1
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Zhang Y, Borch LA, Fischer NH, Meldal M. Hydrodynamic Control of Alzheimer Aβ Fibrillation with Glucosaminic Acid Containing Click-Cyclized β-Bodies. J Am Chem Soc 2024; 146:2654-2662. [PMID: 38126710 DOI: 10.1021/jacs.3c12118] [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: 12/23/2023]
Abstract
It is well established that the dynamic hydration shell plays a vital role in macromolecular functions such as protein-ligand, protein-protein, protein-DNA, and protein-lipid interactions. Here we investigate how the water modality affects conformational changes, solubility, and motion of fibrillar proteins. The hypothesis is that the introduction of a poly hydroxyl amino acid would increase solvation of the fibril forming peptides, preventing their misfolding and aggregation. For the amyloid β (Aβ) peptide, which is considered to be connected with nervous system diseases, including dementia and cognitive decline in Alzheimer's disease, the formation of β-sheet fibrils always occurs with a conformational change and a decrease in the dynamic hydration shell around Aβ(1-42). We present novel cyclic d-amino acid peptides that effectively inhibit fibrillation through affecting the dynamic hydration shell of Aβ(1-42) in vitro. Using de novo design within the software Molecular Operating Environment (MOE), five different peptides that recognize Alzheimer's fibrils were designed and synthesized. Three of them were cyclic all-d-amino acid peptides incorporating the same polyhydroxy building block derived from d-glucosaminic acid (GA). One peptide was the parent cyclic all d-amino acid inhibitor with no GA incorporated, and another was an all l-amino acid linear fibrillation inhibitor. The GA-containing peptides were found to show significantly improved inhibition of Aβ(1-42) aggregation. The inhibition was dramatically improved by the synergistic application of two GA peptides targeting each end of the growing fibril. The present study may facilitate future developments of intervention strategies for Alzheimer's disease and similar neurodegenerative diseases.
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Affiliation(s)
- Yuan Zhang
- Center for Evolutionary Chemical Biology, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Line A Borch
- Center for Evolutionary Chemical Biology, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Niklas H Fischer
- Center for Evolutionary Chemical Biology, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Morten Meldal
- Center for Evolutionary Chemical Biology, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
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2
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The effect of PC20:0 and di-C7-PC amphiphilic surfactants on the aggregation of Aβ1–40 and Aβ1–42 using molecular dynamics simulation. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2023. [DOI: 10.1007/s13738-023-02761-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
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3
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Mathew AT, Baidya ATK, Das B, Devi B, Kumar R. N-glycosylation induced changes in tau protein dynamics reveal its role in tau misfolding and aggregation: A microsecond long molecular dynamics study. Proteins 2023; 91:147-160. [PMID: 36029032 DOI: 10.1002/prot.26417] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/18/2022] [Accepted: 08/23/2022] [Indexed: 01/07/2023]
Abstract
Various posttranslational modifications like hyperphosphorylation, O-GlcNAcylation, and acetylation have been attributed to induce the abnormal folding in tau protein. Recent in vitro studies revealed the possible involvement of N-glycosylation of tau protein in the abnormal folding and tau aggregation. Hence, in this study, we performed a microsecond long all atom molecular dynamics simulation to gain insights into the effects of N-glycosylation on Asn-359 residue which forms part of the microtubule binding region. Trajectory analysis of the stimulations coupled with essential dynamics and free energy landscape analysis suggested that tau, in its N-glycosylated form tends to exist in a largely folded conformation having high beta sheet propensity as compared to unmodified tau which exists in a large extended form with very less beta sheet propensity. Residue interaction network analysis of the lowest energy conformations further revealed that Phe378 and Lys353 are the functionally important residues in the peptide which helped in initiating the folding process and Phe378, Lys347, and Lys370 helped to maintain the stability of the protein in the folded state.
