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Thangavel N, Albratty M. Benchmarked molecular docking integrated molecular dynamics stability analysis for prediction of SARS-CoV-2 papain-like protease inhibition by olive secoiridoids. J King Saud Univ Sci 2023; 35:102402. [PMID: 36338939 PMCID: PMC9617799 DOI: 10.1016/j.jksus.2022.102402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 09/23/2022] [Accepted: 10/24/2022] [Indexed: 05/28/2023]
Abstract
Objectives We performed a virtual screening of olive secoiridoids of the OliveNetTM library to predict SARS-CoV-2 PLpro inhibition. Benchmarked molecular docking protocol that evaluated the performance of two docking programs was applied to execute virtual screening. Molecular dynamics stability analysis of the top-ranked olive secoiridoid docked to PLpro was also carried out. Methods Benchmarking virtual screening used two freely available docking programs, AutoDock Vina 1.1.2. and AutoDock 4.2.1. for molecular docking of olive secoiridoids to a single PLpro structure. Screening also included benchmark structures of known active and decoy molecules from the DEKOIS 2.0 library. Based on the predicted binding energies, the docking programs ranked the screened molecules. We applied the usual performance evaluation metrices to evaluate the docking programs using the predicted ranks. Molecular dynamics of the top-ranked olive secoiridoid bound to PLpro and computation of MM-GBSA energy using three iterations during the last 50 ps of the analysis of the dynamics in Desmond supported the stability prediction. Results and discussions Predictiveness curves suggested that AutoDock Vina has a better predictive ability than AutoDock, although there was a moderate correlation between the active molecules rankings (Kendall's correlation of rank (τ) = 0.581). Interestingly, two same molecules, Demethyloleuropein aglycone, and Oleuroside enriched the top 1 % ranked olive secoiridoids predicted by both programs. Demethyloleuropein aglycone bound to PLpro obtained by docking in AutoDock Vina when analyzed for stability by molecular dynamics simulation for 50 ns displayed an RMSD, RMSF<2 Å, and MM-GBSA energy of -94.54 ± 6.05 kcal/mol indicating good stability. Molecular dynamics also revealed the interactions of Demethyloleuropein aglycone with binding sites 2 and 3 of PLpro, suggesting a potent inhibition. In addition, for 98 % of the simulation time, two phenolic hydroxy groups of Demethyloleuropein aglycone maintained two hydrogen bonds with Asp302 of PLpro, specifying the significance of the groups in receptor binding. Conclusion AutoDock Vina retrieved the active molecules accurately and predicted Demethyloleuropein aglycone as the best inhibitor of PLpro. The Arabian diet consisting of olive products rich in secoiridoids benefits from the PLpro inhibition property and reduces the risk of viral infection.
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Key Words
- AD, AutoDock 4.2.1
- ADV, AutoDock Vina 1.1.2
- BEDROC, Boltzmann enhanced discrimination of ROC
- Benchmarking docking
- DEKOIS, Demanding evaluation kits for objective in-silico screening
- EF, Enrichment factor
- M, Moles
- MD, Molecular dynamics
- MM-GBSA, Molecular mechanics generalized Born surface area
- MW, Molecular weight
- Molecular docking
- Molecular dynamics
- OS, Olive secoiridoids
- Olive secoiridoids
- PC, Predictiveness curve
- PLpro
- PLpro, Papain-like protease
- RIE, Robust initial enhancement
- RMSD, Root mean square deviation
- RMSF, Root mean square fluctuation
- ROC, Receiver operating characteristic curve
- ROC-AUC, Area under ROC
- SARS-CoV-2
- SARS-CoV-2, Severe acute respiratory syndrome coronavirus-2
- TG, Total gain
- g/mol, Grams/mole
- kcal/mol, Kilocalorie/mole
- ns, nanoseconds
- pAUC, partial area under ROC
- pTG, Partial total gain
- ps, picoseconds
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Affiliation(s)
- Neelaveni Thangavel
- Department of Pharmaceutical Chemistry & Pharmacognosy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Mohammed Albratty
- Department of Pharmaceutical Chemistry & Pharmacognosy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
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Casado-Combreras MÁ, Rivero-Rodríguez F, Elena-Real CA, Molodenskiy D, Díaz-Quintana A, Martinho M, Gerbaud G, González-Arzola K, Velázquez-Campoy A, Svergun D, Belle V, De la Rosa MA, Díaz-Moreno I. PP2A is activated by cytochrome c upon formation of a diffuse encounter complex with SET/TAF-Iβ. Comput Struct Biotechnol J 2022; 20:3695-3707. [PMID: 35891793 PMCID: PMC9293736 DOI: 10.1016/j.csbj.2022.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
Cytochrome c activates PP2A by disrupting SET/TAF-Iβ-mediated PP2A inhibition. The “earmuff” domains of SET/TAF-Iβ are sufficient to bind PP2A or cytochrome c. SET/TAF-Iβ ΔC exhibits high flexibility and intrinsic dynamics. Cytochrome c and SET/TAF-Iβ ΔC form a polyconformational encounter complex.
Intrinsic protein flexibility is of overwhelming relevance for intermolecular recognition and adaptability of highly dynamic ensemble of complexes, and the phenomenon is essential for the understanding of numerous biological processes. These conformational ensembles—encounter complexes—lack a unique organization, which prevents the determination of well-defined high resolution structures. This is the case for complexes involving the oncoprotein SET/template-activating factor-Iβ (SET/TAF-Iβ), a histone chaperone whose functions and interactions are significantly affected by its intrinsic structural plasticity. Besides its role in chromatin remodeling, SET/TAF-Iβ is an inhibitor of protein phosphatase 2A (PP2A), which is a key phosphatase counteracting transcription and signaling events controlling the activity of DNA damage response (DDR) mediators. During DDR, SET/TAF-Iβ is sequestered by cytochrome c (Cc) upon migration of the hemeprotein from mitochondria to the cell nucleus. Here, we report that the nuclear SET/TAF-Iβ:Cc polyconformational ensemble is able to activate PP2A. In particular, the N-end folded, globular region of SET/TAF-Iβ (a.k.a. SET/TAF-Iβ ΔC)—which exhibits an unexpected, intrinsically highly dynamic behavior—is sufficient to be recognized by Cc in a diffuse encounter manner. Cc-mediated blocking of PP2A inhibition is deciphered using an integrated structural and computational approach, combining small-angle X-ray scattering, electron paramagnetic resonance, nuclear magnetic resonance, calorimetry and molecular dynamics simulations.
