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Mamatkulov S, Polák J, Razzokov J, Tomaník L, Slavíček P, Dzubiella J, Kanduč M, Heyda J. Unveiling the Borohydride Ion through Force-Field Development. J Chem Theory Comput 2024; 20:1263-1273. [PMID: 38227434 PMCID: PMC10867804 DOI: 10.1021/acs.jctc.3c01020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/17/2024]
Abstract
The borohydride ion, BH4-, is an essential reducing agent in many technological processes, yet its full understanding has been elusive, because of at least two significant challenges. One challenge arises from its marginal stability in aqueous solutions outside of basic pH conditions, which considerably limits the experimental thermodynamic data. The other challenge comes from its unique and atypical hydration shell, stemming from the negative excess charge on its hydrogen atoms, which complicates the accurate modeling in classical atomistic simulations. In this study, we combine experimental and computer simulation techniques to devise a classical force field for NaBH4 and deepen our understanding of its characteristics. We report the first measurement of the ion's activity coefficient and extrapolate it to neutral pH conditions. Given the difficulties in directly measuring its solvation free energies, owing to its instability, we resort to quantum chemistry calculations. This combined strategy allows us to derive a set of nonpolarizable force-field parameters for the borohydride ion for classical molecular dynamics simulations. The derived force field simultaneously captures the solvation free energy, the hydration structure, as well as the activity coefficient of NaBH4 salt across a broad concentration range. The obtained insights into the hydration shell of the BH4- ion are crucial for accurately modeling and understanding its interactions with other molecules, ions, materials, and interfaces.
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Affiliation(s)
- Shavkat Mamatkulov
- Institute
of Material Science of AS, Ch.Aytmatov str.2B, 100084 Tashkent, Uzbekistan
| | - Jakub Polák
- Department
of Physical Chemistry, University of Chemistry
and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Jamoliddin Razzokov
- Institute
of Fundamental and Applied Research, National
Research University TIIAME, Kori Niyoziy 39, 100000 Tashkent, Uzbekistan
- School
of Engineering, Akfa University, Milliy Bog Street 264, 111221 Tashkent, Uzbekistan
| | - Lukáš Tomaník
- Department
of Physical Chemistry, University of Chemistry
and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Petr Slavíček
- Department
of Physical Chemistry, University of Chemistry
and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Joachim Dzubiella
- Applied
Theoretical Physics–Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Str. 3, D-79104 Freiburg, Germany
| | - Matej Kanduč
- Jožef
Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Jan Heyda
- Department
of Physical Chemistry, University of Chemistry
and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
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Zahra AT, Shahzad A, Manzoor A, Razzokov J, Asif QUA, Luo K, Ren G. Structural and thermal analyses in semiconducting and metallic zigzag single-walled carbon nanotubes using molecular dynamics simulations. PLoS One 2024; 19:e0296916. [PMID: 38335221 PMCID: PMC10857726 DOI: 10.1371/journal.pone.0296916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/17/2023] [Indexed: 02/12/2024] Open
Abstract
Equilibrium molecular dynamics (EMD) simulations have been performed to investigate the structural analysis and thermal conductivity (λ) of semiconducting (8,0) and metallic (12,0) zigzag single-walled carbon nanotubes (SWCNTs) for varying ±γ(%) strains. For the first time, the present outcomes provide valuable insights into the relationship between the structural properties of zigzag SWCNTs and corresponding thermal behavior, which is essential for the development of high-performance nanocomposites. The radial distribution function (RDF) has been employed to assess the buckling and deformation understandings of the (8,0) and (12,0) SWCNTs for a wide range of temperature T(K) and varying ±γ(%) strains. The visualization of SWCNTs shows that the earlier buckling and deformation processes are observed for semiconducting SWCNTs as compared to metallic SWCNTs for high T(K) and it also evident through an abrupt increase in RDF peaks. The RDF and visualization analyses demonstrate that the (8,0) SWCNTs can more tunable under compressive than tensile strains, however, the (12,0) zigzag SWCNTs indicate an opposite trend and may tolerate more tensile than compressive strains. Investigations show that the tunable domain of ±γ(%) strains decreases from (-10%≤ γ ≤+19%) to (-5%≤ γ ≤+10%) for (8,0) SWCNTs and the buckling process shifts to lower ±γ(%) for (12,0) SWCNTs with increasing T(K). For intermediate-high T(K), the λ(T) of (12,0) SWCNTs is high but the (8,0) SWCNTs show certainly high λ(T) for low T(K). The present λ(T, ±γ) data are in reasonable agreement with parts of previous NEMD, GK-HNEMD data and experimental investigations with simulation results generally under predicting the λ(T, ±γ) by the ∼1% to ∼20%, regardless of the ±γ(%) strains, depending on T(K). Our simulation data significantly expand the strain range to -10% ≤ γ ≤ +19% for both zigzag SWCNTs, depending on temperature T(K). This extension of the range aims to establish a tunable regime and delve into the intrinsic characteristics of zigzag SWCNTs, building upon previous work.
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Affiliation(s)
- Ama tul Zahra
- Modeling and Simulation Laboratory, Department of Physics, Government College University Faisalabad, Faisalabad, Punjab, Pakistan
| | - Aamir Shahzad
- Modeling and Simulation Laboratory, Department of Physics, Government College University Faisalabad, Faisalabad, Punjab, Pakistan
| | - Alina Manzoor
- Modeling and Simulation Laboratory, Department of Physics, Government College University Faisalabad, Faisalabad, Punjab, Pakistan
| | - Jamoliddin Razzokov
- Institute of Fundamental and Applied Research, National Research University TIIAME, Tashkent, Uzbekistan
- College of Engineering, Central Asian University, Tashkent, Uzbekistan
- Department of Biomedical Engineering, Tashkent State, Technical University, Tashkent, Uzbekistan
| | - Qurat ul Ain Asif
- Modeling and Simulation Laboratory, Department of Physics, Government College University Faisalabad, Faisalabad, Punjab, Pakistan
| | - Kun Luo
- School of Materials Science and Engineering, Changzhou University, Changzhou, P R China
| | - Guogang Ren
- School of Physics, Engineering and Computer Sciences, University of Hertfordshire, Hatfield, United Kingdom
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Rezaei M, Ghasemitarei M, Razzokov J, Yusupov M, Ghorbanalilu M, Ejtehadi MR. In silico study of the impact of oxidation on pyruvate transmission across the hVDAC1 protein channel. Arch Biochem Biophys 2024; 751:109835. [PMID: 38000492 DOI: 10.1016/j.abb.2023.109835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/25/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
The overexpression of voltage dependent anion channels (VDACs), particularly VDAC1, in cancer cells compared to normal cells, plays a crucial role in cancer cell metabolism, apoptosis regulation, and energy homeostasis. In this study, we used molecular dynamics (MD) simulations to investigate the effect of a low level of VDAC1 oxidation (induced e.g., by cold atmospheric plasma (CAP)) on the pyruvate (Pyr) uptake by VDAC1. Inhibiting Pyr uptake through VDAC1 can suppress cancer cell proliferation. Our primary target was to study the translocation of Pyr across the native and oxidized forms of hVDAC1, the human VDAC1. Specifically, we employed MD simulations to analyze the hVDAC1 structure by modifying certain cysteine residues to cysteic acids and methionine residues to methionine sulfoxides, which allowed us to investigate the effect of oxidation. Our results showed that the free energy barrier for Pyr translocation through the native and oxidized channel was approximately 4.3 ± 0.7 kJ mol-1 and 10.8 ± 1.8 kJ mol-1, respectively. An increase in barrier results in a decrease in rate of Pyr permeation through the oxidized channel. Thus, our results indicate that low levels of CAP oxidation reduce Pyr translocation, resulting in decreased cancer cell proliferation. Therefore, low levels of oxidation are likely sufficient to treat cancer cells given the inhibition of Pyr uptake.