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Affiliation(s)
- Alen T Mathew
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
| | - Anurag T K Baidya
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
| | - Bhanuranjan Das
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
| | - Bharti Devi
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
| | - Rajnish Kumar
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
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4
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Chung CW, Stephens AD, Konno T, Ward E, Avezov E, Kaminski CF, Hassanali AA, Kaminski Schierle GS. Intracellular Aβ42 Aggregation Leads to Cellular Thermogenesis. J Am Chem Soc 2022; 144:10034-10041. [PMID: 35616634 PMCID: PMC9185738 DOI: 10.1021/jacs.2c03599] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The aggregation of
Aβ42 is a hallmark of Alzheimer’s
disease. It is still not known what the biochemical changes are inside
a cell which will eventually lead to Aβ42 aggregation. Thermogenesis
has been associated with cellular stress, the latter of which may
promote aggregation. We perform intracellular thermometry measurements
using fluorescent polymeric thermometers to show that Aβ42 aggregation
in live cells leads to an increase in cell-averaged temperatures.
This rise in temperature is mitigated upon treatment with an aggregation
inhibitor of Aβ42 and is independent of mitochondrial damage
that can otherwise lead to thermogenesis. With this, we present a
diagnostic assay which could be used to screen small-molecule inhibitors
to amyloid proteins in physiologically relevant settings. To interpret
our experimental observations and motivate the development of future
models, we perform classical molecular dynamics of model Aβ
peptides to examine the factors that hinder thermal dissipation. We
observe that this is controlled by the presence of ions in its surrounding
environment, the morphology of the amyloid peptides, and the extent
of its hydrogen-bonding interactions with water. We show that aggregation
and heat retention by Aβ peptides are favored under intracellular-mimicking
ionic conditions, which could potentially promote thermogenesis. The
latter will, in turn, trigger further nucleation events that accelerate
disease progression.
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Affiliation(s)
- Chyi Wei Chung
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Amberley D Stephens
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Tasuku Konno
- UK Dementia Research Institute, Department of Clinical Neuroscience, University of Cambridge, Cambridge CB2 0AH, U.K
| | - Edward Ward
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Edward Avezov
- UK Dementia Research Institute, Department of Clinical Neuroscience, University of Cambridge, Cambridge CB2 0AH, U.K
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Ali A Hassanali
- Condensed Matter and Statistical Physics, International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy
| | - Gabriele S Kaminski Schierle
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
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5
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Abstract
Intrinsic fluorescence of nonaromatic amino acids is a puzzling phenomenon with an enormous potential in biophotonic applications. The physical origins of this effect, however, remain elusive. Herein, we demonstrate how specific hydrogen bond networks can modulate fluorescence. We highlight the key role played by short hydrogen bonds, present in the protein structure, on the ensuing fluorescence. We provide detailed experimental and molecular evidence to explain these unusual nonaromatic optical properties. Our findings should benefit the design of novel optically active biomaterials for applications in biosensing and imaging. Fluorescence in biological systems is usually associated with the presence of aromatic groups. Here, by employing a combined experimental and computational approach, we show that specific hydrogen bond networks can significantly affect fluorescence. In particular, we reveal that the single amino acid L-glutamine, by undergoing a chemical transformation leading to the formation of a short hydrogen bond, displays optical properties that are significantly enhanced compared with L-glutamine itself. Ab initio molecular dynamics simulations highlight that these short hydrogen bonds prevent the appearance of a conical intersection between the excited and the ground states and thereby significantly decrease nonradiative transition probabilities. Our findings open the door to the design of new photoactive materials with biophotonic applications.
