exemption. The computational model was less suitable for C-SA PR. Analysis of the results provided valuable information about the shortcomings of this approach. Future studies will focus on the improvement of the computational model by considering explicit water molecules in the active pocket. We believe that this approach has the potential to provide much improved binding energies for complex enzyme drug interactions.
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Affiliation(s)
- Z K Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - T Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - G E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; School of Chemistry and Physics, University of KwaZulu-Natal, 4001 Durban, South Africa
| | - S B Maseko
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - J Lin
- School of Life Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - H G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.
| | - B Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.
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17
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Bani-Yaseen AD. Computational molecular perspectives on the interaction of propranolol with β-cyclodextrin in solution: Towards the drug-receptor mechanism of interaction. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2016.12.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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18
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Protein effects in non-heme iron enzyme catalysis: insights from multiscale models. J Biol Inorg Chem 2016; 21:645-57. [DOI: 10.1007/s00775-016-1374-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/20/2016] [Indexed: 01/09/2023]
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19
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Christensen A, Kubař T, Cui Q, Elstner M. Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications. Chem Rev 2016; 116:5301-37. [PMID: 27074247 PMCID: PMC4867870 DOI: 10.1021/acs.chemrev.5b00584] [Citation(s) in RCA: 246] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Indexed: 12/28/2022]
Abstract
Semiempirical (SE) methods can be derived from either Hartree-Fock or density functional theory by applying systematic approximations, leading to efficient computational schemes that are several orders of magnitude faster than ab initio calculations. Such numerical efficiency, in combination with modern computational facilities and linear scaling algorithms, allows application of SE methods to very large molecular systems with extensive conformational sampling. To reliably model the structure, dynamics, and reactivity of biological and other soft matter systems, however, good accuracy for the description of noncovalent interactions is required. In this review, we analyze popular SE approaches in terms of their ability to model noncovalent interactions, especially in the context of describing biomolecules, water solution, and organic materials. We discuss the most significant errors and proposed correction schemes, and we review their performance using standard test sets of molecular systems for quantum chemical methods and several recent applications. The general goal is to highlight both the value and limitations of SE methods and stimulate further developments that allow them to effectively complement ab initio methods in the analysis of complex molecular systems.
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Affiliation(s)
- Anders
S. Christensen
- Department
of Chemistry and Theoretical Chemistry Institute, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Tomáš Kubař
- Institute of Physical
Chemistry & Center for Functional Nanostructures and Institute of Physical
Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Qiang Cui
- Department
of Chemistry and Theoretical Chemistry Institute, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Marcus Elstner
- Institute of Physical
Chemistry & Center for Functional Nanostructures and Institute of Physical
Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
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20
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Gaus M, Jin H, Demapan D, Christensen AS, Goyal P, Elstner M, Cui Q. DFTB3 Parametrization for Copper: The Importance of Orbital Angular Momentum Dependence of Hubbard Parameters. J Chem Theory Comput 2015; 11:4205-19. [PMID: 26575916 PMCID: PMC4827604 DOI: 10.1021/acs.jctc.5b00600] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the parametrization of a density functional tight binding method (DFTB3) for copper in a spin-polarized formulation. The parametrization is consistent with the framework of 3OB for main group elements (ONCHPS) and can be readily used for biological applications that involve copper proteins/peptides. The key to our parametrization is to introduce orbital angular momentum dependence of the Hubbard parameter and its charge derivative, thus allowing the 3d and 4s orbitals to adopt different sizes and responses to the change of charge state. The parametrization has been tested by applying to a fairly broad set of molecules of biological relevance, and the properties of interest include optimized geometries, ligand binding energies, and ligand proton affinities. Compared to the reference QM level (B3LYP/aug-cc-pVTZ, which is shown here to be similar to the B97-1 and CCSD(T) results, in terms of many properties of interest for a set of small copper containing molecules), our parametrization generally gives reliable structural properties for both Cu(I) and Cu(II) compounds, although several exceptions are also noted. For energetics, the results are more accurate for neutral ligands than for charged ligands, likely reflecting the minimal basis limitation of DFTB3; the results generally outperform NDDO based methods such as PM6 and even PBE with the 6-31+G(d,p) basis. For all ligand types, single-point B3LYP calculations at DFTB3 geometries give results very close (∼1-2 kcal/mol) to the reference B3LYP values, highlighting the consistency between DFTB3 and B3LYP structures. Possible further developments of the DFTB3 model for a better treatment of transition-metal ions are also discussed. In the current form, our first generation of DFTB3 copper model is expected to be particularly valuable as a method that drives sampling in systems that feature a dynamical copper binding site.
