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Mirgaux M, Leherte L, Wouters J. Human indoleamine-2,3-dioxygenase 2 cofactor lability and low substrate affinity explained by homology modeling, molecular dynamics and molecular docking. J Biomol Struct Dyn 2024; 42:4475-4488. [PMID: 37301605 DOI: 10.1080/07391102.2023.2220830] [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: 03/07/2023] [Accepted: 05/28/2023] [Indexed: 06/12/2023]
Abstract
The human indoleamine-2,3-dioxygenase 2 (hIDO2) protein is growing of interest as it is increasingly implicated in multiple diseases (cancer, autoimmune diseases, COVID-19). However, it is only poorly reported in the literature. Its mode of action remains unknown because it does not seem to catalyze the reaction for which it is attributed: the degradation of the L-Tryptophan into N-formyl-kynurenine. This contrasts with its paralog, the human indoleamine-2,3-dioxygenase 1 (hIDO1), which has been extensively studied in the literature and for which several inhibitors are already in clinical trials. Yet, the recent failure of one of the most advanced hIDO1 inhibitors, the Epacadostat, could be caused by a still unknown interaction between hIDO1 and hIDO2. In order to better understand the mechanism of hIDO2, and in the absence of experimental structural data, a computational study mixing homology modeling, Molecular Dynamics, and molecular docking was conducted. The present article highlights an exacerbated lability of the cofactor as well as an inadequate positioning of the substrate in the active site of hIDO2, which might bring part of an answer to its lack of activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manon Mirgaux
- Department of Chemistry, Laboratoire de Chimie Biologique Structurale (CBS), Namur Institute of Structured Matter (NISM), Namur Research Institute for Life Science (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Laurence Leherte
- Department of Chemistry, Laboratoire de Chimie Biologique Structurale (CBS), Namur Institute of Structured Matter (NISM), Namur Research Institute for Life Science (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Johan Wouters
- Department of Chemistry, Laboratoire de Chimie Biologique Structurale (CBS), Namur Institute of Structured Matter (NISM), Namur Research Institute for Life Science (NARILIS), University of Namur (UNamur), Namur, Belgium
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2
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Musavi H, Shokri Afra H, Sadeghkhani F, Ghalehnoei H, Khonakdar-Tarsi A, Mahjoub S. A molecular and computational study of galbanic acid as a regulator of Sirtuin1 pathway in inhibiting lipid accumulation in HepG2 cells. Arch Physiol Biochem 2024:1-9. [PMID: 38712991 DOI: 10.1080/13813455.2024.2336911] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/26/2024] [Indexed: 05/08/2024]
Abstract
INTRODUCTION Sirtuin1 (SIRT1) plays a crucial role in the pathophysiology of non-alcoholic fatty liver disease. We investigated the mechanistic role of galbanic acid (Gal) as a regulator of SIRT1 in silico and in vitro. METHODS HepG2 cells were treated with Gal in the presence or absence of EX-527, a SIRT1-specific inhibitor, for 24 h. Sirtuin1 gene and protein expression were measured by RT-PCR and Western blotting, respectively. It has been docked to the allosteric reign of SIRT1 (PDB ID: 4ZZJ) to study the effect of Gal on SIRT1, and then the protein and complex molecular dynamic (MD) simulations had been studied in 100 ns. RESULTS The semi-quantitative results of Oil red (p < .03) and TG level (p < .009) showed a significant reduction in lipid accumulation by treatment with Gal. Also, a significant increase was observed in the gene and protein expression of SIRT1 (p < .05). MD studies have shown that the average root mean square deviation (RMSD) was about 0.51 Å for protein structure and 0.66 Å for the complex. The average of radius of gyration (Rg) is 2.33 and 2.32 Å for protein and complex, respectively, and the pattern of root mean square fluctuation (RMSF) was almost similar. CONCLUSION Computational studies show that Gal can be a great candidate to use as a SIRT1 ligand because it does not interfere with the structure of the protein, and other experimental studies showed that Gal treatment with SIRT1 inhibitor increases fat accumulation in HepG2 cells.
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Affiliation(s)
- Hadis Musavi
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Hajar Shokri Afra
- Gut and Liver Research Center, Non-communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Farideh Sadeghkhani
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Hossein Ghalehnoei
- Department of Medical Biotechnology, Molecular and Cell Biology Research Center, Faculty of Advanced Technologist in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Abbas Khonakdar-Tarsi
- Department of Clinical Biochemistry and Medical Genetics, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Soleiman Mahjoub
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
- Department of Clinical Biochemistry, School of Medicine, Babol University of Medical Sciences, Babol, Iran
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Tatar Yilmaz G, Yayli N, Tüzüner T, Bozdal G, Salmanli M, Renda G, Korkmaz B, Bozdeveci A, Alpay Karaoğlu Ş. Synthesis, Antimicrobial Activities, and Molecular Modeling Studies of Agents for the Sortase A Enzyme. Chem Biodivers 2024; 21:e202301659. [PMID: 38407541 DOI: 10.1002/cbdv.202301659] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 02/27/2024]
Abstract
Sortase A (SrtA) is an attractive target for developing new anti-infective drugs that aim to interfere with essential virulence mechanisms, such as adhesion to host cells and biofilm formation. Herein, twenty hydroxy, nitro, bromo, fluoro, and methoxy substituted chalcone compounds were synthesized, antimicrobial activities and molecular modeling strategies against the SrtA enzyme were investigated. The most active compounds were found to be T2, T4, and T19 against Streptococcus mutans (S. mutans) with MIC values of 1.93, 3.8, 3.94 μg/mL, and docking scores of -6.46, -6.63, -6.73 kcal/mol, respectively. Also, these three active compounds showed better activity than the chlorohexidine (CHX) (MIC value: 4.88 μg/mL, docking score: -6.29 kcal/mol) in both in vitro and in silico. Structural stability and binding free energy analysis of S.mutans SrtA with active compounds were measured by molecular dynamic (MD) simulations throughout 100 nanoseconds (ns) time. It was observed that the stability of the critical interactions between these compounds and the target enzyme was preserved. To prove further, in vivo biological evaluation studies could be conducted for the most promising precursor compounds T2, T4, and T19, and it might open new avenues to the discovery of more potent SrtA inhibitors.
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Affiliation(s)
- Gizem Tatar Yilmaz
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Karadeniz Technical University, 61080, Trabzon, Turkiye
| | - Nurettin Yayli
- Department of Pharmacognosy, Faculty of Pharmacy, Karadeniz Technical University, 61080, Trabzon, Turkiye
| | - Tamer Tüzüner
- Department of Pediatric Dentistry, Faculty of Dentistry, Karadeniz Technical University, 61080, Trabzon, Turkiye
| | - Gözde Bozdal
- Department of Pharmacognosy, Faculty of Pharmacy, Karadeniz Technical University, 61080, Trabzon, Turkiye
| | - Merve Salmanli
- Department of Pediatric Dentistry, Faculty of Dentistry, Karadeniz Technical University, 61080, Trabzon, Turkiye
| | - Gülin Renda
- Department of Pharmacognosy, Faculty of Pharmacy, Karadeniz Technical University, 61080, Trabzon, Turkiye
| | - Büşra Korkmaz
- Department of Pharmacognosy, Faculty of Pharmacy, Karadeniz Technical University, 61080, Trabzon, Turkiye
| | - Arif Bozdeveci
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdoğan University, 53100, Rize, Turkiye
| | - Şengül Alpay Karaoğlu
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdoğan University, 53100, Rize, Turkiye
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El-Malah AA, Gineinah MM, Khayat MT, Aljahdali AS, Safar MM, Almazmumi HA, Khinkar RM. Design, synthesis, molecular docking, and molecular dynamic studies of novel quinazoline derivatives as phosphodiesterase 7 inhibitors. Front Pharmacol 2024; 15:1389076. [PMID: 38711988 PMCID: PMC11070508 DOI: 10.3389/fphar.2024.1389076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 04/05/2024] [Indexed: 05/08/2024] Open
Abstract
Introduction: Phosphodiesterase 7 (PDE7) is a high-affinity cyclic AMP (cAMP)-specific PDE that is expressed in immune and proinflammatory cells. In this work, we explore the possibility that selective small molecule inhibitors of this enzyme family could provide a novel approach to alleviate the inflammation that is associated with many inflammatory diseases. Methods: A series of novel substituted 4-hydrazinoquinazoline derivatives and fused triazoloquinazolines were designed, synthesized, and evaluated in vitro for their PDE7A inhibition activities, in comparison with Theophylline, a non-selective PDE inhibitor, and BRL50481, a selective PDE7A inhibitor. This series of novel quinazoline derivatives were synthesized via multi-step reactions. The reaction sequence began with selective monohydrazinolysis of compounds 2a,b to give 3a,b. Schiff bases 4a-h were synthesized by the reaction of the quinazolylhydrazines 3a,b with various substituted aromatic aldehydes. The reaction of 4a-h with bromine in acetic acid, in turn, gave fused triazoloquinazolines 5a-h. These compounds were characterized by satisfied spectrum analyses mainly including 1HNMR, 13CNMR, and MS together with elemental analyses. Results and discussion: The results of in vitro PDE7A inhibition activity clearly indicated that compounds 4b, 4g, 5c, and 5f exhibited good potency. Molecular docking and molecular dynamic simulation studies further supported our findings and provided the basis of interaction in terms of conventional hydrogen bonds and π-π stacking patterns. The present results lay the groundwork for developing lead compounds with improved phosphodiesterase seven inhibitory activities.