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6
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Ermakova EA, Makshakova ON, Zuev YF, Sedov IA. Fibril fragments from the amyloid core of lysozyme: An accelerated molecular dynamics study. J Mol Graph Model 2021; 106:107917. [PMID: 33887522 DOI: 10.1016/j.jmgm.2021.107917] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 10/21/2022]
Abstract
Protein aggregation and formation of amyloid fibrils are associated with many diseases and present a ubiquitous problem in protein science. Hen egg white lysozyme (HEWL) can form fibrils both from the full length protein and from its fragments. In the present study, we simulated unfolding of the amyloidogenic fragment of HEWL encompassing residues 49-101 to study the conformational aspects of amyloidogenesis. The accelerated molecular dynamics approach was used to speed up the sampling of the fragment conformers under enhanced temperature. Analysis of conformational transformation and intermediate structures was performed. During the unfolding, the novel short-living and long-living β-structures are formed along with the unstructured random coils. Such β-structure enriched monomers can interact with each other and propagate into fibril-like forms. The stability of oligomers assembled from these monomers was evaluated in the course of MD simulations with explicit water. The residues playing a key role in fibril stabilization were determined. The work provides new insights into the processes occurring at the early stages of amyloid fibril assembly.
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Affiliation(s)
- Elena A Ermakova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia; Sirius University of Science and Technology, Olympic Ave, 1, 354340, Sochi, Russia.
| | - Olga N Makshakova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia; Sirius University of Science and Technology, Olympic Ave, 1, 354340, Sochi, Russia
| | - Yuriy F Zuev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia
| | - Igor A Sedov
- Kazan Federal University, Kremlevskaya Str.,18, 420111, Kazan, Russia; Sirius University of Science and Technology, Olympic Ave, 1, 354340, Sochi, Russia
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7
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Chung CW, Kaminski Schierle GS. Intracellular Thermometry at the Micro-/Nanoscale and its Potential Application to Study Protein Aggregation Related to Neurodegenerative Diseases. Chembiochem 2021; 22:1546-1558. [PMID: 33326160 DOI: 10.1002/cbic.202000765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/14/2020] [Indexed: 11/11/2022]
Abstract
Temperature is a fundamental physical parameter that influences biological processes in living cells. Hence, intracellular temperature mapping can be used to derive useful information reflective of thermodynamic properties and cellular behaviour. Herein, existing publications on different thermometry systems, focusing on those that employ fluorescence-based techniques, are reviewed. From developments based on fluorescent proteins and inorganic molecules to metal nanoclusters and fluorescent polymers, the general findings of intracellular measurements from different research groups are discussed. Furthermore, the contradiction of mitochondrial thermogenesis and nuclear-cytoplasmic temperature differences to current thermodynamic understanding are highlighted. Lastly, intracellular thermometry is proposed as a tool to quantify the energy flow and cost associated with amyloid-β42 (Aβ42) aggregation, a hallmark of Alzheimer's disease.
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Affiliation(s)
- Chyi Wei Chung
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Phillipa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Gabriele S Kaminski Schierle
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Phillipa Fawcett Drive, Cambridge, CB3 0AS, UK
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8
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Shadrack DM, Swai HS, Hassanali A. A computational study on the role of water and conformational fluctuations in Hsp90 in response to inhibitors. J Mol Graph Model 2019; 96:107510. [PMID: 31877402 DOI: 10.1016/j.jmgm.2019.107510] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 12/04/2019] [Accepted: 12/11/2019] [Indexed: 10/25/2022]
Abstract
Molecular chaperone Heat Shock Protein 90 (Hsp90) represents an interesting chemotherapeutic target for cancer treatments as it plays a role in cancer proliferation. Thus, continued effort to identify novel inhibitors of this target is an important task. Drug design using computational approach has gained significant attention in recent years. This work aims to propose docking protocols to re-purpose FDA-approved drugs targeting Hsp90. Sensitivity of results to different docking protocols such apo, holo and receptor ensembles (relaxed complex) structures, the role of water and conformational changes of Hsp90, are described. We show that the protein conformation and water have effects on drug binding. Holo relaxed complex receptors ensembles improves the binding energy of ligands to the protein. We also compare and contrast structural stability of three drugs namely: ezetimibe, pitavastatin and vilazodon in the Hsp90 protein. The results obtained serves as a possible basis towards developing Hsp90 inhibitors.