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Affiliation(s)
- Michael Gaus
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Haiyun Jin
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Darren Demapan
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Anders S Christensen
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Puja Goyal
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology , Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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21
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Khavani M, Izadyar M. Implicit and explicit solvent effects on the selectivity of the cycloaddition reaction of cyclopentadiene and methyl acrylate; a theoretical study. PROGRESS IN REACTION KINETICS AND MECHANISM 2015. [DOI: 10.3184/146867815x14297104685269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The product selectivity of the Diels–Alder reaction between cyclopentadiene and methyl acrylate has been studied through a solvent effect analysis by implicit and explicit solvent models. Two paths for this reaction have been proposed and thermodynamic and kinetic parameters for each path were calculated by the B3LYP functional with 6-311++G(d,p) basis set at 298.15 K. In the explicit solvent model, hydrogen bonds were investigated by the QM/MM method. According to the results, the proportion of the exo product in the gas phase is more than for the endo one, which is in contrast to the solvent phase. HOMO–LUMO analyses in the gas phase and different solvents have been done and solvent effects on the energies of the HOMO–LUMO orbitals were investigated. According to the results, the band gap of the TSs was increased in the presence of the solvents. Finally, natural population analysis has been performed to calculate the electronic charges of some atoms that are involved in the centre of the reaction. The data obtained showed that different solvents, including polar and nonpolar solvents, have different effects on the electronic charges of the atoms. Topological analysis of the structures during the reaction by the quantum theory of atoms in molecules (QTAIM) method in the gas phase and different solvents confirmed a cyclic structure for the transition state.
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Affiliation(s)
- Mohammad Khavani
- Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Izadyar
- Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
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22
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Uma Maheswari J, Muthu S, Sundius T. QM/MM methodology, docking and spectroscopic (FT-IR/FT-Raman, NMR, UV) and Fukui function analysis on adrenergic agonist. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 137:841-855. [PMID: 25277632 DOI: 10.1016/j.saa.2014.07.095] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/09/2014] [Accepted: 07/29/2014] [Indexed: 06/03/2023]
Abstract
The Fourier transform infrared, FT-Raman, UV and NMR spectra of Ternelin have been recorded and analyzed. Harmonic vibrational frequencies have been investigated with the help of HF with 6-31G (d,p) and B3LYP with 6-31G (d,p) and LANL2DZ basis sets. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO method. The polarizability (α) and the first hyperpolarizability (β) values of the investigated molecule have been computed using DFT quantum mechanical calculations. Stability of the molecule arising from hyper conjugative interactions, and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The electron density-based local reactivity descriptors such as Fukui functions were calculated to explain the chemical selectivity or reactivity site in Ternelin. Finally the calculated results were compared to simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra. Molecular docking studies have been carried out in the active site of Ternelin and reactivity with ONIOM was also investigated.
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Affiliation(s)
- J Uma Maheswari
- Department of Physics, Sree Sastha Institute of Engg and Technology, Chembarabakkam, Chennai, Tamil Nadu, India.
| | - S Muthu
- Department of Physics, Sri Venkateswara College of Engineering, Pennalur, Tamil Nadu, India
| | - Tom Sundius
- Department of Physics, University of Helsinki, P.O. Box 64, FIN-00014 Helsinki, Finland
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23
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Mashima A, Kurahashi M, Sasahara K, Yoshida T, Chuman H. Connecting Classical QSAR and LERE Analyses Using Modern Molecular Calculations, LERE-QSAR (VI): Hydrolysis of Substituted Hippuric Acid Phenyl Esters by Trypsin. Mol Inform 2014; 33:802-14. [PMID: 27485426 DOI: 10.1002/minf.201400099] [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: 07/14/2014] [Accepted: 09/14/2014] [Indexed: 11/08/2022]
Abstract
The reaction mechanism of trypsin was studied by applying DFT and ab initio molecular orbital (MO) calculations to complexes of trypsin with a congeneric series of eight para-substituted hippuric acid phenyl esters, for which a previous quantitative structureactivity relationship (QSAR) study revealed nice linearity of Hammett substitution constant σ(-) with logarithmic values of the MichaelisMenten and catalytic rate constants. Based on the LERE procedure, we performed QSAR analyses on each elementary reaction step during the acylation process. The present calculations showed that the rate-determining step during the acylation process is the transition state (TS) between the enzymesubstrate complex (ES) and tetrahedral intermediate (TET), and that the proton transfer occurs from Ser195 to His57, not between His57 and Asp102. The LERE-QSAR analysis statistically suggested that the variation of overall free-energy changes leading to formation of TS is governed mostly by that of activation energies required to form TS from ES. In spite of a very limited number of congeneric ligands in the current work, it is critically essential to clarify and verify physicochemical meanings of a typical QSAR/Chemoinformatics parameter, Hammett σ(-) based on quantum chemical calculations on the proteinligand kinetics; how Hammett σ(-) behaves in terms of proteinligand interaction energies.