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Affiliation(s)
- Afaf A. El-Malah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Magdy M. Gineinah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maan T. Khayat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anfal S. Aljahdali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Marwa M. Safar
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Cairo University, Giza, Egypt
- Department of Pharmacology and Biochemistry, Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - Hadeel A. Almazmumi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Roaa M. Khinkar
- Department of Pharmacy Practice, College of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
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Antonijevic M, Sopkova-de Oliveira Santos J, Dallemagne P, Rochais C. Discovery of a pocket network on the domain 5 of the TrkB receptor - A potential new target in the quest for the new ligands. Mol Inform 2024:e202400043. [PMID: 38619318 DOI: 10.1002/minf.202400043] [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: 02/01/2024] [Revised: 03/06/2024] [Accepted: 03/26/2024] [Indexed: 04/16/2024]
Abstract
The important role that the neurotrophin tyrosine kinase receptor - TrkB has in the pathogenesis of several neurodegenerative conditions such are Alzheimer's disease, Parkinson's disease, Huntington's disease, has been well described. This shouldn't be a surprise, since in the physiological conditions, once activated by brain-derived neurotrophic factor (BDNF) and neurotrophin-4/5 (NT-4/5), the TrkB receptor promotes neuronal survival, differentiation and synaptic function. Considering that the natural ligands for TrkB receptor are large proteins, it is a challenge to discover small molecule capable to mimic their effects. Even though, the surface of receptor that is interacting with BDNF or NT-4/5 is known, there was always a question which pocket and interaction is responsible for activation of it. In order to answer this challenging question, we have used molecular dynamic (MD) simulations and Pocketron algorithm which enabled us to detect, for the first time, a pocket network existing in the interacting domain (d5) of the receptor; to describe them and to see how they are communicating with each other. This new discovery gave us potential new areas on receptor that can be targeted and used for structure-based drug design approach in the development of the new ligands.
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Hur J, Abousleiman YN, Hull KL, Qomi MJA. A ReaxFF Potential for Modeling Organic Matter Degradation with Oxybromine Oxidants. Chemphyschem 2024; 25:e202300860. [PMID: 38263476 DOI: 10.1002/cphc.202300860] [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: 11/13/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 01/25/2024]
Abstract
Oxidation of organic matter with oxybromine oxidants is ushering in a new era of enhanced hydrocarbon recovery. While these potent reagents are being tested in laboratory and field experiments, there is a pressing demand to delineate the molecular processes governing oxidation reactions at geological depth. Here, we parameterize a ReaxFF potential to model the oxidative decompositions of aliphatic and aromatic hydrocarbons in the presence of water-NaBr solutions that contain oxybromine (BrOn)- oxidizers. Our parameterization results in a reliable empirical bond-order potential that accurately calculates bond energies, exhibiting an RMSE of ∼1.18 eV, corresponding to 1.36 % average error. Reproducing bond dissociation and binding energies from Density Functional Theory (DFT), our parameterization proves transferable to aqueous environments. This H/C/O/Na/Br ReaxFF potential accurately reproduces the oxidation pathways of small hydrocarbons with oxybromine oxidizers. This force field captures proton and oxygen transfer, C-C bond tautomerization, and cleavage, leading to ring-opening and chain fragmentation. Molecular dynamic simulations demonstrate the oxidative degradation of aromatic and aliphatic kerogen-like moieties in bulk solutions. We envision that such reactive force fields will be useful to understand better the oxidation reactions of organic matter formed in geological reservoirs for enhanced shale gas recovery and improved carbon dioxide treatments.
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Affiliation(s)
- Jaewoong Hur
- Department of Civil and Environmental Engineering, Henry Samueli School of Engineering, University of California Irvine, E4130 Engineering Gateway, Irvine, CA 92697-2175, United States
| | - Younane N Abousleiman
- Integrated PoroMechanics Institute, The University of Oklahoma, 100 East Boyd Street, RM 710, Norman, Oklahoma, 73019, United States
| | - Katherine L Hull
- Aramco Research Center-Houston Aramco Americas, 16300 Park Row, Houston, Texas, 77084, United States
| | - Mohammad Javad Abdolhosseini Qomi
- Department of Civil and Environmental Engineering, Henry Samueli School of Engineering, University of California Irvine, E4130 Engineering Gateway, Irvine, CA 92697-2175, United States
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Tang Y. Analysis of the binding pattern of NIK inhibitors by computational simulation. J Biomol Struct Dyn 2024; 42:3318-3331. [PMID: 37183664 DOI: 10.1080/07391102.2023.2212782] [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: 10/29/2022] [Accepted: 05/04/2023] [Indexed: 05/16/2023]
Abstract
NF-kappaB-Inducing Kinase (NIK) is a key kinase in the activation of the NF-κB non-classical signalling pathway, which has been shown to be over-activated in patients with inflammatory diseases, immune disorders and malignancies and solid tumours inducing activation of the NF-κB non-classical signalling pathway. The design of ATP-competitive small molecule inhibitors against NIK has been a hot topic in the last decade, and many efficient NIK inhibitors have been identified. In this work, I aim to unravel the mechanism of NIK inhibition by different representative NIK type I 1/2 kinase inhibitors, using ADME, molecular docking, molecular dynamics simulation, MM-PBSA analysis and 3D-QSAR analysis. This work contributes to the understanding of the efficiency of NIK inhibitor binding by revealing the basis of the efficiency of NIK inhibitors, the difference in binding modes between different inhibitors and the overall effect on NIK.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yingkai Tang
- Department of Anatomy, School of Basic Medicine, Bengbu Medical University, Bengbu, China
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8
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Shahab M, de Farias Morais GC, Akash S, Fulco UL, Oliveira JIN, Zheng G, Akter S. A robust computational quest: Discovering potential hits to improve the treatment of pyrazinamide-resistant Mycobacterium tuberculosis. J Cell Mol Med 2024; 28:e18279. [PMID: 38634203 PMCID: PMC11024510 DOI: 10.1111/jcmm.18279] [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: 11/29/2023] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
The rise of pyrazinamide (PZA)-resistant strains of Mycobacterium tuberculosis (MTB) poses a major challenge to conventional tuberculosis (TB) treatments. PZA, a cornerstone of TB therapy, must be activated by the mycobacterial enzyme pyrazinamidase (PZase) to convert its active form, pyrazinoic acid, which targets the ribosomal protein S1. Resistance, often associated with mutations in the RpsA protein, complicates treatment and highlights a critical gap in the understanding of structural dynamics and mechanisms of resistance, particularly in the context of the G97D mutation. This study utilizes a novel integration of computational techniques, including multiscale biomolecular and molecular dynamics simulations, physicochemical and medicinal chemistry predictions, quantum computations and virtual screening from the ZINC and Chembridge databases, to elucidate the resistance mechanism and identify lead compounds that have the potential to improve treatment outcomes for PZA-resistant MTB, namely ZINC15913786, ZINC20735155, Chem10269711, Chem10279789 and Chem10295790. These computational methods offer a cost-effective, rapid alternative to traditional drug trials by bypassing the need for organic subjects while providing highly accurate insight into the binding sites and efficacy of new drug candidates. The need for rapid and appropriate drug development emphasizes the need for robust computational analysis to justify further validation through in vitro and in vivo experiments.
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Affiliation(s)
- Muhammad Shahab
- State key laboratories of Chemical Resources Engineering Beijing, University of Chemical TechnologyBeijingChina
| | | | - Shopnil Akash
- Department of PharmacyDaffodil International UniversityDhakaBangladesh
| | - Umberto Laino Fulco
- Department of Biophysics and Pharmacology, Bioscience CenterFederal University of Rio Grande do NorteNatalRio Grande do NorteBrazil
| | - Jonas Ivan Nobre Oliveira
- Department of Biophysics and Pharmacology, Bioscience CenterFederal University of Rio Grande do NorteNatalRio Grande do NorteBrazil
| | - Guojun Zheng
- State key laboratories of Chemical Resources Engineering Beijing, University of Chemical TechnologyBeijingChina
| | - Shahina Akter
- Bangladesh Council of Scientific and Industrial ResearchDhakaBangladesh
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Jiang C, Li K, Bi Z, Ma S, Zhang J, Liu B, Li J. Developments in Atomistic and Nano Structure Evolution Mechanisms of Molten Slag Using Atomistic Simulation Methods. Nanomaterials (Basel) 2024; 14:464. [PMID: 38470793 DOI: 10.3390/nano14050464] [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: 02/09/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024]
Abstract
Molten slag has different properties depending on its composition. The relationship between its composition, structure, and properties has been the focus of attention in industrial manufacturing processes. This review describes the atomistic scale mechanisms by which oxides of different compositions affect the properties and structure of slag, and depicts the current state of research in the atomic simulation of molten slag. At present, the research on the macroscopic properties of molten slag mainly focuses on viscosity, free-running temperature, melting point, and desulphurization capacity. Regulating the composition has become the most direct and effective way to control slag properties. Analysis of the microevolution mechanism is the fundamental way to grasp the macroscopic properties. The microstructural evolution mechanism, especially at the atomic and nanoscale of molten slag, is reviewed from three aspects: basic oxides, acidic oxides, and amphoteric oxides. The evolution of macroscopic properties is analyzed in depth through the evolution of the atomic structure. Resolution of the macroscopic properties of molten slag by the atomic structure plays a crucial role in the development of fundamental theories of physicochemistry.
