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Shukla R, Kumar A, Kelvin DJ, Singh TR. Disruption of DYRK1A-induced hyperphosphorylation of amyloid-beta and tau protein in Alzheimer's disease: An integrative molecular modeling approach. Front Mol Biosci 2022; 9:1078987. [PMID: 36741918 PMCID: PMC9892649 DOI: 10.3389/fmolb.2022.1078987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/20/2022] [Indexed: 01/20/2023] Open
Abstract
Alzheimer's disease (AD) is a neurological disorder caused by the abnormal accumulation of hyperphosphorylated proteins. Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a dual phosphorylation enzyme which phosphorylates the amyloid-β (Aβ) and neurofibrillary tangles (NFTs). A high throughput virtual screening approach was applied to screen a library of 98,071 compounds against DYRK1A using different programs including AutoDock Vina, Smina, and idock. Based on the binding affinities, we selected 330 compounds for absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis. Various pharmacokinetics parameters were predicted using the admetSAR server, and based on the pharmacokinetics results, 14 compounds were selected for cross-docking analysis using AutoDock. Cross-docking analysis revealed four compounds, namely, ZINC3843365 (-11.07 kcal/mol-1), ZINC2123081 (-10.93 kcal/mol-1), ZINC5220992 (-10.63 kcal/mol-1), and ZINC68569602 (-10.35 kcal/mol-1), which had the highest negative affinity scores compared to the 10 other molecules analyzed. Density functional theory (DFT) analysis was conducted for all the four top-ranked compounds. The molecular interaction stability of these four compounds with DYRK1A has been evaluated using molecular dynamics (MD) simulations on 100 nanoseconds followed by principal component analysis (PCA) and binding free energy calculations. The Gibbs free energy landscape analysis suggested the metastable state and folding pattern of selected docking complexes. Based on the present study outcome, we propose four antagonists, viz., ZINC3843365, ZINC2123081, ZINC5220992, and ZINC68569602 as potential inhibitors against DYRK1A and to reduce the amyloid-β and neurofibrillary tangle burden. These screened molecules can be further investigated using a number of in vitro and in vivo experiments.
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Affiliation(s)
- Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Himachal Pradesh, India
- Centre for Excellence in Healthcare Technologies and Informatics (CEHTI), Jaypee University of Information Technology (JUIT), Waknaghat, Himachal Pradesh, India
| | - Anuj Kumar
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - David J. Kelvin
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
- *Correspondence: David J. Kelvin, ; Tiratha Raj Singh,
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Himachal Pradesh, India
- Centre for Excellence in Healthcare Technologies and Informatics (CEHTI), Jaypee University of Information Technology (JUIT), Waknaghat, Himachal Pradesh, India
- *Correspondence: David J. Kelvin, ; Tiratha Raj Singh,
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Tripathy S, Sahu SK, Azam MA, Jupudi S. Computer-aided identification of lead compounds as Staphylococcal epidermidis FtsZ inhibitors using molecular docking, virtual screening, DFT analysis, and molecular dynamic simulation. J Mol Model 2019; 25:360. [PMID: 31773394 DOI: 10.1007/s00894-019-4238-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 10/20/2019] [Indexed: 01/27/2023]
Abstract
In an effort to face the multiple drug-resistant bacteria, various approaches have been discovered to design potent compounds and search new targets through computational design tools. With an aim to identify selective inhibitors against filamentous temperature-sensitive mutant Z (FtsZ), a library of Phase database compounds have been virtually screened. High-throughput virtual screening of compounds against Staphylococcal epidermidis FtsZ protein (4M8I) was performed using three sequential docking modes like high-throughput virtual screening, Glide standard precision, followed by Glide extra precision. Four top-ranked compounds were selected from molecular mechanics-generalized Born surface area (MM-GBSA) binding energy with better predicted free binding energies of - 89.309, - 54.382, - 53.667, and - 52.133 kcal/mol, respectively. It is also showed that the contribution of van der Waals and electrostatic solvation energy terms are playing a major part to make the hit molecule (T6288784) binding to S. epidermidis FtsZ protein. The result of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and energy gap analysis predicts the molecular reactivity and stability of hit molecules. Subsequently, Lipinski's rule of five and properties of absorption, distribution, metabolism, and excretion (ADME) were to calculate their bioavailability. The average binding energy - 9.67 kcal/mol of the best proposed hit molecule (T6288784) was found with half-maximal inhibitory concentration (IC50) value to be 75.53 nM. A 15-ns molecular dynamics simulation study revealed the stable conformation of hit molecule. On a wide-range research discipline, in silico studies of our proposed compound confirm promising results and can be successfully used towards the development of novel FtsZ inhibitor with better binding affinity. Graphical Abstract.