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Affiliation(s)
- Mahsa Rezaei
- Department of Physics, Shahid Beheshti University, Tehran, 19839-69411, Iran
| | - Maryam Ghasemitarei
- Department of Physics, Sharif University of Technology, 14588-89694, Tehran, Iran; Research Group PLASMANT, Department of Chemistry, University of Antwerp, 2610, Antwerp, Belgium.
| | - Jamoliddin Razzokov
- Institute of Fundamental and Applied Research, National Research University TIIAME, 100000, Tashkent, Uzbekistan; School of Engineering, Central Asian University, Tashkent, 111221, Uzbekistan; Laboratory of Experimental Biophysics, Centre for Advanced Technologies, 100174, Tashkent, Uzbekistan; Department of Chemistry, Termez State University, 190111, Termez, Uzbekistan
| | - Maksudbek Yusupov
- School of Engineering, New Uzbekistan University, 100000, Tashkent, Uzbekistan; Department of Information Technologies, Tashkent International University of Education, 100207, Tashkent, Uzbekistan; Laboratory of Thermal Physics of Multiphase Systems, Arifov Institute of Ion-Plasma and Laser Technologies, Academy of Sciences of Uzbekistan, 100125, Tashkent, Uzbekistan; Department of Power Supply and Renewable Energy Sources, National Research University TIIAME, 100000, Tashkent, Uzbekistan
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Mir SA, Razzokov J, Mukherjee V, Baitharu I, Nayak B. An exploration of the binding prediction of anatoxin-a and atropine to acetylcholinesterase enzyme using multi-level computer simulations. Phys Biol 2023; 21:016002. [PMID: 37963412 DOI: 10.1088/1478-3975/ad0caa] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 11/14/2023] [Indexed: 11/16/2023]
Abstract
Acetylcholinesterase (AChE) is crucial for the breakdown of acetylcholine to acetate and choline, while the inhibition of AChE by anatoxin-a (ATX-a) results in severe health complications. This study explores the structural characteristics of ATX-a and its interactions with AChE, comparing to the reference molecule atropine for binding mechanisms. Molecular docking simulations reveal strong binding affinity of both ATX-a and atropine to AChE, interacting effectively with specific amino acids in the binding site as potential inhibitors. Quantitative assessment using the MM-PBSA method demonstrates a significantly negative binding free energy of -81.659 kJ mol-1for ATX-a, indicating robust binding, while atropine exhibits a stronger binding affinity with a free energy of -127.565 kJ mol-1. Umbrella sampling calculates the ΔGbindvalues to evaluate binding free energies, showing a favorable ΔGbindof -36.432 kJ mol-1for ATX-a and a slightly lower value of -30.12 kJ mol-1for atropine. This study reveals the dual functionality of ATX-a, acting as both a nicotinic acetylcholine receptor agonist and an AChE inhibitor. Remarkably, stable complexes form between ATX-a and atropine with AChE at its active site, exhibiting remarkable binding free energies. These findings provide valuable insights into the potential use of ATX-a and atropine as promising candidates for modulating AChE activity.
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Affiliation(s)
| | - Jamoliddin Razzokov
- Institute of Fundamental and Applied Research, National Research University TIIAME, Kori Niyoziy 39, Tashkent 100000, Uzbekistan
- School of Engineering, Central Asian University, Milliy Bog Street 264, Tashkent 111221, Uzbekistan
- Laboratory of Experimental Biophysics, Centre for Advanced Technologies, Tashkent 100174, Uzbekistan
- Department of Chemistry, Termez State University, Barkamol Avlod Street 43, Termez 190111, Uzbekistan
| | | | - Iswar Baitharu
- Department of Environmental Sciences, Sambalpur University, Odisha 768019, India
| | - Binata Nayak
- School of Life Sciences, Sambalpur University, Odisha 768019, India
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Saidov K, Razzokov J, Parpiev O, Yüzbasi NS, Kovalska N, Blugan G, Ruzimuradov O. Formation of Highly Conductive Interfaces in Crystalline Ionic Liquid-Gated Unipolar MoTe 2/h-BN Field-Effect Transistor. Nanomaterials (Basel) 2023; 13:2559. [PMID: 37764588 PMCID: PMC10536122 DOI: 10.3390/nano13182559] [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] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/06/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023]
Abstract
2H MoTe2 (molybdenum ditelluride) has generated significant interest because of its superconducting, nonvolatile memory, and semiconducting of new materials, and it has a large range of electrical properties. The combination of transition metal dichalcogenides (TMDCs) and two dimensional (2D) materials like hexagonal boron nitride (h-BN) in lateral heterostructures offers a unique platform for designing and engineering novel electronic devices. We report the fabrication of highly conductive interfaces in crystalline ionic liquid-gated (ILG) field-effect transistors (FETs) consisting of a few layers of MoTe2/h-BN heterojunctions. In our initial exploration of tellurium-based semiconducting TMDs, we directed our attention to MoTe2 crystals with thicknesses exceeding 12 nm. Our primary focus centered on investigating the transport characteristics and quantitatively assessing the surface interface heterostructure. Our transconductance (gm) measurements indicate that the very efficient carrier modulation with an ILG FET is two times larger than standard back gating, and it demonstrates unipolarity of the device. The ILG FET exhibited highly unipolar p-type behavior with a high on/off ratio, and it significantly increased the mobility in MoTe2/h-BN heterochannels, achieving improvement as one of the highest recorded mobility increments. Specifically, we observed hole and electron mobility values ranging from 345 cm2 V-1 s-1 to 285 cm2 V-1 s-1 at 80 K. We predict that our ability to observe the intrinsic, heterointerface conduction in the channels was due to a drastic reduction of the Schottky barriers, and electrostatic gating is suggested as a method for controlling the phase transitions in the few layers of TMDC FETs. Moreover, the simultaneous structural phase transitions throughout the sample, achieved through electrostatic doping control, presents new opportunities for developing phase change devices using atomically thin membranes.