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Key Words
- ANP32B, Acidic leucine-rich nuclear phosphoprotein family member B
- BTFA, 3-bromo-1,1,1-trifluoroacetone
- CD, Circular dichroism
- CDK9, Cyclin-dependent kinase 9
- CW, Continuous wave
- Cc, Cytochrome c
- Cytochrome c
- DDR, DNA damage response
- DEER, Double electron–electron resonance
- DLS, Dynamic light scattering
- DMEM, Dulbecco’s modified Eagle’s medium
- DNA, Deoxyribonucleic acid
- DTT, Dithiotreitol
- Dmax, Maximum dimension
- EDTA, Ethylenediamine tetraacetic acid
- EGTA, Ethyleneglycol tetraacetic acid
- EPR, Electron paramagnetic resonance
- Encounter complex
- FBS, Fetal bovine serum
- GUI, Graphical user interface
- HEK, Human embryonic kidney cells
- HRP, Horseradish peroxidase
- I2PP2A, Inhibitor 2 of the protein phosphatase 2A
- I3PP2A, Inhibitor 3 of the protein phosphatase 2A
- INTAC, Integrator-PP2A complex
- IPTG, Isopropyl-β-D-1-thiogalactopyranoside
- ITC, Isothermal titration calorimetry
- Ip/Id, Intensity ratio of NMR resonances between paramagnetic and diamagnetic samples
- LB, Luria-Bertani
- MD, Molecular dynamics
- MTS, (1-acetoxy-2,2,5,5-tetramethyl-δ-3-pyrroline-3-methyl) methanethiosulfonate
- MTSL, (1-oxyl-2,2,5,5-tetramethyl- δ −3-pyrroline-3-methyl) methanethiosulfonate
- MW, Molecular weight
- Molecular dynamics
- NAP1, Nucleosome assembly protein 1
- NAPL, Nucleosome assembly protein L
- NMA, Normal mode analysis
- NMR, Nuclear magnetic resonance
- NPT, Constant number, pressure and temperature
- NVT, Constant number, volume and temperature
- Nuclear magnetic resonance
- OD600, Optical density measured at 600 nm
- OPC, Optimal 3-charge, 4-point rigid water model
- PCR, Polymerase chain reaction
- PME, Particle mesh Ewald
- PMSF, Phenylmethylsulfonyl fluoride
- PP2A, Protein phosphatase 2A
- PRE, Paramagnetic relaxation enhancement
- PVDF, Polyvinylidene fluoride
- Protein phosphatase 2A
- RNA, Ribonucleic acid
- RNApol II, RNA polymerase II
- Rg, Radius of gyration
- SAXS, Small-angle X-ray scattering
- SC, Sample changer
- SDS-PAGE, Sodium dodecylsulfate-polyacrylamide gel electrophoresis
- SDSL, Site-directed spin labeling
- SEC, Size-exclusion chromatography
- SET/TAF-Iβ
- SET/TAF-Iβ ΔC, SET/template-activating factor-Iβ construct lacking its C-terminal domain
- SET/TAF-Iβ, SET/template-activating factor-Iβ
- SPRi, Surface plasmon resonance imaging
- TAF-Iα, Template-activating factor-Iα
- TPBS, Tween 20-phosphate buffered saline
- VPS75, Vacuolar protein sorting-associated protein 75
- WT, Wild type
- XRD, X-ray diffraction
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Affiliation(s)
- Miguel Á Casado-Combreras
- Institute for Chemical Research (IIQ), Scientific Research Centre "Isla de la Cartuja" (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Francisco Rivero-Rodríguez
- Institute for Chemical Research (IIQ), Scientific Research Centre "Isla de la Cartuja" (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Carlos A Elena-Real
- Institute for Chemical Research (IIQ), Scientific Research Centre "Isla de la Cartuja" (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain.,Centre de Biologie Structurale (CBS), INSERM, Centre National de la Recherche Scientifique (CNRS) and Université de Montpellier. 29 rue de Navacelles, 34090 Montpellier, France
| | - Dmitry Molodenskiy
- European Molecular Biology Laboratory, Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607 Hamburg, Germany
| | - Antonio Díaz-Quintana
- Institute for Chemical Research (IIQ), Scientific Research Centre "Isla de la Cartuja" (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Marlène Martinho
- Aix Marseille Univ. Centre National de la Recherche Scientifique (CNRS), BIP UMR7281, Bioénergétique et Ingénierie des protéines, 13402 Marseille, France
| | - Guillaume Gerbaud
- Aix Marseille Univ. Centre National de la Recherche Scientifique (CNRS), BIP UMR7281, Bioénergétique et Ingénierie des protéines, 13402 Marseille, France
| | - Katiuska González-Arzola
- Institute for Chemical Research (IIQ), Scientific Research Centre "Isla de la Cartuja" (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physic of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza. C. de Mariano Esquillor Gómez, Edificio I+D, 50018 Zaragoza, Spain.,Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, C. Pedro Cerbuna, 12, 50009 Zaragoza, Spain.,Instituto de Investigación Sanitaria de Aragón (IIS Aragon), Zaragoza, Spain.,Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), C. de Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607 Hamburg, Germany
| | - Valérie Belle
- Aix Marseille Univ. Centre National de la Recherche Scientifique (CNRS), BIP UMR7281, Bioénergétique et Ingénierie des protéines, 13402 Marseille, France
| | - Miguel A De la Rosa
- Institute for Chemical Research (IIQ), Scientific Research Centre "Isla de la Cartuja" (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Irene Díaz-Moreno
- Institute for Chemical Research (IIQ), Scientific Research Centre "Isla de la Cartuja" (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
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Almalki S, Beigh S, Akhter N, Alharbi RA. In silico epitope-based vaccine design against influenza a neuraminidase protein: Computational analysis established on B- and T-cell epitope predictions. Saudi J Biol Sci 2022; 29:103283. [PMID: 35574284 PMCID: PMC9095894 DOI: 10.1016/j.sjbs.2022.103283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 03/18/2022] [Accepted: 04/17/2022] [Indexed: 11/30/2022] Open
Abstract
Objective Influenza A virus belongs to the most studied virus and its mutant initiates epidemic and pandemics outbreaks. Inoculation is the significant foundation to diminish the risk of infection. To prevent an incidence of influenza from the transmission, various practical approaches require more advancement and progress. More efforts and research must take in front to enhance vaccine efficacy. Methods The present research emphasizes the development and expansion of a universal vaccine for the influenza virus. Research focuses on vaccine design with high efficacy. In this study, numerous computational approaches were used, covering a wide range of elements and ideas in bioinformatics methodology. Various B and T-cell epitopic peptides derived from the Neuraminidase protein N1 are recognized by these approaches. With the implementation of numerous obtained databases and bioinformatics tools, the different immune framework methods of the conserved sequences of N1 neuraminidase were analyzed. NCBI databases were employed to retrieve amino acid sequences. The antigenic nature of the neuraminidase sequence was achieved by the VaxiJen server and Kolaskar and Tongaonkar method. After screening of various B and T cell epitopes, one efficient peptide each from B cell epitope and T cell epitopes was assessed for their antigenic determinant vaccine efficacy. Identical two B cell epitopes were recognized from the N1 protein when analyzed using B-cell epitope prediction servers. The detailed examination of amino acid sequences for interpretation of B and T cell epitopes was achieved with the help of the ABCPred and Immune Epitope Database. Results Computational immunology via immunoinformatic study exhibited RPNDKTG as having its high conservancy efficiency and demonstrated as a good antigenic, accessible surface hydrophilic B-cell epitope. Among T cell epitope analysis, YVNISNTNF was selected for being a conserved epitope. T cell epitope was also analyzed for its allergenicity and cytotoxicity evaluation. YVNISNTNF epitope was found to be a non-allergen and not toxic for cells as well. This T-cell epitope with maximum world populace coverages was scrutinized for its association with the HLA-DRB1*0401 molecule. Results from docking simulation analyses showed YVNISNTNF having lower binding energy, the radius of gyration (Rg), RMSD values, and RMSE values which make the protein structure more stable and increase its ability to become an epitopic peptide for influenza virus vaccination. Conclusions We propose that this epitope analysis may be successfully used as a measurement tool for the robustness of an antigen-antibody reaction between mutant strains in the annual design of the influenza vaccine.