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Affiliation(s)
- Chunhe Jiang
- Technical Support Center for Prevention and Control of Disastrous Accidents in Metal Smelting, University of Science and Technology Beijing, Beijing 100083, China
| | - Kejiang Li
- School of Metallurgical and Ecological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Zhisheng Bi
- School of Metallurgical and Ecological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Shufang Ma
- Aetna Tianlong Tungsten Molybdenum Technology Co., Ltd., No. 11 Fenghui Middle Road, Haidian District, Beijing 100094, China
| | - Jianliang Zhang
- School of Metallurgical and Ecological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- School of Chemical Engineering, The University of Queensland, Saint Lucia, QLD 4072, Australia
| | - Bo Liu
- School of Advanced Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Jiaqi Li
- School of Advanced Engineering, University of Science and Technology Beijing, Beijing 100083, China
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Yi X, Yu H, Ye L. Rational design of transaminases based on comparative analysis of catalytically active and distance-free modes of the high-energy intermediate state. Biotechnol Bioeng 2024; 121:1005-1015. [PMID: 38108196 DOI: 10.1002/bit.28626] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/14/2023] [Accepted: 12/03/2023] [Indexed: 12/19/2023]
Abstract
Bioproduction of chiral amines is limited by low transaminase (TA) activity on nonnatural substrates, leading to the need for protein engineering. To address the challenge of quickly and precisely identifying the engineering targets, a strategy was proposed based on analyzing the mode changes in the high-energy intermediate state (H-state) of the substrate-enzyme complex during catalysis. By substituting the residues with minimal structural changes in catalytically active mode (A-mode) and distance-free mode (F-mode) of the H-state complex with more conserved ones to stabilize it, a TA mutant M5(T295C/L387A/V436A) with 121.9-fold higher activity for synthesizing the (S)-Rivastigmine precursor (S)-1-(3-methoxyphenyl)ethylamine was created. The applicability of this strategy was also validated by engineering another TA for 1.52-fold higher activity and >99% selectivity toward (R)-3-amino-1-butanol biopreparation. The much higher stereoselectivity of the mutant compared with the wild type (28.3%) demonstrated that this strategy is not only advantageous in engineering enzyme activity but also applicable for modulating stereoselectivity.
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Affiliation(s)
- Xiaomin Yi
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Hongwei Yu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Lidan Ye
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
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11
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Hernández-Tanguma A, Ariza-Castolo A. Dynamics of eugenol included in β-cyclodextrin by nuclear magnetic resonance and molecular simulations. Magn Reson Chem 2024. [PMID: 38369602 DOI: 10.1002/mrc.5439] [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: 09/28/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/20/2024]
Abstract
Eugenol-β-cyclodextrin complex has been widely used because of the enhanced stability and conservation of the properties of eugenol. Applications in food and health sciences have been shown previously, which makes this complex an excellent model to understand and develop methodologies for the analysis and prediction of physical properties. In this work, the dynamics of eugenol incorporated into β-cyclodextrin are presented, using NMR relaxation rates, and the predictive capabilities of molecular dynamics simulations are discussed. Results show a hindered rotation of eugenol around the principal inertial axes when located inside β-cyclodextrin. Moreover, a translational movement of the whole complex is demonstrated.
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Affiliation(s)
- Alejandro Hernández-Tanguma
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Armando Ariza-Castolo
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
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12
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Martins NF, Viana MJA, Maigret B. Fungi Tryptophan Synthases: What Is the Role of the Linker Connecting the α and β Structural Domains in Hemileia vastatrix TRPS? A Molecular Dynamics Investigation. Molecules 2024; 29:756. [PMID: 38398508 PMCID: PMC10893352 DOI: 10.3390/molecules29040756] [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: 12/27/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Tryptophan synthase (TRPS) is a complex enzyme responsible for tryptophan biosynthesis. It occurs in bacteria, plants, and fungi as an αββα heterotetramer. Although encoded by independent genes in bacteria and plants, in fungi, TRPS is generated by a single gene that concurrently expresses the α and β entities, which are linked by an elongated peculiar segment. We conducted 1 µs all-atom molecular dynamics simulations on Hemileia vastatrix TRPS to address two questions: (i) the role of the linker segment and (ii) the comparative mode of action. Since there is not an experimental structure, we started our simulations with homology modeling. Based on the results, it seems that TRPS makes use of an already-existing tunnel that can spontaneously move the indole moiety from the α catalytic pocket to the β one. Such behavior was completely disrupted in the simulation without the linker. In light of these results and the αβ dimer's low stability, the full-working TRPS single genes might be the result of a particular evolution. Considering the significant losses that Hemileia vastatrix causes to coffee plantations, our next course of action will be to use the TRPS to look for substances that can block tryptophan production and therefore control the disease.
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Affiliation(s)
- Natália F Martins
- EMBRAPA Agroindústria Tropical, Planalto do Pici, Fortaleza 60511-110, CE, Brazil
| | - Marcos J A Viana
- EMBRAPA Agroindústria Tropical, Planalto do Pici, Fortaleza 60511-110, CE, Brazil
| | - Bernard Maigret
- LORIA, UMR 7504 CNRS, Université de Lorraine, 54000 Vandoeuvre les Nancy, France
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Bouali N, Ahmad I, Patel H, Alhejaili EB, Hamadou WS, Badraoui R, Hadj Lajimi R, Alreshidi M, Siddiqui AJ, Adnan M, Abdulhakeem MA, Bazaid AS, Patel M, Saeed M, Snoussi M, Noumi E. GC-MS screening of the phytochemical composition of Ziziphus honey: ADME properties and in vitro/ in silico study of its antimicrobial activity. J Biomol Struct Dyn 2024; 42:1368-1380. [PMID: 37191027 DOI: 10.1080/07391102.2023.2205945] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 01/23/2023] [Accepted: 03/30/2023] [Indexed: 05/17/2023]
Abstract
A revival interest has been given to natural products as sources of phytocompounds to be used as alternative treatment against infectious diseases. In this context, we aimed to investigate the antimicrobial potential of Ziziphus honey (ZH) against twelve clinical bacterial strains and several yeasts and molds using in vitro and computational approaches. The well-diffusion assay revealed that ZH was able to induce growth inhibition of most Gram-positive and Gram-negative bacteria. The high mean growth inhibition zone (mGIZ) was recorded in E. coli (Clinical strain, 217), S. aureus followed by E. coli ATCC 10536 (mGIZ values: 41.00 ± 1 mm, 40.67 ± 0.57 mm, and 34.67 ± 0.57 mm, respectively). The minimal bactericidal concentrations (MBCs) and minimal fungicidal concentration values (MFCs) from approximately 266.33 mg/mL to over 532.65 mg/mL. Molecular docking results revealed that the identified compounds maltose, 2-furoic acid, isopropyl ester, 2,4-imidazolidinedione, 5-(2-methylpropyl)-(S)- and 3,4,5-trihydroxytoluene, S-Methyl-L-Cysteine, 2-Furancarboxylic acid, L-Valine-N-ethoxycarbonyl, Hexanoic acid, 3,5,5-trimethyl-, Methyl-beta-D-thiogalactoside, gamma-Sitosterol, d-Mannose, 4-O-Methylmannose, 2,4-Imidazolidinedione, 5-(2-methylpropyl)- (S) were found to have good affinity for targeted receptor, respectively. Through a 100-ns dynamic simulation research, binding interactions and stability between promising phytochemicals and the active residues of the studied enzymes were confirmed. The ADMET profiling of all identified compounds revealed that most of them could be qualified as biologically active with good absorption and permeation. Overall, the results highlighted the efficiency of ZH against the tested clinical pathogenic strains. The antimicrobial potential and the potency displayed by the identified compounds could imply their further pharmacological applications.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nouha Bouali
- Department of Biology, University of Hail, College of Science, Ha'il, Saudi Arabia
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Gondur, Dhule, Maharashtra, India
| | - Harun Patel
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Gondur, Dhule, Maharashtra, India
| | | | - Walid Sabri Hamadou
- Department of Biology, University of Hail, College of Science, Ha'il, Saudi Arabia
- Research Unit: Molecular Biology of Leukemia and Lymphoma, Department of Biochemistry, University of Medecine of Sousse, Sousse, Tunisia
| | - Riadh Badraoui
- Department of Biology, University of Hail, College of Science, Ha'il, Saudi Arabia
- Section of Histology - Cytology, University of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Histo-Embryology and Cytogenetics, Medicine Faculty of Sfax, University of Sfax, Sfax, Tunisia
| | - Ramzi Hadj Lajimi
- Department of Chemistry, College of Science, University of Ha'il, Ha'il, Saudi Arabia
- Laboratory of Water, Membranes and Environmental Biotechnologies, Center of Research and Water Technologies, Soliman, Tunisia
| | - Mousa Alreshidi
- Department of Biology, University of Hail, College of Science, Ha'il, Saudi Arabia
- Department of Medical Laboratory Science, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Arif Jamal Siddiqui
- Department of Biology, University of Hail, College of Science, Ha'il, Saudi Arabia
| | - Mohd Adnan
- Department of Biology, University of Hail, College of Science, Ha'il, Saudi Arabia
| | | | - Abdulrahman S Bazaid
- Department of Medical Laboratory Science, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Mitesh Patel
- Department of Biotechnology, Parul Institute of Applied Sciences and Centre of Research for Development, Parul University, Vadodara, India
| | - Mohd Saeed
- Department of Biology, University of Hail, College of Science, Ha'il, Saudi Arabia