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Affiliation(s)
- Kamoladdin Saidov
- Department of Electronics and Radio Engineering, Tashkent University of Information Technologies, Tashkent 100200, Uzbekistan
- Department of Information Technologies, Tashkent International University of Education, Tashkent 100207, Uzbekistan
- Department of Electrical and Computer Engineering, Ajou University in Tashkent, Tashkent 100204, Uzbekistan
| | - Jamoliddin Razzokov
- R&D Center, New Uzbekistan University, Tashkent 100007, Uzbekistan;
- School of Engineering, Central Asian University, Tashkent 111221, Uzbekistan
- Institute of Fundamental and Applied Research, National Research University TIIAME, Tashkent 100000, Uzbekistan
| | - Odilkhuja Parpiev
- Material Sciences Institute, Academy of Sciences of the Republic of Uzbekistan, Tashkent 100084, Uzbekistan;
| | - Nur Sena Yüzbasi
- Laboratory for High Performance Ceramics, Empa, Swiss Federal Laboratories for Materials Science and Technology, 8600 Dübendorf, Switzerland; (N.S.Y.); (N.K.)
| | - Natalia Kovalska
- Laboratory for High Performance Ceramics, Empa, Swiss Federal Laboratories for Materials Science and Technology, 8600 Dübendorf, Switzerland; (N.S.Y.); (N.K.)
| | - Gurdial Blugan
- Laboratory for High Performance Ceramics, Empa, Swiss Federal Laboratories for Materials Science and Technology, 8600 Dübendorf, Switzerland; (N.S.Y.); (N.K.)
| | - Olim Ruzimuradov
- Department of Natural and Mathematic Sciences, Turin Polytechnic University in Tashkent, Tashkent 100095, Uzbekistan
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Abduvokhidov D, Yusupov M, Shahzad A, Attri P, Shiratani M, Oliveira MC, Razzokov J. Unraveling the Transport Properties of RONS across Nitro-Oxidized Membranes. Biomolecules 2023; 13:1043. [PMID: 37509079 PMCID: PMC10377474 DOI: 10.3390/biom13071043] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/13/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023] Open
Abstract
The potential of cold atmospheric plasma (CAP) in biomedical applications has received significant interest, due to its ability to generate reactive oxygen and nitrogen species (RONS). Upon exposure to living cells, CAP triggers alterations in various cellular components, such as the cell membrane. However, the permeation of RONS across nitrated and oxidized membranes remains understudied. To address this gap, we conducted molecular dynamics simulations, to investigate the permeation capabilities of RONS across modified cell membranes. This computational study investigated the translocation processes of less hydrophilic and hydrophilic RONS across the phospholipid bilayer (PLB), with various degrees of oxidation and nitration, and elucidated the impact of RONS on PLB permeability. The simulation results showed that less hydrophilic species, i.e., NO, NO2, N2O4, and O3, have a higher penetration ability through nitro-oxidized PLB compared to hydrophilic RONS, i.e., HNO3, s-cis-HONO, s-trans-HONO, H2O2, HO2, and OH. In particular, nitro-oxidation of PLB, induced by, e.g., cold atmospheric plasma, has minimal impact on the penetration of free energy barriers of less hydrophilic species, while it lowers these barriers for hydrophilic RONS, thereby enhancing their translocation across nitro-oxidized PLB. This research contributes to a better understanding of the translocation abilities of RONS in the field of plasma biomedical applications and highlights the need for further analysis of their role in intracellular signaling pathways.
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Affiliation(s)
- Davronjon Abduvokhidov
- Institute of Fundamental and Applied Research, National Research University TIIAME, Kori Niyoziy 39, Tashkent 100000, Uzbekistan
- Department of Information Technologies, Tashkent International University of Education, Imom Bukhoriy 6, Tashkent 100207, Uzbekistan
- Institute of Material Sciences, Academy of Sciences, Chingiz Aytmatov 2b, Tashkent 100084, Uzbekistan
| | - Maksudbek Yusupov
- R&D Center, New Uzbekistan University, Mustaqillik Avenue 54, Tashkent 100007, Uzbekistan
- Department of Power Supply and Renewable Energy Sources, National Research University TIIAME, Kori Niyoziy 39, Tashkent 100000, Uzbekistan
- Laboratory of Thermal Physics of Multiphase Systems, Arifov Institute of Ion-Plasma and Laser Technologies, Academy of Sciences of Uzbekistan, Tashkent 100125, Uzbekistan
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Aamir Shahzad
- Modeling and Simulation Laboratory, Department of Physics, Government College University Faisalabad (GCUF), Allama Iqbal Road, Faisalabad 38040, Pakistan
| | - Pankaj Attri
- Center of Plasma Nano-Interface Engineering, Kyushu University, Fukuoka 819-0395, Japan
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Masaharu Shiratani
- Center of Plasma Nano-Interface Engineering, Kyushu University, Fukuoka 819-0395, Japan
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Maria C Oliveira
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Jamoliddin Razzokov
- Institute of Fundamental and Applied Research, National Research University TIIAME, Kori Niyoziy 39, Tashkent 100000, Uzbekistan
- School of Engineering, Akfa University, Milliy Bog Street 264, Tashkent 111221, Uzbekistan
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Kari S, Murugesan A, Thiyagarajan R, Kidambi S, Razzokov J, Selvaraj C, Kandhavelu M, Marimuthu P. Bias-force guided simulations combined with experimental validations towards GPR17 modulators identification. Biomed Pharmacother 2023; 160:114320. [PMID: 36716660 DOI: 10.1016/j.biopha.2023.114320] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/17/2023] [Accepted: 01/26/2023] [Indexed: 01/29/2023] Open
Abstract
Glioblastoma Multiforme (GBM) is known to be by far the most aggressive brain tumor to affect adults. The median survival rate of GBM patient's is < 15 months, while the GBM cells aggressively develop resistance to chemo- and radiotherapy with their self-renewal capacity which suggests the pressing need to develop novel preventative measures. We have recently proved that GPR17 -an orphan G protein-coupled receptor- is highly expressed on the GBM cell surface and it has a vital role to play in the disease progression. Despite the progress made on GBM downregulation, there still remain difficulties in developing a promising modulator for GPR17, till date. Here, we have performed robust virtual screening combined with biased-force pulling molecular dynamic (MD) simulations to predict high-affinity GPR17 modulators followed by experimental validation. Initially, the database containing 1379 FDA-approved drugs were screened against the orthosteric binding pocket of the GPR17. The external bias-potentials were then applied to the screened hits during the MD simulations which enabled to predict a spectrum of rupture peak force values that were used to select four approved drugs -ZINC000003792417 (Sacubitril), ZINC000014210457 (Victrelis), ZINC000001536109 (Pralatrexate) and ZINC000003925861 (Vorapaxar)- as top hits. The hits selected turns out to demonstrate unique dissociation pathways, interaction pattern, and change in polar network over time. Subsequently the selected hits with GPR17 were measured by inhibiting the forskolin-stimulated cAMP accumulation in GBM cell lines, LN229 and SNB19. The ex vivo validations shows that Sacubitril drug can act as a full agonist, while Vorapaxar functions as a partial agonist for GPR17. The pEC50 of Sacubitril was identified as 4.841 and 4.661 for LN229 and SNB19, respectively. Small interference of the RNA (siRNA)- silenced the GPR17 to further validate the targeted binding of Sacubitril with GPR17. In the current investigation, we have identified new repurposable GPR17 specific drugs which are likely to increase the opportunity to treat orphan deadly diseases.