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Key Words
- Antigen-antibody reaction
- Docking simulation
- Epitope prediction
- H1N1, Influenza A
- HA, Hemagglutinin
- HAE, Human airway epithelial
- HCP, Health care personal
- HLA, Human leukocyte antigen
- IC50, Half maximal inhibitory concentration
- IEDB, Immune Epitope Database
- Influenza
- KS, Karplus & Schulz flexibility
- MD, Molecular dynamics
- MMPBSA, Molecular Mechanics Poisson-Boltzmann Surface Area
- NA, Neuraminidase
- RMSD, Root means square deviation
- RMSF, Root mean square fluctuation
- Rg, Radius of gyration
- SARS, Severe acute respiratory syndrome
- Toxicity
- pdm09, Pandemic Disease Mexico 2009
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Affiliation(s)
- Shaia Almalki
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Albaha 65431, Saudi Arabia
| | - Saba Beigh
- Department of Public Health, Faculty of Applied Medical Sciences, Albaha University, Albaha 65431, Saudi Arabia
| | - Naseem Akhter
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Albaha 65431, Saudi Arabia
| | - Read A. Alharbi
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Albaha 65431, Saudi Arabia
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4
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Sofia F. Oliveira A, Shoemark DK, Avila Ibarra A, Davidson AD, Berger I, Schaffitzel C, Mulholland AJ. The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. Comput Struct Biotechnol J 2021; 20:139-147. [PMID: 34934478 PMCID: PMC8670790 DOI: 10.1016/j.csbj.2021.12.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 12/12/2022] Open
Abstract
The SARS-CoV-2 spike protein is the first contact point between the SARS-CoV-2 virus and host cells and mediates membrane fusion. Recently, a fatty acid binding site was identified in the spike (Toelzer et al. Science 2020). The presence of linoleic acid at this site modulates binding of the spike to the human ACE2 receptor, stabilizing a locked conformation of the protein. Here, dynamical-nonequilibrium molecular dynamics simulations reveal that this fatty acid site is coupled to functionally relevant regions of the spike, some of them far from the fatty acid binding pocket. Removal of a ligand from the fatty acid binding site significantly affects the dynamics of distant, functionally important regions of the spike, including the receptor-binding motif, furin cleavage site and fusion-peptide-adjacent regions. Simulations of the D614G mutant show differences in behaviour between these clinical variants of the spike: the D614G mutant shows a significantly different conformational response for some structural motifs relevant for binding and fusion. The simulations identify structural networks through which changes at the fatty acid binding site are transmitted within the protein. These communication networks significantly involve positions that are prone to mutation, indicating that observed genetic variation in the spike may alter its response to linoleate binding and associated allosteric communication.
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Key Words
- ACE2, angiotensin-converting 2 enzyme
- CD, connector domain
- CH, central helix
- FA, fatty acid
- FP, fusion peptide
- FPPR, fusion-peptide proximal region
- HR1, heptad repeat 1
- LA, Linoleic acid
- MD, Molecular dynamics
- MERS, middle east respiratory syndrome
- NTD, N-terminal domain
- RBD, receptor binding domain
- RBM, receptor-binding motif
- RMB, receptor binding motif
- SARS, severe acute respiratory syndrome
- SARS-CoV-2, severe acute respiratory syndrome 2
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Affiliation(s)
- A. Sofia F. Oliveira
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
- BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Deborah K. Shoemark
- BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Amaurys Avila Ibarra
- Research Software Engineering, Advanced Computing Research Centre, University of Bristol, Bristol BS1 5QD, UK
| | - Andrew D. Davidson
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Imre Berger
- BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock's Close, Bristol BS8 1TS, UK
| | - Christiane Schaffitzel
- BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
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Remya C, Dileep KV, Koti Reddy E, Mantosh K, Lakshmi K, Sarah Jacob R, Sajith AM, Jayadevi Variyar E, Anwar S, Zhang KYJ, Sadasivan C, Omkumar RV. Neuroprotective derivatives of tacrine that target NMDA receptor and acetyl cholinesterase - Design, synthesis and biological evaluation. Comput Struct Biotechnol J 2021; 19:4517-4537. [PMID: 34471497 PMCID: PMC8379669 DOI: 10.1016/j.csbj.2021.07.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/24/2022] Open
Abstract
The complex and multifactorial nature of neuropsychiatric diseases demands multi-target drugs that can intervene with various sub-pathologies underlying disease progression. Targeting the impairments in cholinergic and glutamatergic neurotransmissions with small molecules has been suggested as one of the potential disease-modifying approaches for Alzheimer’s disease (AD). Tacrine, a potent inhibitor of acetylcholinesterase (AChE) is the first FDA approved drug for the treatment of AD. Tacrine is also a low affinity antagonist of N-methyl-D-aspartate receptor (NMDAR). However, tacrine was withdrawn from its clinical use later due to its hepatotoxicity. With an aim to develop novel high affinity multi-target directed ligands (MTDLs) against AChE and NMDAR, with reduced hepatotoxicity, we performed in silico structure-based modifications on tacrine, chemical synthesis of the derivatives and in vitro validation of their activities. Nineteen such derivatives showed inhibition with IC50 values in the range of 18.53 ± 2.09 – 184.09 ± 19.23 nM against AChE and 0.27 ± 0.05 – 38.84 ± 9.64 μM against NMDAR. Some of the selected compounds also protected rat primary cortical neurons from glutamate induced excitotoxicity. Two of the tacrine derived MTDLs, 201 and 208 exhibited in vivo efficacy in rats by protecting against behavioral impairment induced by administration of the excitotoxic agent, monosodium glutamate. Additionally, several of these synthesized compounds also exhibited promising inhibitory activitiy against butyrylcholinesterase. MTDL-201 was also devoid of hepatotoxicity in vivo. Given the therapeutic potential of MTDLs in disease-modifying therapy, our studies revealed several promising MTDLs among which 201 appears to be a potential candidate for immediate preclinical evaluations.