| | - Mejdi Snoussi
- Department of Biology, University of Hail, College of Science, Ha'il, Saudi Arabia
- Laboratory of Genetics, Biodiversity and Valorisation of Bioressources, High Institute of Biotechnology University of Monastir, Monastir, Tunisia
| | - Emira Noumi
- Department of Biology, University of Hail, College of Science, Ha'il, Saudi Arabia
- Laboratory of Genetics, Biodiversity and Valorisation of Bioressources, High Institute of Biotechnology University of Monastir, Monastir, Tunisia
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Siregar KAAK, Syaifie PH, Jauhar MM, Arda AG, Rochman NT, Kustiawan PM, Mardliyati E. Revealing curcumin therapeutic targets on SRC, PPARG, MAPK8 and HSP90 as liver cirrhosis therapy based on comprehensive bioinformatic study. J Biomol Struct Dyn 2024:1-18. [PMID: 38217310 DOI: 10.1080/07391102.2023.2301534] [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: 08/20/2023] [Accepted: 12/09/2023] [Indexed: 01/15/2024]
Abstract
Cirrhosis naturally progresses through three stages: compensated, decompensated, and late decompensated, which carry an elevated risk of death. Although curcumin's anti-cirrhosis effects have been studied, underlying mechanism in preventing cirrhosis progression and the correlation between curcumin's action with upregulated genes remains insufficiently explored. In this study, we employed network pharmacology approach to construct a drug-target-disease network through bioinformatics and validate the findings with molecular docking and dynamic simulation. The curcumin-targeted liver cirrhosis network encompassed 54 nodes with 282 edges in protein-protein interactions (PPI) network. By utilizing network centrality analysis, we identified eight crucial genes. KEGG enrichment pathway revealed that these crucial genes are involved in pathway of cancer, endocrine resistance, estrogen signaling, chemical carcinogenesis-receptor activation, lipid metabolism, and atherosclerosis. Notably, these eight genes predominantly participate in cancer-related pathways. Further investigation revealed upregulation of four genes and downregulation of four others in hepatocellular carcinoma patients. These upregulated genes-MAPK8, SRC, PPARG, and HSP90AA1-strongly correlated with reduced survival probability in liver hepatocellular carcinoma patients with survival times approximately under 4000 days (∼11 years). Molecular docking and molecular dynamic results exhibited curcumin's superior binding affinities and stability compared to native ligands of MAPK8, SRC, PPARG, and HSP90AA1 within 50 ns simulations. Moreover, MM-GBSA analysis showed stronger binding energy of curcumin to MAPK8, SRC, and HSP90AA1 than native ligand. In conclusion, this study provides valuable insights into curcumin's potential mechanisms in preventing liver cirrhosis progression, specifically in HCC. These findings offer a theoretical basis for further pharmacological research into anti-HCC effect of curcumin.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Khalish Arsy Al Khairy Siregar
- Faculty of Pharmacy, Universitas Muhammadiyah Kalimantan Timur, Samarinda, Indonesia
- Center of Excellence Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
| | - Putri Hawa Syaifie
- Center of Excellence Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
| | | | - Adzani Gaisani Arda
- Center of Excellence Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
| | - Nurul Taufiqu Rochman
- Center of Excellence Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
- Research Center for Advanced Material, National Research and Innovation Agency (BRIN), South Tangerang, Indonesia
| | | | - Etik Mardliyati
- Center of Excellence Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
- Research Center for Vaccine and Drug, National Research and Innovation Agency (BRIN), Bogor, Indonesia
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15
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Junqueira Ribeiro MM. Computer-aided Drug Discovery Approaches in the Identification of Natural Products against SARS-CoV-2: A Review. Curr Comput Aided Drug Des 2024; 20:313-324. [PMID: 36999423 DOI: 10.2174/1573409919666230329090403] [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: 10/02/2022] [Revised: 12/09/2022] [Accepted: 01/19/2023] [Indexed: 03/31/2023]
Abstract
The COVID-19 pandemic is raising a worldwide search for compounds that could act against the disease, mainly due to its mortality. With this objective, many researchers invested in the discovery and development of drugs of natural origin. To assist in this search, the potential of computational tools to reduce the time and cost of the entire process is known. Thus, this review aimed to identify how these tools have helped in the identification of natural products against SARS-CoV-2. For this purpose, a literature review was carried out with scientific articles with this proposal where it was possible to observe that different classes of primary and, mainly, secondary metabolites were evaluated against different molecular targets, mostly being enzymes and spike, using computational techniques, with emphasis on the use of molecular docking. However, it is noted that in silico evaluations still have much to contribute to the identification of an anti- SARS-CoV-2 substance, due to the vast chemical diversity of natural products, identification and use of different molecular targets and computational advancement.
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Güner E, Özkan Ö, Yalcin-Ozkat G, Ölgen S. Determination of Novel SARS-CoV-2 Inhibitors by Combination of Machine Learning and Molecular Modeling Methods. Med Chem 2024; 20:153-231. [PMID: 37957860 DOI: 10.2174/0115734064265609231026063624] [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: 06/25/2023] [Revised: 08/30/2023] [Accepted: 09/25/2023] [Indexed: 11/15/2023]
Abstract
INTRODUCTION Within the scope of the project, this study aimed to find novel inhibitors by combining computational methods. In order to design inhibitors, it was aimed to produce molecules similar to the RdRp inhibitor drug Favipiravir by using the deep learning method. METHODS For this purpose, a Trained Neural Network (TNN) was used to produce 75 molecules similar to Favipiravir by using Simplified Molecular Input Line Entry System (SMILES) representations. The binding properties of molecules to Viral RNA-dependent RNA polymerase (RdRp) were studied by using molecular docking studies. To confirm the accuracy of this method, compounds were also tested against 3CL protease (3CLpro), which is another important enzyme for the progression of SARS-CoV-2. Compounds having better binding energies and RMSD values than favipiravir were searched with similarity analysis on the ChEMBL drug database in order to find similar structures with RdRp and 3CLpro inhibitory activities. RESULTS A similarity search found new 200 potential RdRp and 3CLpro inhibitors structurally similar to produced molecules, and these compounds were again evaluated for their receptor interactions with molecular docking studies. Compounds showed better interaction with RdRp protease than 3CLpro. This result presented that artificial intelligence correctly produced structures similar to favipiravir that act more specifically as RdRp inhibitors. In addition, Lipinski's rules were applied to the molecules that showed the best interaction with RdRp, and 7 compounds were determined to be potential drug candidates. Among these compounds, a Molecular Dynamic simulation study was applied for ChEMBL ID:1193133 to better understand the existence and duration of the compound in the receptor site. CONCLUSION The results confirmed that the ChEMBL ID:1193133 compound showed good Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), hydrogen bonding, and remaining time in the active site; therefore, it was considered that it could be active against the virus. This compound was also tested for antiviral activity, and it was determined that it did not delay viral infection, although it was cytotoxic between 5mg/mL-1.25mg/mL concentrations. However, if other compounds could be tested, it might provide a chance to obtain activity, and compounds should also be tested against the enzymes as well as the other types of viruses.
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Affiliation(s)
- Ersin Güner
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Biruni University, 34010 Topkapı, İstanbul, Turkey
| | - Özgür Özkan
- Teknokent Arı, Pinticks Software Company, Istanbul Technical University, Reşitpaşa Mah. Katar Street, No:4/B204 Sarıyer, İstanbul, Turkey
| | - Gözde Yalcin-Ozkat
- Bioengineering Department, Faculty of Engineering and Architecture, Recep Tayyip Erdogan University, 53100 Rize, Turkey
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Süreyya Ölgen
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Biruni University, 34010 Topkapı, İstanbul, Turkey
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17
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Tohidi S, Aghaie-Khafri M. Cyclophosphamide Loading and Controlled Release in MIL-100(Fe) as an Anti-breast Cancer Carrier: In vivo In vitro Study. Curr Drug Deliv 2024; 21:283-294. [PMID: 37046195 DOI: 10.2174/1567201820666230410120437] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 12/04/2022] [Revised: 02/08/2023] [Accepted: 02/27/2023] [Indexed: 04/14/2023]
Abstract
BACKGROUND Biocompatible MIL-100 (Fe), a metal organic framework material, has recently attracted increasing attention in biomedical engineering. The high surface area, pore volume, and accessible Lewis acid sites make MIL-100 (Fe) a proper candidate for hydrophobic anticancer drug loading and storage. In this study, a novel investigation of cyclophosphamide (CP) -loaded MIL-100(Fe) (MIL- 100(Fe)/CP) and a simulation of drug loading at a molecular level is presented. METHODS This research used a facile synthesis method to prepare MIL-100(Fe), which addresses the high temperature and pressure challenges of synthesis methods. MIL-100(Fe) and MIL-100(Fe)/CP were characterized using x-ray diffraction (XRD), Brunauer-Emmett-Teller (BET), Fourier transform infrared (FTIR), and field emission scanning electron microscopy (FESEM). RESULTS The carriers' drug loading and release behavior are determined by using UV-visible spectrophotometry. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay is applied to examine the biocompatibility and the anticancer effect of MIL-100(Fe)/CP on the human breast cancer cell line (MCF-7). CONCLUSION In vivo antitumor experiments and histological observation reveal inhibition properties of MIL-100(Fe)/CP on the tumor cells. MIL-100(Fe)/CP, with 37.41% drug payload, represents impressive antitumor activity.