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Affiliation(s)
- Sana Kari
- Molecular Signaling Group, Faculty of Medicine and Health Technology, Tampere University and BioMediTech, P.O.Box 553, 33101 Tampere, Finland
| | - Akshaya Murugesan
- Molecular Signaling Group, Faculty of Medicine and Health Technology, Tampere University and BioMediTech, P.O.Box 553, 33101 Tampere, Finland
| | - Ramesh Thiyagarajan
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Kingdom of Saudi Arabia
| | - Srivatsan Kidambi
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, 820 N 16th Street, 207 Othmer Hall, NE 68588, USA
| | - Jamoliddin Razzokov
- Institute of Fundamental and Applied Research, National Research University TIIAME, Kori Niyoziy 39, 100000 Tashkent, Uzbekistan; College of Engineering, Akfa University, Milliy Bog Street 264, 111221 Tashkent, Uzbekistan; Institute of Material Sciences, Academy of Sciences, Chingiz Aytmatov 2b, 100084 Tashkent, Uzbekistan; Department of Physics, National University of Uzbekistan, Universitet 4, 100174 Tashkent, Uzbekistan; Laboratory of Experimental Biophysics, Centre for Advanced Technologies, Universitet 7, 100174 Tashkent, Uzbekistan
| | - Chandrabose Selvaraj
- Department of Biotechnology, Division of Research and Innovation, Saveetha School of Engineering, SIMATS, Chennai 602105, Tamil Nadu, India
| | - Meenakshisundaram Kandhavelu
- Molecular Signaling Group, Faculty of Medicine and Health Technology, Tampere University and BioMediTech, P.O.Box 553, 33101 Tampere, Finland.
| | - Parthiban Marimuthu
- Pharmaceutical Science Laboratory (PSL - Pharmacy) and Structural Bioinformatics Laboratory (SBL - Biochemistry), Faculty of Science and Engineering, Åbo Akademi University, FI-20520 Turku, Finland.
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Razzokov J, Fazliev S, Makhkamov M, Marimuthu P, Baev A, Kurganov E. Effect of Electric Field on α-Synuclein Fibrils: Revealed by Molecular Dynamics Simulations. Int J Mol Sci 2023; 24:ijms24076312. [PMID: 37047286 PMCID: PMC10094641 DOI: 10.3390/ijms24076312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/24/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The self-association of amylogenic proteins to the fibril form is considered a pivotal factor in the pathogenesis of neurodegenerative diseases, including Parkinson’s disease (PD). PD causes unintended or uncontrollable movements in its common symptoms. α-synuclein is the major cause of PD development and thus has been the main target of numerous studies to suppress and sequester its expression or effectively degrade it. Nonetheless, to date, there are no efficient and proven ways to prevent pathological protein aggregation. Recent investigations proposed applying an external electric field to interrupt the fibrils. This method is a non-invasive approach that has a certain benefit over others. We performed molecular dynamics (MD) simulations by applying an electric field on highly toxic fibrils of α-synuclein to gain a molecular-level insight into fibril disruption mechanisms. The results revealed that the applied external electric field induces substantial changes in the conformation of the α-synuclein fibrils. Furthermore, we show the threshold value for electric field strength required to completely disrupt the α-synuclein fibrils by opening the hydrophobic core of the fibril. Thus, our findings might serve as a valuable foundation to better understand molecular-level mechanisms of the α-synuclein fibrils disaggregation process under an applied external electric field.
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Affiliation(s)
- Jamoliddin Razzokov
- Institute of Fundamental and Applied Research, National Research University TIIAME, Kori Niyoziy 39, Tashkent 100000, Uzbekistan
- R&D Center, New Uzbekistan University, Mustaqillik Avenue 54, Tashkent 100007, Uzbekistan
- Institute of Material Sciences, Academy of Sciences, Chingiz Aytmatov 2b, Tashkent 100084, Uzbekistan
- Department of Physics, National University of Uzbekistan, Universitet 4, Tashkent 100174, Uzbekistan
- Correspondence: ; Tel.: +998-90-116-23-20
| | - Sunnatullo Fazliev
- Max Planck School Matter to Life, Jahnstrasse 29, 69120 Heidelberg, Germany
- Faculty of Engineering Sciences, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Mukhriddin Makhkamov
- Laboratory of Experimental Biophysics, Centre for Advanced Technologies, Tashkent 100174, Uzbekistan
| | - Parthiban Marimuthu
- Pharmaceutical Science Laboratory (PSL–Pharmacy) and Structural Bioinformatics Laboratory (SBL–Biochemistry), Faculty of Science and Engineering, Åbo Akademi University, FI-20520 Turku, Finland
| | - Artyom Baev
- Laboratory of Experimental Biophysics, Centre for Advanced Technologies, Tashkent 100174, Uzbekistan
- Department of Biophysics, Biological Faculty, National University of Uzbekistan, Universitet 4, Tashkent 100174, Uzbekistan
| | - Erkin Kurganov
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Fazliev S, Tursunov K, Razzokov J, Sharipov A. Escin's Multifaceted Therapeutic Profile in Treatment and Post-Treatment of Various Cancers: A Comprehensive Review. Biomolecules 2023; 13:biom13020315. [PMID: 36830684 PMCID: PMC9952945 DOI: 10.3390/biom13020315] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/30/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Although modern medicine is advancing at an unprecedented rate, basic challenges in cancer treatment and drug resistance remain. Exploiting natural-product-based drugs is a strategy that has been proven over time to provide diverse and efficient approaches in patient care during treatment and post-treatment periods of various diseases, including cancer. Escin-a plant-derived triterpenoid saponin-is one example of natural products with a broad therapeutic scope. Initially, escin was proven to manifest potent anti-inflammatory and anti-oedematous effects. However, in the last two decades, other novel activities of escin relevant to cancer treatment have been reported. Recent studies demonstrated escin's efficacy in compositions with other approved drugs to accomplish synergy and increased bioavailability to broaden their apoptotic, anti-metastasis, and anti-angiogenetic effects. Here, we comprehensively discuss and present an overview of escin's chemistry and bioavailability, and highlight its biological activities against various cancer types. We conclude the review by presenting possible future directions of research involving escin for medical and pharmaceutical applications as well as for basic research.