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Key Words
- AChE, acetylcholinesterase
- AChEIs, acetylcholinesterase inhibitors
- AChT, acetylthiocholine
- AD, Alzheimer’s disease
- ADME, absorption, distribution, metabolism and excretion
- Acetylcholinesterase
- Alzheimer’s disease
- BBB, blood brain barrier
- Ca2+, calcium
- ChE, Cholinesterases
- DMEM, Dulbecco’s modified Eagle’s medium
- DTNB, 5,5-dithiobis-(2-nitrobenzoic acid)
- ENM, elastic network modeling
- ER, endoplasmic reticulum
- FRET, fluorescence resonance energy transfer
- G6PD, glucose-6-phosphate dehydrogenase
- HBSS, Hank's balanced salt solution
- IP, intraperitoneal
- LBD, Ligand binding domain
- LC-MS, Liquid chromatography-mass spectrometry
- LiCABEDS, Ligand Classifier of Adaptively Boosting Ensemble Decision Stumps
- MAP2, microtubule associated protein 2
- MD, Molecular dynamics
- MTDLs
- MTDLs, multi-target directed ligands
- MWM, Morris water maze
- NBM, neurobasal medium
- NMA, normal mode analysis
- NMDA receptor
- NMDAR, N-methyl-D-aspartate receptor
- Neuroprotection
- OPLS, Optimized potential for liquid simulations
- PBS, phosphate-buffered saline
- PFA, paraformaldehyde
- Polypharmacology
- RMSD, root mean square deviation
- SAR, structure-activity relationships
- SD, standard deviation
- SVM, support vector machine
- Structure-based drug design
- TBI, traumatic brain injury
- TMD, transmembrane domain
- Tacrine
- h-NMDAR, human NMDAR
- hAChE, human AChE
- ppm, parts per million
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Affiliation(s)
- Chandran Remya
- Department of Biotechnology and Microbiology, Kannur University, Dr. Janaki Ammal Campus, Thalassery, Kerala 670661, India
| | - K V Dileep
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,Laboratory for Computational and Structural Biology, Jubilee Center for Medical Research, Jubilee Mission Medical College and Research Institute, Thrissur, Kerala 680005, India
| | - Eeda Koti Reddy
- Division of Chemistry, Department of Sciences and Humanities, Vignan's Foundation for Sciences, Technology and Research -VFSTR (Deemed to be University), Vadlamudi, Guntur, Andhra Pradesh 522 213, India
| | - Kumar Mantosh
- Molecular Neurobiology Division, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695014, India
| | - Kesavan Lakshmi
- Molecular Neurobiology Division, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695014, India
| | - Reena Sarah Jacob
- Molecular Neurobiology Division, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695014, India
| | - Ayyiliyath M Sajith
- Post Graduate and Research Department of Chemistry, Kasargod Govt. College, Kannur University, Kasaragod, India
| | - E Jayadevi Variyar
- Department of Biotechnology and Microbiology, Kannur University, Dr. Janaki Ammal Campus, Thalassery, Kerala 670661, India
| | - Shaik Anwar
- Division of Chemistry, Department of Sciences and Humanities, Vignan's Foundation for Sciences, Technology and Research -VFSTR (Deemed to be University), Vadlamudi, Guntur, Andhra Pradesh 522 213, India
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - C Sadasivan
- Department of Biotechnology and Microbiology, Kannur University, Dr. Janaki Ammal Campus, Thalassery, Kerala 670661, India
| | - R V Omkumar
- Molecular Neurobiology Division, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695014, India
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Jabeen A, Vijayram R, Ranganathan S. A two-stage computational approach to predict novel ligands for a chemosensory receptor. Curr Res Struct Biol 2021; 2:213-221. [PMID: 34235481 PMCID: PMC8244491 DOI: 10.1016/j.crstbi.2020.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 09/29/2020] [Accepted: 10/03/2020] [Indexed: 11/01/2022] Open
Abstract
Olfactory receptor (OR) 1A2 is the member of largest superfamily of G protein-coupled receptors (GPCRs). OR1A2 is an ectopically expressed receptor with only 13 known ligands, implicated in reducing hepatocellular carcinoma progression, with enormous therapeutic potential. We have developed a two-stage screening approach to identify novel putative ligands of OR1A2. We first used a pharmacophore model based on atomic property field (APF) to virtually screen a library of 5942 human metabolites. We then carried out structure-based virtual screening (SBVS) for predicting the potential agonists, based on a 3D homology model of OR1A2. This model was developed using a biophysical approach for template selection, based on multiple parameters including hydrophobicity correspondence, applied to the complete set of available GPCR structures to pick the most appropriate template. Finally, the membrane-embedded 3D model was refined by molecular dynamics (MD) simulations in both the apo and holo forms. The refined model in the apo form was selected for SBVS. Four novel small molecules were identified as strong binders to this olfactory receptor on the basis of computed binding energies.