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Affiliation(s)
- Shabnam Tohidi
- Faculty of Materials Science and Engineering, KN Toosi University of Technology, Tehran, 1999143344, Iran
| | - Mehrdad Aghaie-Khafri
- Faculty of Materials Science and Engineering, KN Toosi University of Technology, Tehran, 1999143344, Iran
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18
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Tripathi SM, Akash S, Rahman MA, Sundriyal S. Identification of synthetically tractable MERS-CoV main protease inhibitors using structure-based virtual screening and molecular dynamics potential of mean force (PMF) calculations. J Biomol Struct Dyn 2023:1-11. [PMID: 37978909 DOI: 10.1080/07391102.2023.2283780] [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: 04/14/2023] [Accepted: 10/01/2023] [Indexed: 11/19/2023]
Abstract
The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a potentially lethal infection that presents a substantial threat to health, especially in Middle East nations. Given that no FDA-approved specific therapy for MERS infection exists, designing and discovering a potent antiviral therapy for MERS-CoV is crucial. One pivotal strategy for inhibiting MERS replication is to focus on the viral main protease (Mpro). In this study, we identify potential novel Mpro inhibitors employing structure-based virtual screening of our recently reported Ugi reaction-derived library (URDL) consisting of cherry-picked molecules from the literature. The key features of the URDL library include synthetic tractability (1-2 pot synthesis) of the molecules scaffold and unexplored chemical space. The hits were ranked based on the docking score, MM-GBSA free energy of binding, and the interaction pattern with the active site residues. A molecular dynamics (MD) simulation study was performed for the first two top-ranked compounds to analyze the stability and free binding energy based on the molecular mechanics Poisson-Boltzmann surface area. The potential mean force calculated from the steered molecular dynamics (SMD) simulations of the hits indicates improved H-bond potential, enhanced conformational stability, and binding affinity toward the target, compared to the cocrystallized ligand. The discovered hits represent novel synthetically tractable scaffolds as potential MERS-CoV Mpro inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shailesh Mani Tripathi
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Rajasthan, India
| | - Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Ashulia, Bangladesh
| | | | - Sandeep Sundriyal
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Rajasthan, India
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K P, Prasanth DSNBK, Shadakshara MKR, Ahmad SF, Seemaladinne R, Rudrapal M, Pasala PK. Citronellal as a Promising Candidate for Alzheimer's Disease Treatment: A Comprehensive Study on In Silico and In Vivo Anti-Acetylcholine Esterase Activity. Metabolites 2023; 13:1133. [PMID: 37999229 PMCID: PMC10672888 DOI: 10.3390/metabo13111133] [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: 10/01/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023] Open
Abstract
One of the primary therapeutic approaches for managing Alzheimer's disease (AD) involves the modulation of Acetylcholine esterase (AChE) activity to elevate acetylcholine (ACh) levels inside the brain. The current study employed computational chemistry approaches to evaluate the inhibitory effects of CTN on AChE. The docking results showed that Citronellal (CTN) and standard Donepezil (DON) have a binding affinity of -6.5 and -9.2 Kcal/mol, respectively, towards AChE. Further studies using molecular dynamics (MD) simulations were carried out on these two compounds. Binding free energy calculations and ligand-protein binding patterns suggested that CTN has a binding affinity of -12.2078. In contrast, DON has a much stronger binding relationship of -47.9969, indicating that the standard DON has a much higher binding affinity than CTN for AChE. In an in vivo study, Alzheimer-type dementia was induced in mice by scopolamine (1.5 mg/kg/day i.p) for 14 days. CTN was administered (25 and 50 mg/kg. i.p) along with scopolamine (SCO) administration. DON (0.5 mg/kg orally) was used as a reference drug. CTN administration significantly improved the mice's behavior as evaluated by the Morris water maze test, evident from decreased escape latency to 65.4%, and in the CPS test, apparent from reduced escape latency to 69.8% compared to the positive control mice. Moreover, CTN significantly increased the activities of antioxidant enzymes such as catalase and superoxide dismutase (SOD) compared to SCO. Furthermore, CTN administration significantly decreased SCO-induced elevated AChE levels in mice. These results were supported by histopathological and in silico molecular docking studies. CTN may be a potential antioxidant and neuroprotective supplement.
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Affiliation(s)
- Pavani K
- Department of Pharmacology, Santhiram College of Pharmacy, Jawaharlal Nehru Technological University Anantapur, Nandyal 518112, Andhra Pradesh, India;
| | - D S. N. B. K. Prasanth
- Department of Pharmacognosy, KVSR Siddhartha College of Pharmaceutical Sciences, Vijayawada 520010, Andhra Pradesh, India;
| | - Murthy K. R. Shadakshara
- Department of Chemical Engineering, Siddaganga Institute of Technology, Tumkur 572103, Karnataka, India;
| | - Sheikh F. Ahmad
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | | | - Mithun Rudrapal
- Department of Pharmaceutical Sciences, School of Biotechnology and Pharmaceutical Sciences, Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur 522213, Andhra Pradesh, India;
| | - Praveen Kumar Pasala
- Department of Pharmacology, Raghavendra Institute of Pharmaceutical Education and Research, JNTUA, Anantapuramu 515721, Andhra Pradesh, India
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Hossain MS, Roney M, Bin Mohd Yunus MY, Shariffuddin JH. Virtual screening, molecular docking, molecular dynamics, and MM-GBSA approaches identify prospective fructose-1,6-bisphosphatase inhibitors from pineapple for diabetes management. J Biomol Struct Dyn 2023:1-16. [PMID: 37916669 DOI: 10.1080/07391102.2023.2276889] [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: 05/24/2023] [Accepted: 10/22/2023] [Indexed: 11/03/2023]
Abstract
Diabetes affects millions globally and poses treatment challenges. Targeting the enzyme fructose-1,6-bisphosphatase (FBPase) in gluconeogenesis and exploring plant-based therapies offer potential solutions for improving diabetes management while supporting sustainability and medicinal advancements. Utilizing pineapple (Ananas comosus L. Merr.) waste as a source of drug precursors could be valuable for health and environmental care due to its medicinal benefits and abundant yearly biomass production. Therefore, this study conducted a virtual screening to identify potential natural compounds from pineapple that could inhibit FBPase activity. A total of 112 compounds were screened for drug-likeness and ADMET properties, and molecular docking simulations were performed on 20 selected compounds using blind docking. The lead compound, butane-2,3-diyl diacetate, was subjected to 100 ns MD simulations, revealing a binding energy of -5.4 kcal/mol comparable to metformin (-5.6 kcal/mol). The MD simulation also confirmed stable complexes with crucial hydrogen bonds. Glu20, Ala24, Thr27, Gly28, Glu29, Leu30, Val160, Met177, Asp178, and Cys179 were identified as key amino acids that stabilized the human liver FBPase-butane-2,3-diyl diacetate complex, while Tyr215 and Asp218 played a crucial role in the human liver FBPase-Metformin complex. Our study indicates that the lead compound has high intestinal solubility. Therefore, it would show rapid bloodstream distribution and effective action on the target protein, making butane-2,3-diyl diacetate a potential antidiabetic drug candidate. However, further investigations in vitro, preclinical, and clinical trials are required to thoroughly assess its efficacy and safety.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Sanower Hossain
- Centre for Sustainability of Mineral and Resource Recovery Technology (Pusat SMaRRT), Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Malaysia
| | - Miah Roney
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Malaysia
| | - Mohd Yusri Bin Mohd Yunus
- Centre for Sustainability of Mineral and Resource Recovery Technology (Pusat SMaRRT), Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Malaysia
- Faculty of Chemical and Process Engineering Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Malaysia
| | - Jun Haslinda Shariffuddin
- Centre for Sustainability of Mineral and Resource Recovery Technology (Pusat SMaRRT), Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Malaysia
- Faculty of Chemical and Process Engineering Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Malaysia
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Daniyan MO. pyGROMODS: a Python package for the generation of input files for molecular dynamic simulation with GROMACS. J Biomol Struct Dyn 2023:1-14. [PMID: 37489036 DOI: 10.1080/07391102.2023.2239929] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The pyGROMODS, an easy-to-use cross-platform python-based package, with a graphical user interface, for the generation of molecular dynamic (MD) input files and running MD simulation (MDS) of proteins, peptides, and protein-ligand complex using GROMACS, is here presented. Four routes, with underlining Python scripts, are implemented in pyGROMODS for the generation of MD input files. They are 'RLmulti' for processing multi-ligand protein complex, 'RLmany' for processing multiple ligands against a single protein target, 'RLsingle' for processing multiple pairs of proteins and ligands, and 'PPmore' for processing peptides or proteins without ligands or non-standard residues. In addition, using the package, the generated input files or appropriate input files from other sources can be uploaded to run MDS with GROMACS. The pyGROMODS is implemented with a unique ability to search the host machine systems for the installation of the required software, update and/or install required Python packages, allow the user to pre-define working directory, and generate unique workflow organization with well-defined folders and files in a well-organized manner. The pyGROMODS, which is released under the MIT License, is freely available for download via the GitHub (https://github.com/Dankem/pyGROMODS) and Zenodo (https://doi.org/10.5281/zenodo.7912747) repositories. The precompiled executables can also be downloaded from Zenodo (https://doi.org/10.5281/zenodo.8087090), and a video tutorial can be downloaded from https://youtu.be/I4OKc6uVx1M.Communicated by Ramaswamy H. Sarma.
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Soudani W, Zaki H, Alaqarbeh M, ELMchichi L, Bouachrine M, Hadjadj-Aoul FZ. Discover the Medication Potential of Algerian Medicinal Plants Against Sars-Cov-2 Main Protease (M pro): Molecular Docking, Molecular Dynamic Simulation, and ADMET Analysis. Chemistry Africa 2023. [PMCID: PMC10238776 DOI: 10.1007/s42250-023-00684-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/16/2023] [Indexed: 07/25/2023]
Abstract
At the end of 2019, the world faced a big challenge and crisis caused by the SARS-CoV-2 virus. It spreads rapidly and is contagious; no treatment has officially been found. Algeria has used medicinal plants native to the country to defend against this pandemic. The objective of this paper is based on a molecular docking study of the active compounds of five Algerian medicinal plants with their target Sars-2Cov-2 virus protease to assess their potential antiviral activity against COVID-19. Innovative software and computerized databases were introduced into the in-silico domain, mainly the Auto-Dock software version 1.5.6. Similar results were obtained for all ligands, with a better chemical affinity of − 5.600 kcal/mol for the protease target 6LU7 and − 5.700 kcal/mol for the protease target 6WTT, with an average of − 4.227 kcal/mol and − 4.221 kcal/mol, respectively. The protease targets 6LU7 and 6WTT. In the ADME-Tox study, the active compounds of Algerian medicinal plants also demonstrated an excellent pharmacokinetic and toxic profile. Best scores were noted for cedrol, camphor, and eucalyptol. A molecular dynamics simulation showed the stability of camphor-6LU7 and cedrol-6LU7 complexes, favoring the biological potential of white artemisia and cypress plants.