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Affiliation(s)
- Sunnatullo Fazliev
- Max Planck School Matter to Life, Jahnstrasse 29, 69120 Heidelberg, Germany
- Faculty of Engineering Sciences, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Khurshid Tursunov
- Department of Inorganic, Physical and Colloidal Chemistry, Tashkent Pharmaceutical Institute, Oybek Street 45, Tashkent 100015, Uzbekistan
- State Center for Expertise and Standardization of Medicines, Medical Devices and Medical Equipment, Agency for the Development of the Pharmaceutical Industry under the Ministry of Health of the Republic of Uzbekistan, Ozod Street 16, Tashkent 100002, Uzbekistan
| | - Jamoliddin Razzokov
- Institute of Fundamental and Applied Research, National Research University TIIAME, Kori Niyoziy 39, Tashkent 100000, Uzbekistan
- College of Engineering, Akfa University, Milliy Bog Street 264, Tashkent 111221, Uzbekistan
- Department of Physics, National University of Uzbekistan, Universitet 4, Tashkent 100174, Uzbekistan
- Laboratory of Experimental Biophysics, Centre for Advanced Technologies, Universitet 7, Tashkent 100174, Uzbekistan
| | - Avez Sharipov
- Department of Inorganic, Physical and Colloidal Chemistry, Tashkent Pharmaceutical Institute, Oybek Street 45, Tashkent 100015, Uzbekistan
- Department of Analytical and Pharmaceutical Chemistry, Institute of Pharmaceutical Education and Research, Yunusota Street 46, Tashkent 100114, Uzbekistan
- Correspondence:
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10
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Shahzad A, Khan IA, Manzoor A, Kashif M, Ahsan M, He M, Razzokov J. Synthesis of nickel nanowires (Ni-NWs) as high ferromagnetic material by electrodeposition technique. Heliyon 2022; 9:e12576. [PMID: 36699268 PMCID: PMC9868378 DOI: 10.1016/j.heliyon.2022.e12576] [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: 08/16/2022] [Revised: 11/14/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022] Open
Abstract
Metallic nanowires (NWs) and their different compounds display incredible prospects for their use in various applications including media storage, sensor and solar cell devices along with the biological drug delivery systems. In this research work, the metallic NWs like nickel nanowires (Ni-NWs) are synthesized successfully by employing electrodeposition process. Anodic aluminum oxide (AAO) templates are employed as a platform with copper metal coating which acts as an active cathode. The synthesized Ni-NWs are examined through various characterization techniques including X-ray diffraction (XRD), scanning electron microscope (SEM) and vibrating sample magnetometer (VSM) to study the crystal structure, surface morphology and magnetic properties, respectively. The XRD analysis shows the development of various diffraction planes like Ni (111), Ni (200), Ni (220) which confirms the formation of polycrystalline nickel NWs. The SEM analysis reveals that the range of diameter and length of nickel NWs are found to be ∼160 to 200 and ∼4 to 11 micron respectively showing high aspect ratio (ranged from ∼200 to 300). The ferromagnetic behavior of Ni-NWs is confirmed by the hysteresis loop carried out for parallel and perpendicular configurations having Hc = 100 and 206 Oe, respectively. The obtained results suggest that the synthesized Ni- NWs may be used for high-density media storage devices.
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Affiliation(s)
- Aamir Shahzad
- Department of Physics, Government College University Faisalabad (GCUF), Allama Iqbal Road, Faisalabad 38040, Pakistan,Corresponding author.
| | - Ijaz Ahmad Khan
- Department of Physics, Government College University Faisalabad (GCUF), Allama Iqbal Road, Faisalabad 38040, Pakistan
| | - Alina Manzoor
- Department of Physics, Government College University Faisalabad (GCUF), Allama Iqbal Road, Faisalabad 38040, Pakistan
| | - Muhammad Kashif
- Department of Physics, Government College University Faisalabad (GCUF), Allama Iqbal Road, Faisalabad 38040, Pakistan
| | - Muhammad Ahsan
- Department of Physics, Government College University Faisalabad (GCUF), Allama Iqbal Road, Faisalabad 38040, Pakistan
| | - Maogang He
- Key Laboratory of Thermo-Fluid Science and Engineering, Ministry of Education (MOE), Xi’an Jiaotong University, Xi’an 710049, P. R. China
| | - Jamoliddin Razzokov
- Institute of Fundamental and Applied Research, National Research University TIIAME, Kori Niyoziy 39, 100000 Tashkent, Uzbekistan
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11
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Sharipov A, Boboev Z, Fazliev S, Gulyamov S, Yunuskhodjayev A, Razzokov J. Development of an Improved Method for the Determination of Iodine/β-Cyclodextrin by Means of HPLC-UV: Validation and the Thyroid-Stimulating Activity Revealed by In Vivo Studies. Pharmaceutics 2021; 13:pharmaceutics13070955. [PMID: 34201915 PMCID: PMC8309194 DOI: 10.3390/pharmaceutics13070955] [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: 05/31/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 12/02/2022] Open
Abstract
Iodine, being an intrinsic part of thyroid hormones, is a vital microelement required for normal growth and development, particularly in children. Inadequate daily intake of iodine causes iodine deficiency, which is responsible for several health disorders, such as cretinism and goiters. Therefore, the development of new drugs and/or food supplements for iodine deficiency is crucial. We synthesized an iodine/β-cyclodextrin complex based on a host–guest model, and in this paper, we outline the development of a new quantitative analysis method. We suggest a robust and reliable high-performance liquid chromatography method to determine the total amount of iodine species in the complex. Moreover, we performed validation of our method. The results of validation presented here show the reliability, accuracy and high precision of the method. Furthermore, for the first time, we show results of in vivo studies for the thyroid-stimulating activity of the iodine/β-cyclodextrin complex. Our findings indicate that the thyroid-stimulating activity of iodine/β-cyclodextrin is comparable to that of potassium iodide, which is the main active pharmaceutical substance of conventional drugs for iodine deficiency.
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Affiliation(s)
- Avez Sharipov
- Department of Inorganic, Physical and Colloidal Chemistry, Tashkent Pharmaceutical Institute, Oybek Street 45, Tashkent 100015, Uzbekistan; (A.S.); (Z.B.); (S.G.)
| | - Zufar Boboev
- Department of Inorganic, Physical and Colloidal Chemistry, Tashkent Pharmaceutical Institute, Oybek Street 45, Tashkent 100015, Uzbekistan; (A.S.); (Z.B.); (S.G.)
- Medical Devices and Medical Equipment, State Centre of Expertize and Standardization of Medicines, Tashkent 100002, Uzbekistan
| | - Sunnatullo Fazliev
- Max Planck School Matter to Life, Jahnstraße 29, 69120 Heidelberg, Germany;
- Faculty of Chemistry and Earth Sciences, Heidelberg University, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
| | - Shokhid Gulyamov
- Department of Inorganic, Physical and Colloidal Chemistry, Tashkent Pharmaceutical Institute, Oybek Street 45, Tashkent 100015, Uzbekistan; (A.S.); (Z.B.); (S.G.)
- College of Pharmacy, Chungbuk National University, 194-21, Osongsaengmyeong 1-ro, OSONG-Eup, Heungdeok-gu, Cheongju City 28160, Chungbuk, Korea
| | | | - Jamoliddin Razzokov
- Department of Inorganic, Physical and Colloidal Chemistry, Tashkent Pharmaceutical Institute, Oybek Street 45, Tashkent 100015, Uzbekistan; (A.S.); (Z.B.); (S.G.)