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Key Words
- APF, Atomic property field
- Amber, Assisted model Building with Energy Refinement
- Atomic property field
- Binding free energy calculation
- CSF, Cerebrospinal fluid
- ECL, Extracellular loop
- GPCR, G protein coupled receptor
- HCMV, Human cytomegalovirus
- HMDB, Human metabolome database
- Hydrophobicity correspondence
- LBVS, Ligand based virtual screening
- LC, Lung carcinoids
- MD, Molecular dynamics
- MMGBSA, Molecular mechanics generalized born surface area
- MMPBSA, Molecular mechanics Poisson–Boltzmann surface area
- Molecular dynamics
- NAFLD, Non-alcoholic fatty liver disease
- NASH, Nonalcoholic steatohepatitis
- OR, olfactory receptor
- OR1A2
- Olfactory receptor
- PMEMD, Particle-Mesh Ewald Molecular Dynamics
- POPC, 1-palmitoyl-2-oleoyl-sn-glycero- 3-phosphatidylcholine
- RMSD, Root mean square deviation
- RMSF, Root mean square fluctuation
- SBVS, Structure based virtual screening
- SSD, Sum of squared difference
- TM, Transmembrane
- Virtual ligand screening
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Affiliation(s)
- Amara Jabeen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Ramya Vijayram
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamilnadu, India
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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7
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Farouk AE, Baig MH, Khan MI, Park T, Alotaibi SS, Dong JJ. Screening of inhibitors against SARS-CoV-2 spike protein and their capability to block the viral entry mechanism: A viroinformatics study. Saudi J Biol Sci 2021; 28:3262-3269. [PMID: 33654454 PMCID: PMC7908882 DOI: 10.1016/j.sjbs.2021.02.066] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/18/2020] [Accepted: 02/19/2021] [Indexed: 01/12/2023] Open
Abstract
SARS-CoV-2, previously named 2019 novel coronavirus (2019-nCoV), has been associated with the global pandemic of acute respiratory distress syndrome. First reported in December 2019 in the Wuhan province of China, this new RNA virus has several folds higher transmission among humans than its other family member (SARS-CoV and MERS-CoV). The SARS-CoV-2 spike receptor-binding domain (RBD) is the region mediating the binding of the virus to host cells via Angiotensin-converting enzyme 2 (ACE2), a critical step of viral. Here in this study, we have utilized in silico approach for the virtual screening of antiviral library extracted from the Asinex database against the Receptor binding domain (RBD) of the S1 subunit of the SARS-CoV-2 spike glycoprotein. Further, the molecules were ranked based on their binding affinity against RBD, and the top 15 molecules were selected. The affinity of these selected molecules to interrupt the ACE2-Spike interaction was also studied. It was found that the chosen molecules were demonstrating excellent binding affinity against spike protein, and these molecules were also very effectively interrupting the ACE2-RBD interaction. Furthermore, molecular dynamics (MD) simulation studies were utilized to investigate the top 3 selected molecules' stability in the ACE2-RBD complexes. To the best of our knowledge, this is the first study where molecules' inhibitory potential against the Receptor binding domain (RBD) of the S1 subunit of the SARS-CoV-2 spike glycoprotein and their inhibitory potential against the ACE2-Spike has been studied. We believe that these compounds can be further tested as a potential therapeutic option against COVID-19.
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Affiliation(s)
- Abd-ElAziem Farouk
- Department of Biotechnology, College of Science, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Mohammad Hassan Baig
- Department of Family Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Mohd Imran Khan
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Taehwan Park
- University-Industry Foundation, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Saqer S Alotaibi
- Department of Biotechnology, College of Science, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Jae-June Dong
- Department of Family Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
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8
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Parida PK, Paul D, Chakravorty D. Nature's therapy for COVID-19: Targeting the vital non-structural proteins (NSP) from SARS-CoV-2 with phytochemicals from Indian medicinal plants. Phytomed Plus 2021; 1:100002. [PMID: 35403083 PMCID: PMC7691168 DOI: 10.1016/j.phyplu.2020.100002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/06/2020] [Accepted: 11/24/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Containing COVID-19 is still a global challenge. It has affected the "normal" world by targeting its economy and health sector. The effect is shifting of focus of research from life threatening diseases like cancer. Thus, we need to develop a medical solution at the earliest. The purpose of this present work was to understand the efficacy of 22 rationally screened phytochemicals from Indian medicinal plants obtained from our previous work, following drug-likeness properties, against 6 non-structural-proteins (NSP) from SARS-CoV-2. METHODS 100 ns molecular dynamics simulations were performed, and relative binding free energies were computed by MM/PBSA. Further, principal component analysis, dynamic cross correlation and hydrogen bond occupancy were analyzed to characterize protein-ligand interactions. Biological pathway enrichment analysis was also carried out to elucidate the therapeutic targets of the phytochemicals in comparison to SARS-CoV-2. RESULTS The potential binding modes and favourable molecular interaction profile of 9 phytochemicals, majorly from Withania somnifera with lowest free binding energies, against the SARS-CoV-2 NSP targets were identified. It was understood that phytochemicals and 2 repurposed drugs with steroidal moieties in their chemical structures formed stable interactions with the NSPs. Additionally, human target pathway analysis for SARS-CoV-2 and phytochemicals showed that cytokine mediated pathway and phosphorylation pathways were with the most significant p-value. CONCLUSIONS To summarize this work, we suggest a global approach of targeting multiple proteins of SARS-CoV-2 with phytochemicals as a natural alternative therapy for COVID-19. We also suggest that these phytochemicals need to be tested experimentally to confirm their efficacy.
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Key Words
- ACPYPE, AnteChamberPYthon Parser interface
- ATP, Adenosine tri phosphate
- Binding energy
- COVID-19, Corona Virus Disease 2019
- DCCM, Dynamic Cross Correlation Matrix
- GO, Gene Ontology enrichment
- H-bond, Hydrogen Bond
- HIV, Human Immuno Deficiency Virus
- India
- JAK-STAT, The Janus kinase (JAK)-signal transducer and activator of transcription (STAT)
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MAPK, Mitogen-activated protein kinase
- MD, Molecular dynamics
- MM/PBSA, Molecular Mechanics/Poisson–Boltzmann (Generalized Born) surface area
- Molecular dynamics simulation
- NSP, Non Structural Proteins
- PCA, Principal Component Analysis
- PME, Particle-Mesh-Ewald summation
- Pathway enrichment
- Phytochemicals
- RMSD, Root mean square deviation
- RMSF, Root mean square fluctuations
- RNA, Ribonucleic Acid
- RdRp, RNA-dependent RNA polymerase
- Rg, Radius of gyration (Rg)
- SARS-CoV, Severe acute respiratory syndrome/coronavirus
- SARS-CoV-2
- SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2
- vdW, van der Waal's energy.
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Affiliation(s)
| | - Dipak Paul
- Noor Enzymes Private Limited, 37-B, Darga Road, Kolkata 700 017, India
| | - Debamitra Chakravorty
- Novel Techsciences (OPC) Private Limited, 37-B, Darga Road, 1st Floor, Kolkata 700 017, India
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9
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Sheik Amamuddy O, Musyoka TM, Boateng RA, Zabo S, Tastan Bishop Ö. Determining the unbinding events and conserved motions associated with the pyrazinamide release due to resistance mutations of Mycobacterium tuberculosis pyrazinamidase. Comput Struct Biotechnol J 2020; 18:1103-1120. [PMID: 32489525 PMCID: PMC7251373 DOI: 10.1016/j.csbj.2020.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/23/2020] [Accepted: 05/06/2020] [Indexed: 01/04/2023] Open
Abstract
WT and 82 Mtb PZase-PZA complexes were established using molecular modelling. AMBER force field parameters for the PZase Fe2+ cofactor were established. Statistically guided network analysis described late PZA unbinding events. MBS and nearby residue mutations lead to premature PZA release from PZase. Cofactor destabilisation was found in only some PZase mutants.