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Affiliation(s)
- Wafa Soudani
- Therapeutic Chemistry Laboratory, Department of Pharmacy, Annaba Faculty of Medicine, 23000 Annaba, Algeria
| | - Hanane Zaki
- Biotechnology, Bioresources and Bioinformatics Laboratory, Higher School of Technology, 54000 Khenifra, Morocco
| | - Marwa Alaqarbeh
- National Agricultural Research Center, Al-Baqa, 19381 Jordan
| | - Larbi ELMchichi
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University of Meknes, 50000 Meknes, Morocco
| | - Mohammed Bouachrine
- Biotechnology, Bioresources and Bioinformatics Laboratory, Higher School of Technology, 54000 Khenifra, Morocco
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University of Meknes, 50000 Meknes, Morocco
| | - Fatima Zohra Hadjadj-Aoul
- Therapeutic Chemistry Laboratory, Department of Pharmacy, Algiers Faculty of Medicine, 16000 Algiers, Algeria
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Azad I, Khan T, Ahmad N, Khan AR, Akhter Y. Updates on drug designing approach through computational strategies: a review. Future Sci OA 2023; 9:FSO862. [PMID: 37180609 PMCID: PMC10167725 DOI: 10.2144/fsoa-2022-0085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/12/2023] [Indexed: 05/16/2023] Open
Abstract
The drug discovery and development (DDD) process in pursuit of novel drug candidates is a challenging procedure requiring lots of time and resources. Therefore, computer-aided drug design (CADD) methodologies are used extensively to promote proficiency in drug development in a systematic and time-effective manner. The point in reference is SARS-CoV-2 which has emerged as a global pandemic. In the absence of any confirmed drug moiety to treat the infection, the science fraternity adopted hit and trial methods to come up with a lead drug compound. This article is an overview of the virtual methodologies, which assist in finding novel hits and help in the progression of drug development in a short period with a specific medicinal solution.
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Affiliation(s)
- Iqbal Azad
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Tahmeena Khan
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Naseem Ahmad
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Abdul Rahman Khan
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, UP, 2260025, India
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24
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Motta S, Bonati L. TCDD-Induced Allosteric Perturbation of the AhR:ARNT Binding to DNA. Int J Mol Sci 2023; 24:ijms24119339. [PMID: 37298290 DOI: 10.3390/ijms24119339] [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: 04/05/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that mediates the biological and toxicological effects of structurally diverse chemicals, including halogenated aromatic hydrocarbons. In this work, we investigate the effects of the binding of the AhR prototypical ligand, TCDD, on the stability of the AhR:ARNT complex, as well as the mechanisms by which ligand-induced perturbations propagate to the DNA recognition site responsible for gene transcription. To this aim, a reliable structural model of the overall quaternary structure of the AhR:ARNT:DRE complex is proposed, based on homology modelling. The model shows very good agreement with a previous one and is supported by experimental evidence. Moreover, molecular dynamics simulations are performed to compare the dynamic behaviour of the AhR:ARNT heterodimer in the presence or absence of the TCDD. Analysis of the simulations, performed by an unsupervised machine learning method, shows that TCDD binding to the AhR PASB domain influences the stability of several inter-domain interactions, in particular at the PASA-PASB interface. The inter-domain communication network suggests a mechanism by which TCDD binding allosterically stabilizes the interactions at the DNA recognition site. These findings may have implications for the comprehension of the different toxic outcomes of AhR ligands and drug design.
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Affiliation(s)
- Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Laura Bonati
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, 20126 Milan, Italy
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25
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Araque I, Ramírez J, Vergara R, Mella J, Aránguiz P, Espinoza L, Vera W, Montenegro I, Salas CO, Villena J, Cuellar MA. Cytotoxic Activity, Topoisomerase I Inhibition and In Silico Studies of New Sesquiterpene-aryl Ester Derivatives of (-) Drimenol. Molecules 2023; 28:molecules28093959. [PMID: 37175368 PMCID: PMC10179937 DOI: 10.3390/molecules28093959] [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: 03/27/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
In this study, we aimed to evaluate two sets of sesquiterpene-aryl derivatives linked by an ester bond, their cytotoxic activities, and their capacity to activate caspases 3/7 and inhibit human topoisomerase I (TOP1). A total of 13 compounds were synthesized from the natural sesquiterpene (-)-drimenol and their cytotoxic activity was evaluated in vitro against three cancer cell lines: PC-3 (prostate cancer), HT-29 (colon cancer), MCF-7 (breast cancer), and an immortalized non-tumoral cell line (MCF-10). From the results, it was observed that 6a was the most promising compound due to its cytotoxic effect on three cancer cell lines and its selectivity, 6a was 100-fold more selective than 5-FU in MCF-7 and 20-fold in PC-3. It was observed that 6a also induced apoptosis by caspases 3/7 activity using a Capsase-Glo-3/7 assay kit and inhibited TOP1. A possible binding mode of 6a in a complex with TOP1-DNA was proposed by docking and molecular dynamics studies. In addition, 6a was predicted to have a good pharmacokinetic profile for oral administration. Therefore, through this study, it was demonstrated that the drimane scaffold should be considered in the search of new antitumoral agents.
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Affiliation(s)
- Ileana Araque
- Facultad de Farmacia, Escuela de Química y Farmacia, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso 2340000, Chile
| | - Javiera Ramírez
- Facultad de Farmacia, Escuela de Química y Farmacia, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso 2340000, Chile
| | - Rut Vergara
- Centro de Investigaciones Biomédicas, Escuela de Medicina, Facultad de Medicina, Universidad de Valparaíso, Viña del Mar 2520000, Chile
| | - Jaime Mella
- Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2340000, Chile
- Centro de Investigación Farmacopea Chilena (CIFAR), Universidad de Valparaíso, Valparaíso 2340000, Chile
| | - Pablo Aránguiz
- Escuela de Química y Farmacia, Facultad de Medicina, Universidad Andrés Bello, Viña del Mar 2520000, Chile
| | - Luis Espinoza
- Departamento de Química, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2340000, Chile
| | - Waleska Vera
- Facultad de Farmacia, Escuela de Química y Farmacia, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso 2340000, Chile
- Centro de Investigación Farmacopea Chilena (CIFAR), Universidad de Valparaíso, Valparaíso 2340000, Chile
| | - Iván Montenegro
- Centro de Investigación Farmacopea Chilena (CIFAR), Universidad de Valparaíso, Valparaíso 2340000, Chile
- Facultad de Medicina, Escuela de Obstetricia y Puericultura, Universidad de Valparaíso, Angamos 655, Reñaca, Viña del Mar 2520000, Chile
| | - Cristian O Salas
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, Santiago de Chile 7820436, Chile
| | - Joan Villena
- Centro de Investigaciones Biomédicas, Escuela de Medicina, Facultad de Medicina, Universidad de Valparaíso, Viña del Mar 2520000, Chile
| | - Mauricio A Cuellar
- Facultad de Farmacia, Escuela de Química y Farmacia, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso 2340000, Chile
- Centro de Investigación Farmacopea Chilena (CIFAR), Universidad de Valparaíso, Valparaíso 2340000, Chile
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Shalayel MHF, Al-Mazaideh GM, Alanezi AA, Almuqati AF, Alotaibi M. Diosgenin and Monohydroxy Spirostanol from Prunus amygdalus var amara Seeds as Potential Suppressors of EGFR and HER2 Tyrosine Kinases: A Computational Approach. Pharmaceuticals (Basel) 2023; 16:ph16050704. [PMID: 37242487 DOI: 10.3390/ph16050704] [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: 03/08/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Cancer continues to be leading cause of death globally, with nearly 7 million deaths per year. Despite significant progress in cancer research and treatment, there remain several challenges to overcome, including drug resistance, the presence of cancer stem cells, and high interstitial fluid pressure in tumors. To tackle these challenges, targeted therapy, specifically targeting HER2 (Human Epidermal Growth Factor Receptor 2) as well as EGFR (Epidermal Growth Factor Receptor), is considered a promising approach in cancer treatment. In recent years, phytocompounds have gained recognition as a potential source of chemopreventive and chemotherapeutic agents in tumor cancer treatment. Phytocompounds are compounds derived from medicinal plants that have the potential to treat and prevent cancer. This study aimed to investigate phytocompounds from Prunus amygdalus var amara seeds as inhibitors against EGFR and HER2 enzymes using in silico methods. In this study, fourteen phytocompounds were isolated from Prunus amygdalus var amara seeds and subjected to molecular docking studies to determine their ability to bind to EGFR and HER2 enzymes. The results showed that diosgenin and monohydroxy spirostanol exhibited binding energies comparable to those of the reference drugs, tak-285, and lapatinib. Furthermore, the drug-likeness and ADMET predictions, performed using the admetSAR 2.0 web-server tool, suggested that diosgenin and monohydroxy spirostanol have similar safety and ADMET properties as the reference drugs. To get deeper insight into the structural steadiness and flexibility of the complexes formed between these compounds and theEGFR and HER2 proteins, molecular dynamics simulations were performed for 100 ns. The results showed that the hit phytocompounds did not significantly affect the stability of the EGFR and HER2 proteins and were able to form stable interactions with the catalytic binding sites of the proteins. Additionally, the MM-PBSA analysis revealed that the binding free energy estimates for diosgenin and monohydroxy spirostanol is comparable to the reference drug, lapatinib. This study provides evidence that diosgenin and monohydroxy spirostanol may have the potential to act as dual suppressors of EGFR and HER2. Additional in vivo and in vitro research are needed to certify these results and assess their efficacy and safety as cancer therapy agents. The experimental data reported and these results are in agreement.