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Affiliation(s)
- Akira Mashima
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Masahiro Kurahashi
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Katsunori Sasahara
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Tatsusada Yoshida
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Hiroshi Chuman
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508.
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24
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Silva JRA, Roitberg AE, Alves CN. Catalytic mechanism of L,D-transpeptidase 2 from Mycobacterium tuberculosis described by a computational approach: insights for the design of new antibiotics drugs. J Chem Inf Model 2014; 54:2402-10. [PMID: 25149147 DOI: 10.1021/ci5003069] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Tuberculosis is perhaps the most persistent human disease caused by an infections bacterium, Mycobacterium tuberculosis. The L,D-transpeptidase enzyme catalyzes the formation of 3 → 3 peptidoglycan cross-links of the Mtb cell wall and facilitates resistance against classical β-lactams. Herein, the experimentally proposed mechanism for LdtMt2 was studied by performing QM/MM MD simulations. The whole mechanistic process includes two stages: acylation and deacylation. During the acylation step, two steps were observed: the first step is a thiolate/imidazole ion-pair in the zwitterionic form, and the second step is the nucleophilic attack on the carboxyl carbon of the natural substrate accompanied by the breaking of the peptide bond on substrate. In the deacylation step the acyl-enzyme suffers a nucleophilic attack on the carboxyl carbon by the amine group of the second substrate. Our free energy results obtained by PMF analysis reveal that the first step (acylation) is the rate-limiting step in the whole catalytic mechanism in accordance with the experimental proposal. Also, the residues responsible for binding of the substrate and transition state stabilization were identified by energy decomposition methods.
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Affiliation(s)
- José Rogério A Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará , Belém, PA 66075-110, Brazil
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25
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Cao Y, Han S, Yu L, Qian H, Chen JZ. MD and QM/MM studies on long-chain L-α-hydroxy acid oxidase: substrate binding features and oxidation mechanism. J Phys Chem B 2014; 118:5406-17. [PMID: 24801764 DOI: 10.1021/jp5022399] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Long-chain L-α-hydroxy acid oxidase (LCHAO) is a flavin mononucleotide (FMN)-dependent oxidase that dehydrogenates l-α-hydroxy acids to keto acids. There were two different mechanisms, named as hydride transfer (HT) mechanism and carbanion (CA) mechanism, respectively, proposed about the catalytic process for the FMN-dependent L-α-hydroxy acid oxidases on the basis of biochemical data. However, crystallographic and kinetic studies could not provide enough evidence to prove one of the mechanisms or eliminate the alternative. In the present studies, theoretical computations were carried out to study the molecular mechanism for LCHAO-catalyzed dehydrogenation of L-lactate. Our molecular dynamics (MD) simulations indicated that L-lactate prefers to bind with LCHAO in a hydride transfer mode rather than a carbanion mode. Quantum mechanics/molecular mechanics (QM/MM) calculations were further carried out to obtain the optimized structures of reactants, transition states, and products at the level of ONIOM-EE (B3LYP/6-311++G(d,p)//B3LYP/6-31G(d,p):AMBER). Quantum chemical studies indicated that LCHAO-catalyzed dehydrogenation of L-lactate would be a stepwise catalytic reaction in a hydride transfer mechanism but not a carbanion mechanism. MD simulations, binding free energy calculations, and QM/MM computations were also implemented on the complex between L-lactate and Y129F mutant LCHAO. By comparing the Y129F mutant system with the wild-type system, it was further confirmed that the key residue Tyr129 in the active site of LCHAO would not affect L-lactate's binding to LCHAO but play an important role on the catalytic reaction process through an H-bond interaction.