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Affiliation(s)
- Daniel M Shadrack
- Department of Health and Biomedical Sciences, School of Life Science and Bioengieering, The Nelson Mandela African Institution of Science and Technology, P.O.Box 447, Arusha, Tanzania; International Centre for Theoretical Physics, Strada Costiera, 11, 34151, Trieste, Italy; Department of Chemistry, FaNAS, St John's University of Tanzania, P.O.Box 47, Dodoma, Tanzania.
| | - Hulda S Swai
- Department of Health and Biomedical Sciences, School of Life Science and Bioengieering, The Nelson Mandela African Institution of Science and Technology, P.O.Box 447, Arusha, Tanzania
| | - Ali Hassanali
- International Centre for Theoretical Physics, Strada Costiera, 11, 34151, Trieste, Italy.
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9
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Jong KH, Azar YT, Grisanti L, Stephens AD, Jones STE, Credgington D, Kaminski Schierle GS, Hassanali A. Low energy optical excitations as an indicator of structural changes initiated at the termini of amyloid proteins. Phys Chem Chem Phys 2019; 21:23931-23942. [PMID: 31661536 DOI: 10.1039/c9cp04648h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There is a growing body of experimental work showing that protein aggregates associated with amyloid fibrils feature intrinsic fluorescence. In order to understand the microscopic origin of this behavior observed in non-aromatic aggregates of peptides and proteins, we conducted a combined experimental and computational study on the optical properties of amyloid-derived oligopeptides in the near-UV region. We have focused on a few model systems having charged termini (zwitterionic) or acetylated termini. For the zwitterionic system, we were able to simulate the longer tail absorption in the near UV (250-350 nm), supporting the experimental results in terms of excitation spectra. We analyzed the optical excitations responsible for the low-energy absorption and found a large role played by charge-transfer states around the termini. These charge-transfer excitations are very sensitive to the conformation of the peptide and in realistic fibrils may involve inter and intra chain charge reorganization.
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Affiliation(s)
- Kwang Hyok Jong
- Condensed Matter and Statistical Physics, International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy.
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10
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Yang W, Tan P, Fu X, Hong L. Prediction of amyloid aggregation rates by machine learning and feature selection. J Chem Phys 2019; 151:084106. [PMID: 31470712 DOI: 10.1063/1.5113848] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A novel data-based machine learning algorithm for predicting amyloid aggregation rates is reported in this paper. Based on a highly nonlinear projection from 16 intrinsic features of a protein and 4 extrinsic features of the environment to the protein aggregation rate, a feedforward fully connected neural network (FCN) with one hidden layer is trained on a dataset composed of 21 different kinds of amyloid proteins and tested on 4 rest proteins. FCN shows a much better performance than traditional algorithms, such as multivariable linear regression and support vector regression, with an average accuracy higher than 90%. Furthermore, by the correlation analysis and the principal component analysis, seven key features, folding energy, HP patterns for helix, sheet and helices cross membrane, pH, ionic strength, and protein concentration, are shown to constitute a minimum feature set for characterizing the amyloid aggregation kinetics.