Pyrazinamide (PZA) is the only first-line antitubercular drug active against latent Mycobacterium tuberculosis (Mtb). It is activated to pyrazinoic acid by the pncA-encoded pyrazinamidase enzyme (PZase). Despite the emergence of PZA drug resistance, the underlying mechanisms of resistance remain unclear. This study investigated part of these mechanisms by modelling a PZA-bound wild type and 82 mutant PZase structures before applying molecular dynamics (MD) with an accurate Fe2+ cofactor coordination geometry. After observing nanosecond-scale PZA unbinding from several PZase mutants, an algorithm was developed to systematically detect ligand release via centre of mass distances (COM) and ligand average speed calculations, before applying the statistically guided network analysis (SGNA) method to investigate conserved protein motions associated with ligand unbinding. Ligand and cofactor perspectives were also investigated. A conserved pair of lid-destabilising motions was found. These consisted of (1) antiparallel lid and side flap motions; (2) the contractions of a flanking region within the same flap and residue 74 towards the core. Mutations affecting the hinge residues (H51 and H71), nearby residues or L19 were found to destabilise the lid. Additionally, other metal binding site (MBS) mutations delocalised the Fe2+ cofactor, also facilitating lid opening. In the early stages of unbinding, a wider variety of PZA poses were observed, suggesting multiple exit pathways. These findings provide insights into the late events preceding PZA unbinding, which we found to occur in some resistant PZase mutants. Further, the algorithm developed here to identify unbinding events coupled with SGNA can be applicable to other similar problems.
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Key Words
- 3D, Three-dimensional
- ACPYPE, AnteChamber Python Parser interface
- Amber force field parameters
- CHPC, Center for High Performance Computing
- COM, Center of mass
- Drug resistance
- Drug unbinding
- FDA, Food and Drug Administration
- HTMD, High throughput molecular dynamics
- INH, Isoniazid
- MBS, Metal binding site
- MCBP, Metal Center Parameter Builder
- MD, Molecular dynamics
- MDR-TB, Multidrug-resistant tuberculosis
- Missense mutations
- Molecular dynamics simulations
- PBC, Periodic boundary conditions
- PDB, Protein Data bank
- POA, Pyrazinoic acid
- PZA, Pyrazinamide
- PZase, Pyrazinamidase
- QM, Quantum Mechanics
- RIF, Rifampicin
- SGNA, Statistically guided network analysis
- Statistically guided network analysis
- TB, Tuberculosis
- VAPOR, Variant Analysis Portal
- WHO, World Health Organization
- WT, Wild type
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Affiliation(s)
- Olivier Sheik Amamuddy
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Thommas Mutemi Musyoka
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Rita Afriyie Boateng
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Sophakama Zabo
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
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10
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Fassi EMA, Sgrignani J, D'Agostino G, Cecchinato V, Garofalo M, Grazioso G, Uguccioni M, Cavalli A. Oxidation State Dependent Conformational Changes of HMGB1 Regulate the Formation of the CXCL12/HMGB1 Heterocomplex. Comput Struct Biotechnol J 2019; 17:886-894. [PMID: 31333815 PMCID: PMC6617219 DOI: 10.1016/j.csbj.2019.06.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/28/2019] [Accepted: 06/18/2019] [Indexed: 12/15/2022] Open
Abstract
High-mobility Group Box 1 (HMGB1) is an abundant protein present in all mammalian cells and involved in several processes. During inflammation or tissue damage, HMGB1 is released in the extracellular space and, depending on its redox state, can form a heterocomplex with CXCL12. The heterocomplex acts exclusively via the chemokine receptor CXCR4 enhancing leukocyte recruitment. Here, we used multi-microsecond molecular dynamics (MD) simulations to elucidate the effect of the disulfide bond on the structure and dynamics of HMGB1. The results of the MD simulations show that the presence or lack of the disulfide bond between Cys23 and Cys45 modulates the conformational space explored by HMGB1, making the reduced protein more suitable to form a complex with CXCL12.
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Key Words
- CXCL12
- CXCL12, C-X-C motif chemokine 12
- CXCR4, C-X-C chemokine receptor type 4
- Conformational ensemble
- HMGB1
- HMGB1, High-mobility Group Box 1
- MD, Molecular dynamics
- Molecular dynamics
- Protein-protein docking
- RMSD, Root mean square deviation
- RoG, Radius of gyration
- SASA, Solvent accessible surface area
- TLR2 or TLR4, Toll-like Receptor 2 or 4
- ds-HMGB1, Disulfide High-mobility Group Box 1
- fr-HMGB1, Full reduced High-mobility Group Box 1
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Affiliation(s)
- Enrico M A Fassi
- Institute for Research in Biomedicine, Università della Svizzera Italiana, CH-6500 Bellinzona, Switzerland
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, CH-6500 Bellinzona, Switzerland
| | - Gianluca D'Agostino
- Institute for Research in Biomedicine, Università della Svizzera Italiana, CH-6500 Bellinzona, Switzerland
| | - Valentina Cecchinato
- Institute for Research in Biomedicine, Università della Svizzera Italiana, CH-6500 Bellinzona, Switzerland
| | - Maura Garofalo
- Institute for Research in Biomedicine, Università della Svizzera Italiana, CH-6500 Bellinzona, Switzerland.,University of Lausanne (UNIL), CH-1015, Lausanne, Switzerland
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milan, Italy
| | - Mariagrazia Uguccioni
- Institute for Research in Biomedicine, Università della Svizzera Italiana, CH-6500 Bellinzona, Switzerland.,Humanitas University, Department of Biomedical Sciences, 20090, Pieve Emanuele, Milan, Italy
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, CH-6500 Bellinzona, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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11
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Zeb A, Son M, Yoon S, Kim JH, Park SJ, Lee KW. Computational Simulations Identified Two Candidate Inhibitors of Cdk5/p25 to Abrogate Tau-associated Neurological Disorders. Comput Struct Biotechnol J 2019; 17:579-590. [PMID: 31073393 PMCID: PMC6495220 DOI: 10.1016/j.csbj.2019.04.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/14/2019] [Accepted: 04/17/2019] [Indexed: 01/26/2023] Open
Abstract
Deregulation of Cdk5 is a hallmark in neurodegenerative diseases and its complex with p25 forms Cdk5/p25, thereby causes severe neuropathological insults. Cdk5/p25 abnormally phosphorylates tau protein, and induces tau-associated neurofibrillary tangles in neurological disorders. Therefore, the pharmacological inhibition of Cdk5/p25 alleviates tau-associated neurological disorders. Herein, computational simulations probed two candidate inhibitors of Cdk5/p25. Structure-based pharmacophore investigated the essential complementary chemical features of ATP-binding site of Cdk5 in complex with roscovitine. Resultant pharmacophore harbored polar interactions with Cys83 and Asp86 residues and non-polar interactions with Ile10, Phe80, and Lys133 residues of Cdk5. The chemical space of selected pharmacophore was comprised of two hydrogen bond donors, one hydrogen bond acceptor, and three hydrophobic features. Decoy test validation of pharmacophore obtained highest Guner-Henry score (0.88) and enrichment factor score (7.23). The screening of natural product drug-like databases by validated pharmacophore retrieved 1126 compounds as candidate inhibitors of Cdk5/p25. The docking of candidate inhibitors filtered 10 molecules with docking score >80.00 and established polar and non-polar interactions with the ATP-binding site residues of Cdk5/p25. Finally, molecular dynamics simulation and binding free energy analyses identified two candidate inhibitors of Cdk5/p25. During 30 ns simulation, the candidate inhibitors established <3.0 Å root mean square deviation and stable hydrogen bond interactions with the ATP-binding site residues of Cdk5/p25. The final candidate inhibitors obtained lowest binding free energies of -122.18 kJ/mol and - 117.26 kJ/mol with Cdk5/p25. Overall, we recommend two natural product candidate inhibitors to target the pharmacological inhibition of Cdk5/p25 in tau-associated neurological disorders.