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Affiliation(s)
- Yang Cao
- Institute of Materia Medica, College of Pharmaceutical Sciences, Zijingang Campus, Zhejiang University , 866 Yuhangtang Rd., Hangzhou, Zhejiang 310058, China
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26
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Cao Y, Chen ZJ, Jiang HD, Chen JZ. Computational Studies of the Regioselectivities of COMT-Catalyzed Meta-/Para-O Methylations of Luteolin and Quercetin. J Phys Chem B 2014; 118:470-81. [DOI: 10.1021/jp410296s] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yang Cao
- Institute
of Materia Medica,
College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Zhong-Jian Chen
- Institute
of Materia Medica,
College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Hui-Di Jiang
- Institute
of Materia Medica,
College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Jian-Zhong Chen
- Institute
of Materia Medica,
College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
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27
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Gaus M, Cui Q, Elstner M. Density functional tight binding: application to organic and biological molecules. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1156] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Michael Gaus
- Department of Chemistry and Theoretical Chemistry Institute University of Wisconsin Madison WI 53706 USA
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute University of Wisconsin Madison WI 53706 USA
| | - Marcus Elstner
- Karlsruhe Institute of Technology Physical Chemistry, Kaiserstrasse 12 D‐76131 Karlsruhe Germany
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28
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Rao W, Koh MJ, Li D, Hirao H, Chan PWH. Gold-catalyzed cycloisomerization of 1,6-diyne carbonates and esters to 2,4a-dihydro-1H-fluorenes. J Am Chem Soc 2013; 135:7926-32. [PMID: 23627597 DOI: 10.1021/ja4032727] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A synthetic method to prepare 2,4a-dihydro-1H-fluorenes efficiently from gold(I)-catalyzed 1,2-acyloxy migration/cyclopropenation/Nazarov cyclization of 1,6-diyne carbonates and esters is described. The suggested reaction pathway provides rare examples of [2,3]-sigmatropic rearrangement in this class of compounds as well as the involvement of an in situ formed cyclopropene intermediate in gold catalysis. Experimental and ONIOM(QM:QM') [our own n-layered integrated molecular orbital and molecular mechanics(quantum mechanics:quantum mechanics')] computational studies based on the proposed Au carbenoid species provide insight into this unique selectivity.
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Affiliation(s)
- Weidong Rao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
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29
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Pang X, Han K, Cui Q. A simple but effective modeling strategy for structural properties of non-heme Fe(II) sites in proteins: test of force field models and application to proteins in the AlkB family. J Comput Chem 2013; 34:1620-35. [PMID: 23666816 DOI: 10.1002/jcc.23305] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 03/09/2013] [Accepted: 04/03/2013] [Indexed: 12/25/2022]
Abstract
To facilitate computational study of proteins in the AlkB family and related α-ketoglutarate/Fe(II)-dependent dioxygenases, we have tested a simple modeling strategy for the non-heme Fe(II) site in which the iron is represented by a simple +2 point charge with Lennard-Jones parameters. Calculations for an AlkB active site model in the gas phase and ∼150 ns molecular dynamics (MD) simulations for two enzyme-dsDNA complexes (E. coli AlkB-dsDNA and ABH2-dsDNA) suggest that this simple modeling strategy provides a satisfactory description of structural properties of the Fe(II) site in AlkB enzymes, provided that care is exercised to control the binding mode of carboxylate (Asp) to the iron. MD simulations using the model for AlkB-dsDNA and ABH2-dsDNA systems find that although the structural features for the latter are overall in good agreement with the crystal structure, the dsDNA, and AlkB-dsDNA interface undergo substantial changes during the MD simulations from the crystal structure. Even for ABH2, new interactions form between a long loop region and dsDNA upon structural relaxation of the loop, supporting the role of this loop in DNA binding despite the lack of interactions between them in the crystal structure. Analysis of DNA backbone torsional distributions helps identify regions that adopt strained conformations. Collectively, the results highlight that crystal packing may have a significant impact on the structure of protein-DNA complexes; the simulations also provide additional insights regarding why AlkB and ABH2 prefer single-strand and double-strand DNA, respectively, as substrate.