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Affiliation(s)
- Wuyue Yang
- Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing 100084, China
| | - Pengzhen Tan
- Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing 100084, China
| | - Xianjun Fu
- Institute for Literature and Culture of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Liu Hong
- Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing 100084, China
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11
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Stephens AD, Kaminski Schierle GS. The role of water in amyloid aggregation kinetics. Curr Opin Struct Biol 2019; 58:115-123. [DOI: 10.1016/j.sbi.2019.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 05/30/2019] [Accepted: 06/06/2019] [Indexed: 12/16/2022]
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12
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Xu Z, Zhang Q, Shi J, Zhu W. Underestimated Noncovalent Interactions in Protein Data Bank. J Chem Inf Model 2019; 59:3389-3399. [PMID: 31294978 DOI: 10.1021/acs.jcim.9b00258] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Noncovalent interactions (NCIs) play essential roles in the structure and function of biomacromolecules. There are various NCIs, e.g., hydrogen bonds (HBs), cation-π and π-π interactions, and ionic bonds, among which HBs are the most widespread and well-studied. By utilizing the ratio of the observed HBs over pseudo HBs (1.0 Å longer than the HB distance criteria without angle constraints), we demonstrated that HBs in both protein-ligand and protein-protein interfaces are overlooked in structures deposited in PDB. After the QM/MM optimization of 12 protein-ligand complexes, we showed that the overlooked HBs could be recovered. With a systematic search in the PDB, we found that the HB number per residue (NHB/R) in proteins decreases as structural resolution becomes lower, implying that HBs are overlooked even today, regardless of the type of refinement approach used. Similarly, cation-π, π-π, and ionic interactions were found to be significantly lost, manifesting the universal underestimation of various NCIs. Considering the vital role of NCIs, it is important to recover the NCIs to facilitate drug design, to explore protein-protein interaction, and to study protein structure and function.
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Affiliation(s)
- Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Qian Zhang
- Department of Computer Science and Technology , East China Normal University , Shanghai 200241 , China
| | - Jiye Shi
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China.,Open Studio for Druggability Research of Marine Natural Products , Pilot National Laboratory for Marine Science and Technology (Qingdao) , Qingdao 266237 , China
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13
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Lupia A, Moraca F, Bagetta D, Maruca A, Ambrosio FA, Rocca R, Catalano R, Romeo I, Talarico C, Ortuso F, Artese A, Alcaro S. Computer-based techniques for lead identification and optimization II: Advanced search methods. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2018-0114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
This paper focuses on advanced computational techniques for identifying and optimizing lead molecules, such as metadynamics and a novel dynamic 3D pharmacophore analysis method called Dynophores. In this paper, the first application of the funnel metadynamics of the Berberine binding to G-quadruplex DNA is depicted, disclosing hints for drug design, in particular clarifying water’s role and suggesting the design of derivatives able to replace the solvent-mediated interactions between ligand and DNA to achieve more potent and selective activity. Secondly, the novel dynamic pharmacophore approach is an extension of the classic 3D pharmacophores, with statistical and sequential information about the conformational flexibility of a molecular system derived from molecular dynamics (MD) simulations.
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Affiliation(s)
- Antonio Lupia
- Department of Health Sciences , University “Magna Græcia” of Catanzaro , Viale Europa , 88100 Catanzaro , Italy
- “Magna Græcia” University of Catanzaro , Net4Science Academic Spin-Off , “S. Venuta” Catanzaro , Italy
| | - Federica Moraca
- Department of Health Sciences , University “Magna Græcia” of Catanzaro , Viale Europa , 88100 Catanzaro , Italy