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Affiliation(s)
- Mohammed Helmy Faris Shalayel
- Department of Pharmacy Practice, College of Pharmacy, University of Hafr Al Batin, Hafr Al Batin 31991, Saudi Arabia
| | - Ghassab M Al-Mazaideh
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hafr Al Batin, Hafr Al Batin 31991, Saudi Arabia
| | - Abdulkareem A Alanezi
- Department of Pharmaceutics, College of Pharmacy, University of Hafr Al Batin, Hafr Al Batin 31991, Saudi Arabia
| | - Afaf F Almuqati
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hafr Al Batin, Hafr Al Batin 31991, Saudi Arabia
| | - Meshal Alotaibi
- Department of Pharmacy Practice, College of Pharmacy, University of Hafr Al Batin, Hafr Al Batin 31991, Saudi Arabia
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27
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Yuan N, Ye L, Sun Y, Wu H, Xiao Z, Fu W, Chen Z, Pei Y, Min Y, Wang D. Molecular Integrative Analysis of the Inhibitory Effects of Dipeptides on Amyloid β Peptide 1-42 Polymerization. Int J Mol Sci 2023; 24:ijms24087673. [PMID: 37108834 PMCID: PMC10141046 DOI: 10.3390/ijms24087673] [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: 03/04/2023] [Revised: 04/02/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
The major pathological feature of Alzheimer's disease (AD) is the aggregation of amyloid β peptide (Aβ) in the brain. Inhibition of Aβ42 aggregation may prevent the advancement of AD. This study employed molecular dynamics, molecular docking, electron microscopy, circular dichroism, staining of aggregated Aβ with ThT, cell viability, and flow cytometry for the detection of reactive oxygen species (ROS) and apoptosis. Aβ42 polymerizes into fibrils due to hydrophobic interactions to minimize free energy, adopting a β-strand structure and forming three hydrophobic areas. Eight dipeptides were screened by molecular docking from a structural database of 20 L-α-amino acids, and the docking was validated by molecular dynamics (MD) analysis of binding stability and interaction potential energy. Among the dipeptides, arginine dipeptide (RR) inhibited Aβ42 aggregation the most. The ThT assay and EM revealed that RR reduced Aβ42 aggregation, whereas the circular dichroism spectroscopy analysis showed a 62.8% decrease in β-sheet conformation and a 39.3% increase in random coiling of Aβ42 in the presence of RR. RR also significantly reduced the toxicity of Aβ42 secreted by SH-SY5Y cells, including cell death, ROS production, and apoptosis. The formation of three hydrophobic regions and polymerization of Aβ42 reduced the Gibbs free energy, and RR was the most effective dipeptide at interfering with polymerization.
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Affiliation(s)
- Nan Yuan
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Lianmeng Ye
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Yan Sun
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Hao Wu
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Zhengpan Xiao
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Wanmeng Fu
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Zuqian Chen
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Yechun Pei
- One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
- Department of Biosciences, School of Life Sciences, Hainan University, Haikou 570228, China
| | - Yi Min
- Department of Biosciences, School of Life Sciences, Hainan University, Haikou 570228, China
| | - Dayong Wang
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
- Key Laboratory of Tropical Biological Resources of the Ministry of China, Hainan University, Haikou 570228, China
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28
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Galashev A, Abramova K. Molecular Dynamics Simulation of Thin Silicon Carbide Films Formation by the Electrolytic Method. Materials (Basel) 2023; 16:3115. [PMID: 37109951 PMCID: PMC10144933 DOI: 10.3390/ma16083115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/13/2023] [Accepted: 04/13/2023] [Indexed: 06/19/2023]
Abstract
Silicon carbide is successfully implemented in semiconductor technology; it is also used in systems operating under aggressive environmental conditions, including high temperatures and radiation exposure. In the present work, molecular dynamics modeling of the electrolytic deposition of silicon carbide films on copper, nickel, and graphite substrates in a fluoride melt is carried out. Various mechanisms of SiC film growth on graphite and metal substrates were observed. Two types of potentials (Tersoff and Morse) are used to describe the interaction between the film and the graphite substrate. In the case of the Morse potential, a 1.5 times higher adhesion energy of the SiC film to graphite and a higher crystallinity of the film was observed than is the case of the Tersoff potential. The growth rate of clusters on metal substrates has been determined. The detailed structure of the films was studied by the method of statistical geometry based on the construction of Voronoi polyhedra. The film growth based on the use of the Morse potential is compared with a heteroepitaxial electrodeposition model. The results of this work are important for the development of a technology for obtaining thin films of silicon carbide with stable chemical properties, high thermal conductivity, low thermal expansion coefficient, and good wear resistance.
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Affiliation(s)
- Alexander Galashev
- Institute of High-Temperature Electrochemistry, Ural Branch of Russia Academy of Science, Academicheskaya Str., 20, Yekaterinburg 620990, Russia
- Institute of Chemical Engineering, Ural Federal University Named after the First President of Russia B.N. Yeltsin, Mira Str., 19, Yekaterinburg 620002, Russia
| | - Ksenia Abramova
- Institute of High-Temperature Electrochemistry, Ural Branch of Russia Academy of Science, Academicheskaya Str., 20, Yekaterinburg 620990, Russia
- Institute of Chemical Engineering, Ural Federal University Named after the First President of Russia B.N. Yeltsin, Mira Str., 19, Yekaterinburg 620002, Russia
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29
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Sary HG, Khedr MA, Orabi KY. Novel Vulgarin Derivatives: Chemical Transformation, In Silico and In Vitro Studies. Molecules 2023; 28:molecules28083421. [PMID: 37110654 PMCID: PMC10143240 DOI: 10.3390/molecules28083421] [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: 03/16/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Vulgarin, an eudesmanolide sesquiterpene isolated from Artemisia judaica, was refluxed with iodine to produce two derivatives (1 and 2), which were purified and spectroscopically identified as naproxen methyl ester analogs. The reaction mechanism by which 1 and 2 were formed is explained using a sigmatropic reaction with a 1,3 shift. The scaffold hopping via lactone ring opening enabled the new derivatives of vulgarin (1 and 2) to fit well inside the COX-2 active site with ΔG of -7.73 and -7.58 kcal/mol, respectively, which was better than that of naproxen (ΔG of -7.04 kcal/mol). Moreover, molecular dynamic simulations showed that 1 was able to achieve a faster steady-state equilibrium than naproxen. The novel derivative 1 showed promising cytotoxic activities against HepG-2, HCT-116, MCF-7, and A-549 cancer cell lines compared to those of vulgarin and naproxen.
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Affiliation(s)
- Hanan G Sary
- Department of Pharmaceutical Chemistry, College of Pharmacy, Kuwait University, Safat 13110, Kuwait
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Cairo 11566, Egypt
| | - Mohammed A Khedr
- Department of Pharmaceutical Chemistry, College of Pharmacy, Kuwait University, Safat 13110, Kuwait
| | - Khaled Y Orabi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Kuwait University, Safat 13110, Kuwait
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30
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Harmak H, Redouane S, Charoute H, Aniq Filali O, Barakat A, Rouba H. In silico exploration and molecular dynamics of deleterious SNPs on the human TERF1 protein triggering male infertility. J Biomol Struct Dyn 2023; 41:14665-14688. [PMID: 36995171 DOI: 10.1080/07391102.2023.2193995] [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: 11/15/2022] [Accepted: 02/18/2023] [Indexed: 03/31/2023]
Abstract
By limiting chromosome erosion and end-to-end fusions, telomere integrity is critical for chromosome stability and cell survival. During mitotic cycles or due to environmental stresses, telomeres become progressively shorter and dysfunctional, thus triggering cellular senescence, genomic instability and cell death. To avoid such consequences, the telomerase action, as well as the Shelterin and CST complexes, assure the telomere's protection. Telomeric repeat binding factor 1 (TERF1), which is one of the primary components of the Shelterin complex, binds directly to the telomere and controls its length and function by regulating the telomerase activity. Several reports about TERF1 gene variations have been associated with different diseases, and some of them have linked these variations to male infertility. Hence, this paper can be advantageous to investigate the association between the missense variants of the TERF1 gene and the susceptibility to male infertility. The stepwise prediction of SNPs pathogenicity followed in this study was based on stability and conservation analysis, post-translational modification, secondary structure, functional interaction prediction, binding energy evaluation and finally molecular dynamic simulation. Prediction matching among the tools revealed that out of 18 SNPs, only four (rs1486407144, rs1259659354, rs1257022048 and rs1320180267) were predicted as the most damaging and highly deleterious SNPs affecting the TERF1 protein and its molecular dynamics when interacting with the TERB1 protein by influencing the function, structural stability, flexibility and compaction of the overall complex. Interestingly, these polymorphisms should be considered during genetic screening so they can be used effectively as genetic biomarkers for male infertility diagnosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Houda Harmak
- Laboratory of Genomics and Human Genetics, 1, Place Louis Pasteur, Institut Pasteur du Maroc, Casablanca, Morocco
- Laboratory of Physiopathology, Molecular Genetics and Biotechnology, Department of Biology, Faculty of Sciences Ain Chock, Hassan II University, Casablanca, Morocco
| | - Salaheddine Redouane
- Laboratory of Genomics and Human Genetics, 1, Place Louis Pasteur, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Hicham Charoute
- Research Unit of Epidemiology, Biostatistics and Bioinformatics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Ouafaa Aniq Filali
- Laboratory of Physiopathology, Molecular Genetics and Biotechnology, Department of Biology, Faculty of Sciences Ain Chock, Hassan II University, Casablanca, Morocco
| | - Abdelhamid Barakat
- Laboratory of Genomics and Human Genetics, 1, Place Louis Pasteur, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Hassan Rouba
- Laboratory of Genomics and Human Genetics, 1, Place Louis Pasteur, Institut Pasteur du Maroc, Casablanca, Morocco
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31
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Makki AA, Ibraheem W, Alzain AA. Cytosporone E analogues as BRD4 inhibitors for cancer treatment: molecular docking and molecular dynamic investigations. J Biomol Struct Dyn 2023; 41:12643-12653. [PMID: 36644887 DOI: 10.1080/07391102.2023.2167122] [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: 10/31/2022] [Accepted: 01/05/2023] [Indexed: 01/17/2023]
Abstract
Cancer is considered one of the worldwide life-threatening and leading causes of human mortality. In 2020, 19,292,789 cancer cases and 9,958,133 cancer deaths have been estimated worldwide. Therefore, efforts have been devoted to discover novel anticancer agents. Bromodomains have a vital role in the regulation of transcription. Many reports have shown that bromodomain-containing protein 4 (BRD4) is an important target for cancer therapeutics. In this study, several in silico approaches were utilized to discover new inhibitors against the BRD4 protein using the Schrodinger suite. A library of 27 cytosporone E derivatives was docked into the active site of the BRD4 protein. Docked ligands showed docking scores ranging between -11.289 to -3.992 Kcal/mol. Ligands 1-4 showed better binding affinities with docking scores ranging from -11.289 to -8.917 Kcal/mol compared to the reference ligand BI-2536 (-8.426 Kcal/mol). These ligands displayed favorable MM-GBSA free binding energy. Also, ligands 1-4 were subjected to molecular dynamics simulations for 100 ns to get insight into the ligand-binding stability. These compounds exhibited an average RMSD below 2.8 Å, indicating the stability of the compounds with BRD4 protein. Further, Moreover, ligands 1-3 displayed favorable AMDET properties (absorption, distribution, metabolism, excretion, and toxicity). These new compounds might be potential leads to combat cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alaa A Makki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Walaa Ibraheem
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Abdulrahim A Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
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32
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Dahri M, Miri Jahromi A, Nikzad A, Mohammadgholian M, Rahmanian M, Abolmaali SS, Maleki R. Novel bioengineered MBenes for the treatment of Alzheimer's disease: An in-Sillico study. J Biomol Struct Dyn 2022; 40:12268-12276. [PMID: 34427178 DOI: 10.1080/07391102.2021.1969288] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Alzheimer's disease is a neurodegenerative disease caused by the deposition and accumulation of amyloid-β (Aβ) peptides in the brain neurons. Current medications are not a definitive cure for this disease, but they can hamper the signs and symptoms of Alzheimer's disease. Therefore, prevention is the best way to deal with this disease. In this study, the novel structures based on MBenes (such as Cd2B, Mo2B, Cu2B, and Ta2B) are proposed to prevent amyloid-β accumulation in Alzheimer's disease. Regarding the remarkable MBene properties such as tunability, biocompatibility, and low manufacturing cost, the effect of these structures on amyloid-β deformation was explored using molecular dynamics simulation. To provide an atomic analysis of Beta-amyloid behavior in the presence of these structures, the compaction, contact area, and stability of Beta-amyloid were investigated. The results indicated the satisfactory performance of MBenes on the destabilization of amyloid-β structures. Moreover, given the higher interactions between Cd2B and amyloid-β, the instability, compaction, and the contact area of amyloid-β particles were investigated in this complex. The findings confirmed Cd2B as the best structure to prevent amyloid-β accumulation. The results of this investigation paved the way for the development of these structures as a medicinal agent to prevent Alzheimer's disease.