- Department of Physics and Chemistry, Tashkent Institute of Irrigation and Agricultural Mechanization Engineers, Kori Niyoziy 39, Tashkent 100000, Uzbekistan
- Department of Physics, National University of Uzbekistan, Tashkent 100174, Uzbekistan
- Institute of Material Sciences, Academy of Sciences, Chingiz Aytmatov 2b, Tashkent 100084, Uzbekistan
- College of Engineering, Akfa University, Kichik Halqa Yuli Street 17, Tashkent 100095, Uzbekistan
- Correspondence:
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Sharipov A, Tursunov K, Fazliev S, Azimova B, Razzokov J. Hypoglycemic and Anti-Inflammatory Effects of Triterpene Glycoside Fractions from Aeculus hippocastanum Seeds. Molecules 2021; 26:molecules26133784. [PMID: 34206308 PMCID: PMC8270310 DOI: 10.3390/molecules26133784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/07/2021] [Accepted: 06/14/2021] [Indexed: 11/30/2022] Open
Abstract
Horse chestnut (Aesculus hippocastanum L.)-derived drugs have shown their potential in biomedical applications. The seed of A. hippocastanum contains various kinds of chemical compounds including phenolics, flavonoids, coumarins, and triterpene saponins. Here, we investigated the chemical components in A. hippocastanum L. grown in Uzbekistan, which has not yet been studied in detail. We identified 30 kinds of triterpene saponins in an extract of A. hippocastanum L. Classifying extracted saponins into eight fractions, we next studied the hypoglycemic and the anti-inflammatory activities of escin and its derivatives through in vivo experiments. We came by data indicating the highest (SF-1 and SF-2) and the lowest (SF-5 and SF-8) antidiabetic and anti-inflammatory effects of those eight fractions. These results imply the prospective use of A. hippocastanum L. grown in Uzbekistan in the production of pharmaceutical drugs to treat diabetes and inflammation.
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Affiliation(s)
- Avez Sharipov
- Department of Inorganic, Physical and Colloidal Chemistry, Tashkent Pharmaceutical Institute, Oybek Street 45, Tashkent 100015, Uzbekistan; (A.S.); (K.T.); (B.A.)
| | - Khurshid Tursunov
- Department of Inorganic, Physical and Colloidal Chemistry, Tashkent Pharmaceutical Institute, Oybek Street 45, Tashkent 100015, Uzbekistan; (A.S.); (K.T.); (B.A.)
| | - Sunnatullo Fazliev
- Max Planck School Matter to Life, Jahnstrasse 29, 69120 Heidelberg, Germany;
- Faculty of Chemistry and Earth Sciences, Heidelberg University, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
| | - Bahtigul Azimova
- Department of Inorganic, Physical and Colloidal Chemistry, Tashkent Pharmaceutical Institute, Oybek Street 45, Tashkent 100015, Uzbekistan; (A.S.); (K.T.); (B.A.)
| | - Jamoliddin Razzokov
- Department of Physics and Chemistry, Tashkent Institute of Irrigation and Agricultural Mechanization Engineers, Kori Niyoziy 39, Tashkent 100000, Uzbekistan
- Department of Physics, National University of Uzbekistan, Tashkent 100174, Uzbekistan
- Institute of Material Sciences, Academy of Sciences, Chingiz Aytmatov 2b, Tashkent 100084, Uzbekistan
- Correspondence:
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13
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Yusupov M, Privat-Maldonado A, Cordeiro RM, Verswyvel H, Shaw P, Razzokov J, Smits E, Bogaerts A. Oxidative damage to hyaluronan-CD44 interactions as an underlying mechanism of action of oxidative stress-inducing cancer therapy. Redox Biol 2021; 43:101968. [PMID: 33895486 PMCID: PMC8099558 DOI: 10.1016/j.redox.2021.101968] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/20/2021] [Accepted: 04/06/2021] [Indexed: 12/15/2022] Open
Abstract
Multiple cancer therapies nowadays rely on oxidative stress to damage cancer cells. Here we investigated the biological and molecular effect of oxidative stress on the interaction between CD44 and hyaluronan (HA), as interrupting their binding can hinder cancer progression. Our experiments demonstrated that the oxidation of HA decreased its recognition by CD44, which was further enhanced when both CD44 and HA were oxidized. The reduction of CD44-HA binding negatively affected the proliferative state of cancer cells. Our multi-level atomistic simulations revealed that the binding free energy of HA to CD44 decreased upon oxidation. The effect of HA and CD44 oxidation on CD44-HA binding was similar, but when both HA and CD44 were oxidized, the effect was much larger, in agreement with our experiments. Hence, our experiments and computations support our hypothesis on the role of oxidation in the disturbance of CD44-HA interaction, which can lead to the inhibition of proliferative signaling pathways inside the tumor cell to induce cell death.
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Affiliation(s)
- Maksudbek Yusupov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium.
| | - Angela Privat-Maldonado
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium; Solid Tumor Immunology Group, Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium.
| | - Rodrigo M Cordeiro
- Centro de Ciências Naturais e Humanas, Universidade Federal Do ABC, Avenida Dos Estados 5001, CEP 09210-580, Santo André, SP, Brazil
| | - Hanne Verswyvel
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium; Solid Tumor Immunology Group, Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium
| | - Priyanka Shaw
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium; Solid Tumor Immunology Group, Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium
| | - Jamoliddin Razzokov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium; Tashkent Institute of Irrigation and Agricultural Mechanization Engineers, Kori Niyoziy 39, 100000, Tashkent, Uzbekistan; Institute of Material Sciences, Uzbek Academy of Sciences, Chingiz Aytmatov 2b, 100084, Tashkent, Uzbekistan
| | - Evelien Smits
- Solid Tumor Immunology Group, Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium
| | - Annemie Bogaerts
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium.
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14
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Razzokov J, Fazliev S, Yusupov M, Sharipov A, Ruziev Z, Mamatkulov S. Effect of mutation and disulfide bond formation on the catalytic site of monomeric cytoglobin: a molecular level insight. Plasma Med 2021. [DOI: 10.1615/plasmamed.2021041420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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15
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Marimuthu P, Razzokov J, Eshonqulov G. Disruption of conserved polar interactions causes a sequential release of Bim mutants from the canonical binding groove of Mcl1. Int J Biol Macromol 2020; 158:364-374. [PMID: 32376253 DOI: 10.1016/j.ijbiomac.2020.04.243] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/25/2020] [Accepted: 04/27/2020] [Indexed: 12/15/2022]
Abstract
Mcl1 is an important anti-apoptotic member of the Bcl2 family proteins that are upregulated in several cancer malignancies. The canonical binding groove (CBG) located at the surface of Mcl1 exhibits a critical role in binding partners selectively via the BH3-domain of pro-apoptotic Bcl2 family members that trigger the downregulation of Mcl1 function. There are several crystal structures of point-mutated pro-apoptotic Bim peptides in complex with Mcl1. However, the mechanistic effects of such point-mutations towards peptide binding and complex stability still remain unexplored. Here, the effects of the reported point mutations in Bim peptides and their binding mechanisms to Mcl1 were computationally evaluated using atomistic-level steered molecular dynamics (SMD) simulations. A range of external-forces and constant-velocities were applied to the Bim peptides to uncover the mechanistic basis of peptide dissociation from the CBG of Mcl1. Although the peptides showed similarities in their dissociation pathways, the peak rupture forces varied significantly. According to simulations results, the disruption of the conserved polar contacts at the complex interface causes a sequential release of the peptides from the CBG of Mcl1. Overall, the results obtained from the current study may provide valuable insights for the development of novel anti-cancer peptide-inhibitors that can downregulate Mcl1's function.