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Key Words
- 2D, Two-dimentional
- 3D, Three-dimentional
- AD, Alzheimer's disease
- ADMET, Absorption, distribution, metabolism, excretion, and toxicity
- ASP, Astex statistical potential
- Aβ, Amyloid beta
- BBB, Blood-brain barrier
- CGMC, Cyclin-dependent kinases, mitogen-activated protein kinases, glycogen synthase kinases, and Cdk-like kinases
- Cdk5, Cyclin-dependent kinase 5
- Cdk5/p25 inhibitors
- Cdks, Cyclin-dependent kinases
- DS, Discovery Studio
- EF, Enrichment factor
- GA, Genetic algorithm
- GFA, Genetic Function Approximation
- GH, Guner-Henry
- GOLD, Genetic optimization of ligand docking
- GROMACS, Groningen Machine for Chemical Simulation
- H-bond, Hydrogen bond
- HBA, Hydrogen bond acceptor
- HBD, Hydrogen bond donor
- HD, Hungtington's disease
- HYP, Hydrophobic
- IBS, InterBioScreen
- K, kelvin
- MD, Molecular dynamics
- MPTP, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine
- Molecular docking
- Molecular dynamics simulation
- NPT, Number particle, pressure, and temperature
- NVT, Number of particles, volume, and temperature
- P5, A 24-residues mimetic peptide of p35
- PD, Parkinson's disease
- PDB, Protein databank
- PLP, Piecewise linear potential
- PME, Particle mesh ewald
- RMSD, Root mean square deviation
- ROF, Rule of five
- Structure-based pharmacophore modeling
- TAT, Twin-arginine targeting
- TIP3P, Transferable intermolecular potential with 3 points
- Tau-pathogenesis
- ZNPD, Zinc Natural Product Database
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Affiliation(s)
- Amir Zeb
- Division of Life Science, Division of Applied Life Sciences (BK21 Plus), Research Institute of Natural Sciences (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Gyeongnam, Republic of Korea
| | - Minky Son
- Division of Life Science, Division of Applied Life Sciences (BK21 Plus), Research Institute of Natural Sciences (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Gyeongnam, Republic of Korea
| | - Sanghwa Yoon
- Division of Life Science, Division of Applied Life Sciences (BK21 Plus), Research Institute of Natural Sciences (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Gyeongnam, Republic of Korea
| | - Ju Hyun Kim
- Department of Chemistry (BK21 Plus), Research Institute of Natural Science (RINS), Geyongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Gyeongnam, Republic of Korea
| | - Seok Ju Park
- Department of Internal Medicine, College of Medicine, Busan Paik Hospital, Inje University, Busan 47392, Republic of Korea
| | - Keun Woo Lee
- Division of Life Science, Division of Applied Life Sciences (BK21 Plus), Research Institute of Natural Sciences (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Gyeongnam, Republic of Korea
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12
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Makuch K, Markiewicz M, Pasenkiewicz-Gierula M. Asymmetric Spontaneous Intercalation of Lutein into a Phospholipid Bilayer, a Computational Study. Comput Struct Biotechnol J 2019; 17:516-26. [PMID: 31011410 DOI: 10.1016/j.csbj.2019.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 04/01/2019] [Accepted: 04/02/2019] [Indexed: 01/05/2023] Open
Abstract
Lutein, a hydroxylated carotenoid, is a pigment synthesised by plants and bacteria. Animals are unable to synthesise lutein, nevertheless, it is present in animal tissues, where its only source is dietary intake. Both in plants and animals, carotenoids are associated mainly with membranes where they carry out important physiological functions. Their trafficking to and insertion into membranes are not well recognised due to experimental difficulties. In this paper, a computational approach is used to elucidate details of the dynamics and energetics of lutein intercalation from the water to the phospholipid bilayer phase. The dynamics is studied using molecular dynamics simulation, and the energetics using umbrella sampling. Lutein spontaneous insertion into the bilayer and translocation across it proceed via formation of hydrogen bonds between its hydroxyl groups and water and/or phospholipid oxygen atoms as well as desolvation of its polyene chain. As lutein molecule is asymmetric, its bilayer intercalation is also asymmetric. The course of events and timescale of the intercalation are different from those of helical peptides. The time of full lutein intercalation ranges from 20 to 100 ns and its final orientation is predominately vertical. Nevertheless, some lutein molecules are in the final horizontal position and some aggregate in the water phase and remain there for the whole simulation time. The highest energy barrier for the intercalation process is ~2.2 kcal/mol and the energy gain is ~18 kcal/mol. The results obtained for lutein can be applied to other xanthophylls and molecules of a similar structure. Lutein as an amphiphilic molecule readily intercalates into a lipid bilayer. MD simulations with dense sampling revealed details of the intercalation process. Time of full lutein membrane intercalation ranges from 20 to 100 ns. Lutein intercalation from the ε ring end is less probable than from the β ring end. Horizontal position of lutein in the bilayer is less probable than vertical.