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Affiliation(s)
- Xueqin Pang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, People's Republic of China
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30
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Muthu S, Maheswari JU, Sundius T. Molecular structural, non-linear optical, second order perturbation and Fukui studies of Indole-3-Aldehyde using density functional calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 106:299-309. [PMID: 23416887 DOI: 10.1016/j.saa.2012.12.080] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 12/19/2012] [Accepted: 12/21/2012] [Indexed: 06/01/2023]
Abstract
Indole-3-Aldehyde is a new organic non-linear material having good second harmonic generation. The optimized molecular geometry, harmonic vibrational frequencies, infrared intensities of Indole-3-Aldehyde (I3A, C9H7NO) in the ground state were carried out by using density functional theory (B3LYP) method with 6-31G(d,p) basis set. A detailed interpretation of the infrared spectrum of Indole-3-Aldehyde is reported. The vibrational frequencies are calculated and compared with experimental FT-IR spectra. The theoretical spectrograms of FT-IR of the title compound have been constructed in addition, theoretical information like ONIOM, potential energy surface, NBO, and Fukui function are also calculated. Unambiguous vibrational assignment of all the fundamentals was made using the potential energy distribution.
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Affiliation(s)
- S Muthu
- Department of Physics, Sri Venkateswara College of Engineering, Pennalur, Tamil Nadu, India
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31
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Kochman MA, Morrison CA. Hybrid QM/QM Simulations of Excited-State Intramolecular Proton Transfer in the Molecular Crystal 7-(2-Pyridyl)-indole. J Chem Theory Comput 2013; 9:1182-92. [DOI: 10.1021/ct3008149] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michal̷ A. Kochman
- School of Chemistry and
EaSTCHEM Research School, The
University of Edinburgh, King’s Buildings, West Mains Road,
Edinburgh, EH9 3JJ, United Kingdom
| | - Carole A. Morrison
- School of Chemistry and
EaSTCHEM Research School, The
University of Edinburgh, King’s Buildings, West Mains Road,
Edinburgh, EH9 3JJ, United Kingdom
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32
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Lundberg M, Borowski T. Oxoferryl species in mononuclear non-heme iron enzymes: Biosynthesis, properties and reactivity from a theoretical perspective. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.03.047] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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33
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Yoshida T, Hitaoka S, Mashima A, Sugimoto T, Matoba H, Chuman H. Combined QM/MM (ONIOM) and QSAR approach to the study of complex formation of matrix metalloproteinase‑9 with a series of biphenylsulfonamides−LERE-QSAR analysis (V). J Phys Chem B 2012; 116:10283-9. [PMID: 22845734 DOI: 10.1021/jp305476x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We previously proposed a novel QSAR (quantitative structure-activity relationship) procedure called LERE (linear expression by representative energy terms)-QSAR involving molecular calculations such as an ab initio fragment molecular orbital ones. In the present work, we applied LERE-QSAR to complex formation of matrix metalloproteinase-9 (MMP-9) with a series of substituted biphenylsulfonamides. The results shows that the overall free-energy change accompanying complex formation is due to predominantly the contribution from the electrostatic interaction with the zinc atom in the active site of MMP-9. Carbonic anhydrase (CA) belongs to the zinc-containing protease family. In contrast to the current case of MMP-9, the overall free-energy change during complex formation of CA with a series of benzenesulfonamides is due to the contributions from the solvation and dissociation free-energy changes, as previously reported. Comparison of the two sets of results indicates quantitative differences in the relative contributions of free-energy components to the overall free-energy change between the two data sets, corresponding with those in the respective classical QSAR equations. The LERE-QSAR procedure was demonstrated to quantitatively reveal differences in the binding mechanisms between the two cases involving similar but different zinc-containing proteins at the electronic and atomic levels.