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Affiliation(s)
- Parthiban Marimuthu
- Structural Bioinformatics Laboratory (SBL), Biochemistry and Pharmacy, Faculty of Science and Engineering, Åbo Akademi University, FI-20520 Turku, Finland.
| | - Jamoliddin Razzokov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Gofur Eshonqulov
- Department of Physics, National University of Uzbekistan, 100174 Tashkent, Uzbekistan
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16
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Attri P, Razzokov J, Yusupov M, Koga K, Shiratani M, Bogaerts A. Influence of osmolytes and ionic liquids on the Bacteriorhodopsin structure in the absence and presence of oxidative stress: A combined experimental and computational study. Int J Biol Macromol 2020; 148:657-665. [DOI: 10.1016/j.ijbiomac.2020.01.179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/16/2020] [Accepted: 01/19/2020] [Indexed: 12/17/2022]
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17
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Cordeiro RM, Yusupov M, Razzokov J, Bogaerts A. Parametrization and Molecular Dynamics Simulations of Nitrogen Oxyanions and Oxyacids for Applications in Atmospheric and Biomolecular Sciences. J Phys Chem B 2020; 124:1082-1089. [DOI: 10.1021/acs.jpcb.9b08172] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rodrigo M. Cordeiro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados 5001, CEP 09210-580 Santo André (SP), Brazil
| | - Maksudbek Yusupov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Jamoliddin Razzokov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Annemie Bogaerts
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
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18
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Vanmeert M, Razzokov J, Mirza MU, Weeks SD, Schepers G, Bogaerts A, Rozenski J, Froeyen M, Herdewijn P, Pinheiro VB, Lescrinier E. Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins. Nucleic Acids Res 2019; 47:11976-11977. [PMID: 31713624 PMCID: PMC7145540 DOI: 10.1093/nar/gkz1090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Michiel Vanmeert
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Jamoliddin Razzokov
- Research group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Muhammad Usman Mirza
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium.,Centre for Research in Molecular Medicine (CRiMM), University of Lahore, Pakistan
| | - Stephen D Weeks
- Biocrystallography, KU Leuven, Herestraat 49, box 822, 3000 Leuven, Belgium
| | - Guy Schepers
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Annemie Bogaerts
- Research group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Jef Rozenski
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Mathy Froeyen
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Vitor B Pinheiro
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium.,University College London, Department of Structural and Molecular Biology, Gower Street, London, WC1E 6BT, UK
| | - Eveline Lescrinier
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
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19
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Vanmeert M, Razzokov J, Mirza MU, Weeks SD, Schepers G, Bogaerts A, Rozenski J, Froeyen M, Herdewijn P, Pinheiro VB, Lescrinier E. Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins. Nucleic Acids Res 2019; 47:7130-7142. [PMID: 31334814 PMCID: PMC6649754 DOI: 10.1093/nar/gkz551] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/24/2019] [Accepted: 06/12/2019] [Indexed: 02/06/2023] Open
Abstract
Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be used for the storage of genetic information. In vivo XNA applications could be developed into novel biocontainment strategies, but are currently limited by the challenge of developing XNA processing enzymes such as polymerases, ligases and nucleases. Here, we present a structure-guided modelling-based strategy for the rational design of those enzymes essential for the development of XNA molecular biology. Docking of protein domains to unbound double-stranded nucleic acids is used to generate a first approximation of the extensive interaction of nucleic acid processing enzymes with their substrate. Molecular dynamics is used to optimise that prediction allowing, for the first time, the accurate prediction of how proteins that form toroidal complexes with nucleic acids interact with their substrate. Using the Chlorella virus DNA ligase as a proof of principle, we recapitulate the ligase's substrate specificity and successfully predict how to convert it into an XNA-templated XNA ligase.
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Affiliation(s)
- Michiel Vanmeert
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Jamoliddin Razzokov
- Research group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Muhammad Usman Mirza
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
- Centre for Research in Molecular Medicine (CRiMM), University of Lahore, Pakistan
| | - Stephen D Weeks
- Biocrystallography, KU Leuven, Herestraat 49, box 822, 3000 Leuven, Belgium
| | - Guy Schepers
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Annemie Bogaerts
- Research group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Jef Rozenski
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Mathy Froeyen
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Vitor B Pinheiro
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
- University College London, Department of Structural and Molecular Biology, Gower Street, London, WC1E 6BT, UK
| | - Eveline Lescrinier
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
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20
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Abstract
The aggregation of insoluble amyloid beta (Aβ) peptides in the brain is known to trigger the onset of neurodegenerative diseases, such as Alzheimer’s disease. In spite of the massive number of investigations, the underlying mechanisms to destabilize the Aβ aggregates are still poorly understood. Some studies indicate the importance of oxidation to destabilize the Aβ aggregates. In particular, oxidation induced by cold atmospheric plasma (CAP) has demonstrated promising results in eliminating these toxic aggregates. In this paper, we investigate the effect of oxidation on the stability of an Aβ pentamer. By means of molecular dynamics simulations and umbrella sampling, we elucidate the conformational changes of Aβ pentamer in the presence of oxidized residues, and we estimate the dissociation free energy of the terminal peptide out of the pentamer form. The calculated dissociation free energy of the terminal peptide is also found to decrease with increasing oxidation. This indicates that Aβ pentamer aggregation becomes less favorable upon oxidation. Our study contributes to a better insight in one of the potential mechanisms for inhibition of toxic Aβ peptide aggregation, which is considered to be the main culprit to Alzheimer’s disease.
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Affiliation(s)
- J Razzokov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium.
| | - M Yusupov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium
| | - A Bogaerts
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium
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21
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Razzokov J, Naderi S, van der Schoot P. Nanoscale insight into silk-like protein self-assembly: effect of design and number of repeat units. Phys Biol 2018; 15:066010. [PMID: 30124438 DOI: 10.1088/1478-3975/aadb5e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
By means of replica exchange molecular dynamics simulations we investigate how the length of a silk-like, alternating diblock oligopeptide influences its secondary and quaternary structure. We carry out simulations for two protein sizes consisting of three and five blocks, and study the stability of a single protein, a dimer, a trimer and a tetramer. Initial configurations of our simulations are β-roll and β-sheet structures. We find that for the triblock the secondary and quaternary structures upto and including the tetramer are unstable: the proteins melt into random coil structures and the aggregates disassemble either completely or partially. We attribute this to the competition between conformational entropy of the proteins and the formation of hydrogen bonds and hydrophobic interactions between proteins. This is confirmed by our simulations on the pentablock proteins, where we find that, as the number of monomers in the aggregate increases, individual monomers form more hydrogen bonds whereas their solvent accessible surface area decreases. For the pentablock β-sheet protein, the monomer and the dimer melt as well, although for the β-roll protein only the monomer melts. For both trimers and tetramers remain stable. Apparently, for these the entropy loss of forming β-rolls and β-sheets is compensated for in the free-energy gain due to the hydrogen-bonding and hydrophobic interactions. We also find that the middle monomers in the trimers and tetramers are conformationally much more stable than the ones on the top and the bottom. Interestingly, the latter are more stable on the tetramer than on the trimer, suggesting that as the number of monomers increases protein-protein interactions cooperatively stabilize the assembly. According to our simulations, the β-roll and β-sheet aggregates must be approximately equally stable.