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Affiliation(s)
- Swayansiddha Tripathy
- University Department of Pharmaceutical Sciences, Utkal University, Vani Vihar, Bhubaneswar, Odisha, 751004, India.
| | - Susanta Kumar Sahu
- University Department of Pharmaceutical Sciences, Utkal University, Vani Vihar, Bhubaneswar, Odisha, 751004, India
| | - Mohammed Afzal Azam
- Department of Pharmaceutical Chemistry, J.S.S. College of Pharmacy, Ooty, Udhagamandalam, Tamil Nadu, 643001, India
| | - Srikanth Jupudi
- Department of Pharmaceutical Chemistry, J.S.S. College of Pharmacy, Ooty, Udhagamandalam, Tamil Nadu, 643001, India
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Miranda-Quintana RA, Chattaraj PK, Ayers PW. Finite temperature grand canonical ensemble study of the minimum electrophilicity principle. J Chem Phys 2017; 147:124103. [DOI: 10.1063/1.4996443] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
| | - Pratim K. Chattaraj
- Department of Chemistry and Center for Theoretical Studies, Indian Institute of Technology, Kharagpur 721302, India
| | - Paul W. Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
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Ranasinghe DS, Margraf JT, Jin Y, Bartlett RJ. Does the ionization potential condition employed in QTP functionals mitigate the self-interaction error? J Chem Phys 2017; 146:034102. [PMID: 28109216 DOI: 10.1063/1.4973727] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Though contrary to conventional wisdom, the interpretation of all occupied Kohn-Sham eigenvalues as vertical ionization potentials is justified by several formal and numerical arguments. Similarly, the performance of density functional approximations (DFAs) for fractionally charged systems has been extensively studied as a measure of one- and many-electron self-interaction errors (MSIEs). These complementary perspectives (initially recognized in ab initio dft) are shown to lead to the unifying concept that satisfying Bartlett's IP theorem in DFA's mitigates self-interaction errors. In this contribution, we show that the IP-optimized QTP functionals (reparameterization of CAM-B3LYP where all eigenvalues are approximately equal to vertical IPs) display reduced self-interaction errors in a variety of tests including the He2+ potential curve. Conversely, the MSIE-optimized rCAM-B3LYP functional also displays accurate orbital eigenvalues. It is shown that the CAM-QTP and rCAM-B3LYP functionals show improved dissociation limits, fundamental gaps and thermochemical accuracy compared to their parent functional CAM-B3LYP.
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Affiliation(s)
| | - Johannes T Margraf
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | - Yifan Jin
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | - Rodney J Bartlett
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
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Molecular Docking, Molecular Dynamics Simulations, Computational Screening to Design Quorum Sensing Inhibitors Targeting LuxP of Vibrio harveyi and Its Biological Evaluation. Appl Biochem Biotechnol 2016; 181:192-218. [DOI: 10.1007/s12010-016-2207-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 08/05/2016] [Indexed: 10/21/2022]
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Franco-Pérez M, Gázquez JL, Vela A. Electronic chemical response indexes at finite temperature in the canonical ensemble. J Chem Phys 2015; 143:024112. [DOI: 10.1063/1.4923260] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Marco Franco-Pérez
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, México, D. F. 09340, México
- Departamento de Química, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional 2508, México, D. F. 07360, México
| | - José L. Gázquez
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, México, D. F. 09340, México
- Departamento de Química, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional 2508, México, D. F. 07360, México
| | - Alberto Vela
- Departamento de Química, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional 2508, México, D. F. 07360, México
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Levy M, Anderson JSM, Zadeh FH, Ayers PW. Kinetic and electron-electron energies for convex sums of ground state densities with degeneracies and fractional electron number. J Chem Phys 2014; 140:18A538. [DOI: 10.1063/1.4871734] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Ayers PW, Levy M. Tight constraints on the exchange-correlation potentials of degenerate states. J Chem Phys 2014; 140:18A537. [DOI: 10.1063/1.4871732] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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Cai J, Xing Y, Yang M, Zhao X. Preparation of modified γ-alumina as stationary phase in gas–solid chromatography and its separation performance for hydrogen isotopes. ADSORPTION 2013. [DOI: 10.1007/s10450-013-9499-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Sarkar U, Khatua M, Chattaraj PK. A tug-of-war between electronic excitation and confinement in a dynamical context. Phys Chem Chem Phys 2012; 14:1716-27. [DOI: 10.1039/c1cp22862e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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