- Department of Chemical Sciences , University of Napoli Federico II , Via Cinthia 4 , I-80126 Napoli , Italy
- “Magna Græcia” University of Catanzaro , Net4Science Academic Spin-Off , “S. Venuta” Catanzaro , Italy
| | - Donatella Bagetta
- Department of Health Sciences , University “Magna Græcia” of Catanzaro , Viale Europa , 88100 Catanzaro , Italy
- “Magna Græcia” University of Catanzaro , Net4Science Academic Spin-Off , “S. Venuta” Catanzaro , Italy
| | - Annalisa Maruca
- Department of Health Sciences , University “Magna Græcia” of Catanzaro , Viale Europa , 88100 Catanzaro , Italy
- “Magna Græcia” University of Catanzaro , Net4Science Academic Spin-Off , “S. Venuta” Catanzaro , Italy
| | | | - Roberta Rocca
- Department of Health Sciences , University “Magna Græcia” of Catanzaro , Viale Europa , 88100 Catanzaro , Italy
- Department of Experimental and Clinical Medicine , Magna Graecia University and Translational Medicinal Oncology Unit, Salvatore Venuta University Campus , Catanzaro , Italy
- “Magna Græcia” University of Catanzaro , Net4Science Academic Spin-Off , “S. Venuta” Catanzaro , Italy
| | - Raffaella Catalano
- Department of Health Sciences , University “Magna Græcia” of Catanzaro , Viale Europa , 88100 Catanzaro , Italy
- “Magna Græcia” University of Catanzaro , Net4Science Academic Spin-Off , “S. Venuta” Catanzaro , Italy
| | - Isabella Romeo
- Department of Health Sciences , University “Magna Græcia” of Catanzaro , Viale Europa , 88100 Catanzaro , Italy
- “Magna Græcia” University of Catanzaro , Net4Science Academic Spin-Off , “S. Venuta” Catanzaro , Italy
| | - Carmine Talarico
- Department of Health Sciences , University “Magna Græcia” of Catanzaro , Viale Europa , 88100 Catanzaro , Italy
| | - Francesco Ortuso
- Department of Health Sciences , University “Magna Græcia” of Catanzaro , Viale Europa , 88100 Catanzaro , Italy
- “Magna Græcia” University of Catanzaro , Net4Science Academic Spin-Off , “S. Venuta” Catanzaro , Italy
| | - Anna Artese
- Department of Health Sciences , University “Magna Græcia” of Catanzaro , Viale Europa , 88100 Catanzaro , Italy
- “Magna Græcia” University of Catanzaro , Net4Science Academic Spin-Off , “S. Venuta” Catanzaro , Italy
| | - Stefano Alcaro
- Department of Health Sciences , University “Magna Græcia” of Catanzaro , Viale Europa , 88100 Catanzaro , Italy
- “Magna Græcia” University of Catanzaro , Net4Science Academic Spin-Off , “S. Venuta” Catanzaro , Italy
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14
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Rezaei Motlagh S, Harun R, Awang Biak DR, Hussain SA, Wan Ab Karim Ghani WA, Khezri R, Wilfred CD, Elgharbawy AAM. Screening of Suitable Ionic Liquids as Green Solvents for Extraction of Eicosapentaenoic Acid (EPA) from Microalgae Biomass Using COSMO-RS Model. Molecules 2019; 24:E713. [PMID: 30781457 PMCID: PMC6412376 DOI: 10.3390/molecules24040713] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/18/2019] [Accepted: 01/20/2019] [Indexed: 11/24/2022] Open
Abstract
Omega-3 poly unsaturated fatty acids (PUFA) particularly eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA), have many health benefits including reducing the risk of cancer and cardiovascular disease. Recently, the use of ionic liquids (ILs) in lipid extraction from microalgae provides the potential to overcome common drawbacks, offers several other benefits. To date, very limited researches are available to focus on extracting microalgae lipid and PUFA in particular by using ILs. The objective of current work is to screen the potential ILs that can be applied in EPA extraction. In this study, fast ILs screening was performed with the help of a conductor like screening model for real solvents (COSMO-RS) and the ILs with higher capacity values for use in extraction of EPA were compared. According to the results, the highest capacity for EPA extraction among 352 screened cation/anion combinations belongs to [TMAm][SO₄]. It is expected to achieve a higher yield of EPA once applying this combination as the solvent in the process of extraction. ILs with small anions were observed to have higher capacities, as well possessing higher charge density compared to larger ones, and therefore, they are more preferable for extraction purposes. Moreover, shorter alkyl chain cations are preferred when using imidazolium-based IL, which agrees with experimental data.