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Affiliation(s)
- Jamoliddin Razzokov
- Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium. Faculteit Technische Natuurkunde, Technische Universiteit Eindhoven, Postbus 513, 5600 MB Eindhoven, Netherlands
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22
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De Backer J, Razzokov J, Hammerschmid D, Mensch C, Hafideddine Z, Kumar N, van Raemdonck G, Yusupov M, Van Doorslaer S, Johannessen C, Sobott F, Bogaerts A, Dewilde S. The effect of reactive oxygen and nitrogen species on the structure of cytoglobin: A potential tumor suppressor. Redox Biol 2018; 19:1-10. [PMID: 30081385 PMCID: PMC6084017 DOI: 10.1016/j.redox.2018.07.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 06/04/2018] [Revised: 07/15/2018] [Accepted: 07/22/2018] [Indexed: 12/12/2022] Open
Abstract
Many current anti-cancer therapies rely on increasing the intracellular reactive oxygen and nitrogen species (RONS) contents with the aim to induce irreparable damage, which subsequently results in tumor cell death. A novel tool in cancer therapy is the use of cold atmospheric plasma (CAP), which has been found to be very effective in the treatment of many different cancer cell types in vitro as well as in vivo, mainly through the vast generation of RONS. One of the key determinants of the cell's fate will be the interaction of RONS, generated by CAP, with important proteins, i.e. redox-regulatory proteins. One such protein is cytoglobin (CYGB), a recently discovered globin proposed to be involved in the protection of the cell against oxidative stress. In this study, the effect of plasma-produced RONS on CYGB was investigated through the treatment of CYGB with CAP for different treatment times. Spectroscopic analysis of CYGB showed that although chemical modifications occur, its secondary structure remains intact. Mass spectrometry experiments identified these modifications as oxidations of mainly sulfur-containing and aromatic amino acids. With longer treatment time, the treatment was also found to induce nitration of the heme. Furthermore, the two surface-exposed cysteine residues of CYGB were oxidized upon treatment, leading to the formation of intermolecular disulfide bridges, and potentially also intramolecular disulfide bridges. In addition, molecular dynamics and docking simulations confirmed, and further show, that the formation of an intramolecular disulfide bond, due to oxidative conditions, affects the CYGB 3D structure, thereby opening the access to the heme group, through gate functioning of His117. Altogether, the results obtained in this study (1) show that plasma-produced RONS can extensively oxidize proteins and (2) that the oxidation status of two redox-active cysteines lead to different conformations of CYGB.
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Affiliation(s)
- Joey De Backer
- Research Group PPES, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium.
| | - Jamoliddin Razzokov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium
| | - Dietmar Hammerschmid
- Research Group PPES, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium; Biomolecular & Analytical Mass Spectrometry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Carl Mensch
- Research Group Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Zainab Hafideddine
- Research Group PPES, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium; The Laboratory of Biophysics and Biomedical Physics, Department of Physics, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium
| | - Naresh Kumar
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium
| | - Geert van Raemdonck
- Center for Proteomics, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Maksudbek Yusupov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium
| | - Sabine Van Doorslaer
- The Laboratory of Biophysics and Biomedical Physics, Department of Physics, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium
| | - Christian Johannessen
- Research Group Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Annemie Bogaerts
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium
| | - Sylvia Dewilde
- Research Group PPES, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium.
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23
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Kumar N, Shaw P, Razzokov J, Yusupov M, Attri P, Uhm HS, Choi EH, Bogaerts A. Enhancement of cellular glucose uptake by reactive species: a promising approach for diabetes therapy. RSC Adv 2018; 8:9887-9894. [PMID: 35540836 PMCID: PMC9078705 DOI: 10.1039/c7ra13389h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/03/2018] [Indexed: 12/16/2022] Open
Abstract
It is generally known that antidiabetic activity is associated with an increased level of glucose uptake in adipocytes and skeletal muscle cells. However, the role of exogenous reactive oxygen and nitrogen species (RONS) in muscle development and more importantly in glucose uptake is largely unknown. We investigate the effect of RONS generated by cold atmospheric plasma (CAP) in glucose uptake. We show that the glucose uptake is significantly enhanced in differentiated L6 skeletal muscle cells after CAP treatment. We also observe a significant increase of the intracellular Ca++ and ROS level, without causing toxicity. One of the possible reasons for an elevated level of glucose uptake as well as intracellular ROS and Ca++ ions is probably the increased oxidative stress leading to glucose transport. Influenence of biocompatible microsecond dielectric barrier discharge (μs-DBD) plasma in glucose uptake and cell differentiation.![]()
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Affiliation(s)
- Naresh Kumar
- Department of Chemistry
- University of Antwerp
- Belgium
| | | | | | | | - Pankaj Attri
- Department of Chemistry
- University of Antwerp
- Belgium
| | - Han Sup Uhm
- Plasma Bioscience Research Center/Department of Electrical and Biological Physics
- Kwangwoon University
- Seoul 139-701
- Korea
| | - Eun Ha Choi
- Plasma Bioscience Research Center/Department of Electrical and Biological Physics
- Kwangwoon University
- Seoul 139-701
- Korea
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24
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Razzokov J, Naderi S, van der Schoot P. Prediction of the structure of a silk-like protein in oligomeric states using explicit and implicit solvent models. Soft Matter 2014; 10:5362-5374. [PMID: 24937549 DOI: 10.1039/c4sm00384e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We perform Replica Exchange Molecular Dynamics (REMD) simulations on a silk-like protein design with amino-acid sequence [(Gly-Ala)3-Gly-Glu]5 to investigate the stability of a single protein, a dimer, a trimer and a tetramer made up of these proteins starting from β-roll and β-sheet structures in both explicit (TIP3P) and implicit (GBSA) solvent models. Our simulation results for the implicit solvent model agree with those for the explicit solvent model for simulation times up to the longest tested, being 30 ns per replica. From this we infer that the implicit solvent model that we use is reliable, allowing us to reach much longer time scales (up to 200 ns per replica). We find that the self-assembly of fibers of these proteins in solution must be a nucleated process, involving nuclei made up of at least three monomers. We also find that the conformation of the protein changes upon assembly, i.e., there is a transition from a disordered globular state to an ordered β-sheet structure in the self-assembled state of aggregates containing more than two monomers. This indicates that autosteric effects must be important in the polymerization of this protein, reminiscent of what is observed for β-amyloids. Our findings are consistent with recent experimental results on a protein with an amino acid sequence similar to that of the protein we study.
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Affiliation(s)
- Jamoliddin Razzokov
- Institute Ion-Plasma and Laser Technologies, Academy of Sciences of Uzbekistan, Dormon yoli Str. 33, 100125, Tashkent, Uzbekistan.
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