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Affiliation(s)
- Tatsusada Yoshida
- Institute of Health Biosciences, The University of Tokushima Graduate School , 1-78 Shomachi, Tokushima 770-8505, Japan
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Guo W, Wu A, Zhang IY, Xu X. XO: An extended ONIOM method for accurate and efficient modeling of large systems. J Comput Chem 2012; 33:2142-60. [DOI: 10.1002/jcc.23051] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 06/04/2012] [Accepted: 06/05/2012] [Indexed: 11/10/2022]
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Bruschi M, Bertini L, Bonačić-Koutecký V, De Gioia L, Mitrić R, Zampella G, Fantucci P. Speciation of Copper–Peptide Complexes in Water Solution Using DFTB and DFT Approaches: Case of the [Cu(HGGG)(Py)] Complex. J Phys Chem B 2012; 116:6250-60. [DOI: 10.1021/jp210409c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Maurizio Bruschi
- Department of Environmental Science, University of Milano-Bicocca, Piazza della Scienza
1, I-20126 Milano, Italy
| | - Luca Bertini
- Department of Biotechnologies
and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy
| | - Vlasta Bonačić-Koutecký
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse
2, D-12489 Berlin, Germany
| | - Luca De Gioia
- Department of Biotechnologies
and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy
| | - Roland Mitrić
- Fachbereich Physik, Freie Universität zu Berlin, Arnimallee 14,
D-14195 Berlin, Germany
| | - Giuseppe Zampella
- Department of Biotechnologies
and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy
| | - Piercarlo Fantucci
- Department of Biotechnologies
and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy
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Lundberg M. Understanding cross-boundary events in ONIOM QM:QM' calculations. J Comput Chem 2011; 33:406-15. [DOI: 10.1002/jcc.21982] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 09/18/2011] [Accepted: 10/05/2011] [Indexed: 12/31/2022]
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Parthasarathi R, Tian J, Redondo A, Gnanakaran S. Quantum Chemical Study of Carbohydrate–Phospholipid Interactions. J Phys Chem A 2011; 115:12826-40. [DOI: 10.1021/jp204015j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- R. Parthasarathi
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Jianhui Tian
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Antonio Redondo
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - S. Gnanakaran
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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Trani F, Scalmani G, Zheng G, Carnimeo I, Frisch MJ, Barone V. Time-Dependent Density Functional Tight Binding: New Formulation and Benchmark of Excited States. J Chem Theory Comput 2011; 7:3304-13. [DOI: 10.1021/ct200461y] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fabio Trani
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
- INFN Sezione di Pisa, Pisa, Italy
| | - Giovanni Scalmani
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Guishan Zheng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Ivan Carnimeo
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
- INFN Sezione di Pisa, Pisa, Italy
| | - Michael J. Frisch
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
- INFN Sezione di Pisa, Pisa, Italy
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Hirao H, Morokuma K. [Recent progress in the theoretical studies of structure, function, and reaction of biological molecules]. YAKUGAKU ZASSHI 2011; 131:1151-61. [PMID: 21804318 DOI: 10.1248/yakushi.131.1151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Essential biomolecular functions often involve electron-related events such as chemical reactions and photoluminescence phenomena. Theoretical description of such electronic processes requires the use of quantum mechanics (QM), but the number of atoms that can be handled with QM is usually smaller than the number of atoms present in a single protein. A reasonable strategy is therefore to give priority to a few tens or hundreds of atoms in the system and deal with them quantum mechanically. Lower-priority atoms influence the event occurring in the higher-priority area; therefore, their effect should also be taken into account. Under these circumstances, a reasonable approach is to apply two or more different theoretical methods to differently prioritized subsystems. QM can be combined, for example, with less accurate yet much less demanding molecular mechanics (MM). Our own N-layered integrated molecular orbital and molecular mechanics (ONIOM) method allows for such hybrid calculations, and our group has been applying it to a wide range of biology-related problems. In this paper, we briefly explain the theoretical background and the procedure for the theoretical investigation of biological systems. Subsequently, we provide an overview of some of our recent studies of metalloenzymes and photobiology-related problems.
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Affiliation(s)
- Hajime Hirao
- Fukui Institute for Fundamental Chemistry, Kyoto University, Japan
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Chung LW, Hirao H, Li X, Morokuma K. The ONIOM method: its foundation and applications to metalloenzymes and photobiology. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.85] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Ramalho TC, Caetano MS, Josa D, Luz GP, Freitas EA, da Cunha EFF. Molecular Modeling ofMycobacterium TuberculosisdUTpase: Docking and Catalytic Mechanism Studies. J Biomol Struct Dyn 2011; 28:907-17. [DOI: 10.1080/07391102.2011.10508617] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Trani F, Barone V. Silicon Nanocrystal Functionalization: Analytic Fitting of DFTB Parameters. J Chem Theory Comput 2011; 7:713-9. [PMID: 26596303 DOI: 10.1021/ct1006086] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A density functional tight binding (DFTB) scheme has been applied to functionalized silicon nanocrystals. Using an analytic functional representation of DFTB parameters, the scheme has been used to compute the adsorption energies in the organic functionalization of reconstructed Si(100) and H-terminated Si(111) surfaces of hundreds-of-atoms nanocrystals. We adopt an ONIOM(QM:QM') approach that corrects the overbinding of DFTB, obtaining nice agreement with high-level reaction energies and structural configurations.
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Affiliation(s)
- Fabio Trani
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.,Infn Sezione di Pisa
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.,Infn Sezione di Pisa
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