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Affiliation(s)
- Shiva Rezaei Motlagh
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University Putra Malaysia, UPM, Serdang, Selangor 43400, Malaysia.
| | - Razif Harun
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University Putra Malaysia, UPM, Serdang, Selangor 43400, Malaysia.
| | - Dayang Radiah Awang Biak
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University Putra Malaysia, UPM, Serdang, Selangor 43400, Malaysia.
| | - Siti Aslina Hussain
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University Putra Malaysia, UPM, Serdang, Selangor 43400, Malaysia.
| | - Wan Azlina Wan Ab Karim Ghani
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University Putra Malaysia, UPM, Serdang, Selangor 43400, Malaysia.
| | - Ramin Khezri
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University Putra Malaysia, UPM, Serdang, Selangor 43400, Malaysia.
| | - Cecilia Devi Wilfred
- Department of Fundamental and Applied Sciences, Centre of Research in Ionic Liquids (CORIL), Universiti Teknologi Petronas, UTP, Bandar Seri Iskandar, Perak 32610, Malaysia.
| | - Amal A M Elgharbawy
- International Institute for Halal Research and Training (INHART), International Islamic University Malaysia, Gombak, Kuala Lumpur 50728, Malaysia.
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15
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Jong K, Ansari N, Grisanti L, Hassanali A. Understanding the quantum mechanical properties of hydrogen bonds in solvated biomolecules from cluster calculations. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.05.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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16
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Jong K, Hassanali AA. A Data Science Approach to Understanding Water Networks Around Biomolecules: The Case of Tri-Alanine in Liquid Water. J Phys Chem B 2018; 122:7895-7906. [DOI: 10.1021/acs.jpcb.8b03644] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- KwangHyok Jong
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
- SISSA—Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy
- Department of Physics, Kim Il Sung University, Ryongnam Dong, Taesong District, Pyongyang, D. P. R. Korea
| | - Ali A. Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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17
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Dandekar R, Hassanali AA. Hierarchical lattice models of hydrogen-bond networks in water. Phys Rev E 2018; 97:062113. [PMID: 30011567 DOI: 10.1103/physreve.97.062113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Indexed: 06/08/2023]
Abstract
We develop a graph-based model of the hydrogen-bond network in water, with a view toward quantitatively modeling the molecular-level correlational structure of the network. The networks formed are studied by the constructing the model on two infinite-dimensional lattices. Our models are built bottom up, based on microscopic information coming from atomistic simulations, and we show that the predictions of the model are consistent with known results from ab initio simulations of liquid water. We show that simple entropic models can predict the correlations and clustering of local-coordination defects around tetrahedral waters observed in the atomistic simulations. We also find that orientational correlations between bonds are longer ranged than density correlations, determine the directional correlations within closed loops, and show that the patterns of water wires within these structures are also consistent with previous atomistic simulations. Our models show the existence of density and compressibility anomalies, as seen in the real liquid, and the phase diagram of these models is consistent with the singularity-free scenario previously proposed by Sastry and coworkers [Phys. Rev. E 53, 6144 (1996)1063-651X10.1103/PhysRevE.53.6144].