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Key Words
- Energy barrier
- Hydrogen bond
- Hydrophobic effect
- MD, Molecular dynamics
- Molecular dynamics
- OH-LUT, Lutein hydroxyl group
- Op, Oe, Og, Oc collective names for the non-esterified phosphate, esterified phosphate, glycerol, and carbonyl oxygen atoms, respectively
- Ow, Water oxygen atom
- PC, Phosphatidylcholine
- Palmitoyl-oleoyl PC, POPC
- US, Umbrella sampling
- Umbrella sampling
- Xanthophyll
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Xing J, Mei H, Huang S, Zhang D, Pan X. An Energetically Favorable Ligand Entrance Gate of a Multidrug Transporter Revealed by Partial Nudged Elastic Band Simulations. Comput Struct Biotechnol J 2019; 17:319-323. [PMID: 30899446 PMCID: PMC6406077 DOI: 10.1016/j.csbj.2019.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 11/08/2022] Open
Abstract
P-glycoprotein (P-gp) is a multidrug transporter, which harnesses the chemical energy of ATP to power the efflux of diverse chemotherapeutics out of cells and thus contributes to the development of multidrug resistance (MDR) in cancer. It has been proved that the ligand-binding pocket of P-gp is located at the transmembrane domains (TMDs). However, the access of ligands into the binding pocket remains to be elucidated, which definitely hinder the development of P-gp inhibitors. Herein, the access pathways of a well-known substrate rhodamine-123 and a cyclopeptide inhibitor QZ-Leu were characterized by time-independent partial nudged elastic band (PNEB) simulations. The decreasing free energies along the PNEB-optimized access pathway indicated that TM4/6 cleft may be an energetically favorable entrance gate for ligand entry into the binding pocket of P-gp. The results can be reconciled with a range of experimental studies, further corroborating the reliability of the gate revealed by computational simulations. Our atomic level description of the ligand access pathway provides valuable insights into the gating mechanism for drug uptake and transport by P-gp and other multidrug transporters. P-gp contributes to the development of multidrug resistance in cancer. The entrance of drugs into P-gp binding pocket has yet to be elucidated. An energetically favorable entrance gate was revealed by PNEB simulations. The computational results were reconciled with the experimental data. The atomic simulations provide insights into the gating mechanism of P-gp.
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Affiliation(s)
- Juan Xing
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), College of Bioengineering, Chongqing University, Chongqing 400045, China.,Department of Pathophysiology, College of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Hu Mei
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), College of Bioengineering, Chongqing University, Chongqing 400045, China
| | - ShuHeng Huang
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), College of Bioengineering, Chongqing University, Chongqing 400045, China
| | - Duo Zhang
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), College of Bioengineering, Chongqing University, Chongqing 400045, China
| | - XianChao Pan
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), College of Bioengineering, Chongqing University, Chongqing 400045, China.,Department of Medicinal Chemistry, College of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, China
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14
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Topno NS, Kannan M, Krishna R. Interacting mechanism of ID3 HLH domain towards E2A/E12 transcription factor - An Insight through molecular dynamics and docking approach. Biochem Biophys Rep 2015; 5:180-190. [PMID: 28955822 PMCID: PMC5600450 DOI: 10.1016/j.bbrep.2015.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 11/24/2015] [Accepted: 12/01/2015] [Indexed: 10/29/2022] Open
Abstract
Inhibitor of DNA binding protein 3 (ID3) has long been characterized as an oncogene that implicates its functional role through its Helix-Loop-Helix (HLH) domain upon protein-protein interaction. An insight into the dimerization brought by this domain helps in identifying the key residues that favor the mechanism behind it. Molecular dynamics (MD) simulations were performed for the HLH proteins ID3 and Transcription factor E2-alpha (E2A/E12) and their ensemble complex (ID3-E2A/E12) to gather information about the HLH domain region and its role in the interaction process. Further evaluation of the results by Principal Component Analysis (PCA) and Free Energy Landscape (FEL) helped in revealing residues of E2A/E12: Lys570, Ala595, Val598, and Ile599 and ID3: Glu53, Gln63, and Gln66 buried in their HLH motifs imparting key roles in dimerization process. Furthermore the T-pad analysis results helped in identifying the key fluctuations and conformational transitions using the intrinsic properties of the residues present in the domain region of the proteins thus specifying their crucial role towards molecular recognition. The study provides an insight into the interacting mechanism of the ID3-E2A/E12 complex and maps the structural transitions arising in the essential conformational space indicating the key structural changes within the helical regions of the motif. It thereby describes how the internal dynamics of the proteins might regulate their intrinsic structural features and its subsequent functionality.
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Affiliation(s)
- Nishith Saurav Topno
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Muthu Kannan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Ramadas Krishna
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
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Pang YP. Low-mass molecular dynamics simulation for configurational sampling enhancement: More evidence and theoretical explanation. Biochem Biophys Rep 2015; 4:126-133. [PMID: 29124195 PMCID: PMC5668912 DOI: 10.1016/j.bbrep.2015.08.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/30/2015] [Accepted: 08/31/2015] [Indexed: 11/28/2022] Open
Abstract
It has been reported recently that classical, isothermal-isobaric molecular dynamics (NTP MD) simulations at a time step of 1.00 fs of the standard-mass time (Δt=1.00 fssmt) and a temperature of ≤340 K using uniformly reduced atomic masses by tenfold offers better configurational sampling than standard-mass NTP MD simulations at the same time step. However, it has long been reported that atomic masses can also be increased to improve configurational sampling because higher atomic masses permit the use of a longer time step. It is worth investigating whether standard-mass NTP MD simulations at Δt=2.00 or 3.16 fssmt can offer better or comparable configurational sampling than low-mass NTP MD simulations at Δt=1.00 fssmt. This article reports folding simulations of two β-hairpins showing that the configurational sampling efficiency of NTP MD simulations using atomic masses uniformly reduced by tenfold at Δt=1.00 fssmt is statistically equivalent to and better than those using standard masses at Δt=3.16 and 2.00 fssmt, respectively. The results confirm that, relative to those using standard masses at routine Δt=2.00 fssmt, the low-mass NTP MD simulations at Δt=1.00 fssmt are a simple and generic technique to enhance configurational sampling at temperatures of ≤340 K.
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Affiliation(s)
- Yuan-Ping Pang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Stabile 12-26, 200 First Street SW, Rochester, MN 55905, USA
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