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Affiliation(s)
- Rahul Dandekar
- Condensed Matter and Statistical Physics Section, International Center for Theoretical Physics, Strada Costiera 11, Trieste, Italy
| | - Ali A Hassanali
- Condensed Matter and Statistical Physics Section, International Center for Theoretical Physics, Strada Costiera 11, Trieste, Italy
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18
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Jeszenői N, Schilli G, Bálint M, Horváth I, Hetényi C. Analysis of the influence of simulation parameters on biomolecule-linked water networks. J Mol Graph Model 2018; 82:117-128. [DOI: 10.1016/j.jmgm.2018.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/27/2018] [Accepted: 04/21/2018] [Indexed: 12/11/2022]
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19
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Vajda T, Perczel A. The impact of water on the ambivalent behavior and paradoxical phenomenon of the amyloid-β fibril protein. Biomol Concepts 2017; 8:213-220. [PMID: 29211680 DOI: 10.1515/bmc-2017-0027] [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: 08/24/2017] [Accepted: 10/20/2017] [Indexed: 11/15/2022] Open
Abstract
The crucial role of water in amyloid-β(Aβ) fibril proteins is evaluated in several ways including the water's thermodynamic and kinetic solvation effects. As regards the water's character, its hindered-rotation barriers are also considered. The following protein molecules considered here are: the Aβ40 (PDB ID: 2LMN), Aβ42 (PDB ID: 5KK3 and 2NAO) and the double-layered Aβ17-42 fibril. We discuss: (i) extracellular Aβ40 and Aβ42 fibril monomers exhibit an ambivalent propensity to transform into a helical form toward the N-term region and a β-strand-like form near the C-terminal; (ii) interfacial water molecules play a crucial role in protein-protein interactions, as molecular dynamics simulations have shown a significant impact on the protein-protein binding; (iii) it is shown that the spontaneous dimerization process of the Aβ42 fibril protein in water occurs via a two-step nucleation-accommodation mechanism; (iv) MD simulations of the double-layered Aβ17-42 fibril model show that the C↔C interface appears more energetically favorable than the N↔N interface due to large hydrophobic contacts; (v) the water's role in the HET-s prion and in the Aβ fibrillar aggregates; (vi) it was found that the monomer-oligomer equilibrium spontaneously dissociates into stable monomeric species when they are incubated up to 3 μm for a longer time (>1 week) in a physiological buffer.
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Wang L, Fried SD, Markland TE. Proton Network Flexibility Enables Robustness and Large Electric Fields in the Ketosteroid Isomerase Active Site. J Phys Chem B 2017; 121:9807-9815. [DOI: 10.1021/acs.jpcb.7b06985] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lu Wang
- Department
of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Stephen D. Fried
- Medical Research
Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Thomas E. Markland
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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21
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Bhattacharya A, Bhowmik S, Singh AK, Kodgire P, Das AK, Mukherjee TK. Direct Evidence of Intrinsic Blue Fluorescence from Oligomeric Interfaces of Human Serum Albumin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:10606-10615. [PMID: 28930631 DOI: 10.1021/acs.langmuir.7b02463] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The molecular origin behind the concentration-dependent intrinsic blue fluorescence of human serum albumin (HSA) is not known yet. This unusual blue fluorescence is believed to be a characteristic feature of amyloid-like fibrils of protein/peptide and originates due to the delocalization of peptide bond electrons through the extended hydrogen bond networks of cross-β-sheet structure. Herein, by combining the results of spectroscopy, size exclusion chromatography, native gel electrophoresis, and confocal microscopy, we have shown that the intrinsic blue fluorescence of HSA exclusively originates from oligomeric interfaces devoid of any amyloid-like fibrillar structure. Our study suggests that this low energy fluorescence band is not due to any particular residue/sequence, but rather it is a common feature of self-assembled peptide bonds. The present findings of intrinsic blue fluorescence from oligomeric interfaces pave the way for future applications of this unique visual phenomenon for early stage detection of various protein aggregation related human diseases.
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Affiliation(s)
- Arpan Bhattacharya
- Discipline of Chemistry, Indian Institute of Technology Indore , Khandwa Road, Indore 453552, Madhya Pradesh, India
| | - Soumitra Bhowmik
- Discipline of Chemistry, Indian Institute of Technology Indore , Khandwa Road, Indore 453552, Madhya Pradesh, India
| | - Amit K Singh
- Centre of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore , Khandwa Road, Indore 453552, Madhya Pradesh, India
| | - Prashant Kodgire
- Centre of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore , Khandwa Road, Indore 453552, Madhya Pradesh, India
| | - Apurba K Das
- Discipline of Chemistry, Indian Institute of Technology Indore , Khandwa Road, Indore 453552, Madhya Pradesh, India
| | - Tushar Kanti Mukherjee
- Discipline of Chemistry, Indian Institute of Technology Indore , Khandwa Road, Indore 453552, Madhya Pradesh, India
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