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Affiliation(s)
- Mohammad Dahri
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Department of Physics, Tehran University, Tehran, Iran.,Center for Nanotechnology in Drug Delivery, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Miri Jahromi
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Department of Physics, Tehran University, Tehran, Iran
| | - Arash Nikzad
- The University of British Columbia, Vancouver, Canada
| | - Maryam Mohammadgholian
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Department of Physics, Tehran University, Tehran, Iran
| | - Mohammad Rahmanian
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samira Sadat Abolmaali
- Center for Nanotechnology in Drug Delivery, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Pharmaceutical Nanotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Maleki
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Department of Physics, Tehran University, Tehran, Iran
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Nakayama M, Goto S, Goto S. Physical Characteristics of von Willebrand Factor Binding with Platelet Glycoprotein Ibɑ Mutants at Residue 233 Causing Various Biological Functions. TH Open 2022; 6:e421-e428. [PMID: 36632284 PMCID: PMC9729063 DOI: 10.1055/a-1937-9940] [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] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/05/2022] [Indexed: 01/14/2023]
Abstract
Glycoprotein (GP: HIS 1 -PRO 265 ) Ibɑ is a receptor protein expressed on the surface of the platelet. Its N-terminus domain binds with the A1 domain (ASP 1269 -PRO 1472 ) of its ligand protein von Willebrand factor (VWF) and plays a unique role in platelet adhesion under blood flow conditions. Single amino acid substitutions at residue 233 from glycine (G) to alanine (A), aspartic acid (D), or valine (V) are known to cause biochemically distinct functional alterations known as equal, loss, and gain of function, respectively. However, the underlying physical characteristics of VWF binding with GPIbɑ in wild-type and the three mutants exerting different biological functions are unclear. Here, we aimed to test the hypothesis: biological characteristics of macromolecules are influenced by small changes in physical parameters. The position coordinates and velocity vectors of all atoms and water molecules constructing the wild-type and the three mutants of GPIbɑ (G233A, G233D, and G233V) bound with VWF were calculated every 2 × 10 -15 seconds using the CHARMM (Chemistry at Harvard Macromolecular Mechanics) force field for 9 × 10 -10 seconds. Six salt bridges were detected for longer than 50% of the calculation period for the wild-type model generating noncovalent binding energy of -1096 ± 137.6 kcal/mol. In contrast, only four pairs of salt bridges were observed in G233D mutant with noncovalent binding energy of -865 ± 139 kcal/mol. For G233A and G233V, there were six and five pairs of salt bridges generating -929.8 ± 88.5 and -989.9 ± 94.0 kcal/mol of noncovalent binding energy, respectively. Our molecular dynamic simulation showing a lower probability of salt bridge formation with less noncovalent binding energy in VWF binding with the biologically loss of function G233D mutant of GPIbɑ as compared with wild-type, equal function, and gain of function mutant suggests that biological functions of macromolecules such as GPIbɑ are influenced by their small changes in physical characteristics.
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Affiliation(s)
- Masamitsu Nakayama
- Department of Medicine (Cardiology), Tokai University School of Medicine, Isehara, Japan
| | - Shinichi Goto
- Department of Medicine (Cardiology), Tokai University School of Medicine, Isehara, Japan
| | - Shinya Goto
- Department of Medicine (Cardiology), Tokai University School of Medicine, Isehara, Japan,Address for correspondence Shinya Goto, MD, PhD Department of Medicine (Cardiology), Tokai University School of Medicine143 Shimokasuya, IseharaJapan
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Zeng Q, Zhu J. Analysis of Adhesion at the Interface of Steamed Bread and Eggshell. Molecules 2022; 27:molecules27238179. [PMID: 36500271 PMCID: PMC9737473 DOI: 10.3390/molecules27238179] [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] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/08/2022] [Accepted: 11/19/2022] [Indexed: 11/25/2022]
Abstract
The adhesion phenomenon of polymers occurs in nature and in human activity. In the present paper, an adhesion system of steamed bread and eggshell was observed in formation when steamed bread and eggshells were placed in close contact and cooled slightly in the ambient air. The adhesion phenomena and mechanism of the adhesion interface between the steamed bread and eggshell were investigated and systematically discussed. Strong-bond interfaces were observed by scanning electron microscope (SEM). The formation process and mechanism of the strong-bond adhesion were also analyzed molecular dynamics simulation technology, and the results are discussed. The simulation analyses showed that the starch molecules at the calcite (104) crystal face were diffused in a water vapor environment, and the formation and solidification of multiple hydrogen bonds in the starch chain and oxygen atoms in the calcium carbonate were observed in detail during cooling. The diffusion rate of hydrogen atoms in hydroxyl groups on the calcite surface decreased gradually with the decrease of the cooling temperature of the steamed bread's upper surface. The strong adhesion of the steamed bread and eggshell is attributed to the synthetic effect of the absorption, diffusion, surface chemistry, and the formation of multiple hydrogen bonds between the starch from the steamed bread and the calcium carbonate crystals in eggshell. The interesting findings are helpful for the design of strong bonds, and provide an idea for new environmentally friendly adhesive materials.
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Shkolin AV, Strizhenov EM, Chugaev SS, Men’shchikov IE, Gaidamavichute VV, Grinchenko AE, Zherdev AA. Natural Gas Storage Filled with Peat-Derived Carbon Adsorbent: Influence of Nonisothermal Effects and Ethane Impurities on the Storage Cycle. Nanomaterials (Basel) 2022; 12:4066. [PMID: 36432352 PMCID: PMC9694911 DOI: 10.3390/nano12224066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Adsorbed natural gas (ANG) is a promising solution for improving the safety and storage capacity of low-pressure gas storage systems. The structural-energetic and adsorption properties of active carbon ACPK, synthesized from cheap peat raw materials, are presented. Calculations of the methane-ethane mixture adsorption on ACPK were performed using the experimental adsorption isotherms of pure components. It is shown that the accumulation of ethane can significantly increase the energy capacity of the ANG storage. Numerical molecular modeling of the methane-ethane mixture adsorption in slit-like model micropores has been carried out. The molecular effects associated with the displacement of ethane by methane molecules and the formation of a molecule layered structure are shown. The integral molecular adsorption isotherm of the mixture according to the molecular modeling adequately corresponds to the ideal adsorbed solution theory (IAST). The cyclic processes of gas charging and discharging from the ANG storage based on the ACPK are simulated in three modes: adiabatic, isothermal, and thermocontrolled. The adiabatic mode leads to a loss of 27-33% of energy capacity at 3.5 MPa compared to the isothermal mode, which has a 9.4-19.5% lower energy capacity compared to the thermocontrolled mode, with more efficient desorption of both methane and ethane.
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Affiliation(s)
- Andrey V. Shkolin
- Research Institute of Power Engineering, Bauman Moscow State Technical University, Baumanskaya 2-ya str. 5, 105005 Moscow, Russia
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninskii Prospect, 31, Build. 4, 119071 Moscow, Russia
| | - Evgeny M. Strizhenov
- Research Institute of Power Engineering, Bauman Moscow State Technical University, Baumanskaya 2-ya str. 5, 105005 Moscow, Russia
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninskii Prospect, 31, Build. 4, 119071 Moscow, Russia
| | - Sergey S. Chugaev
- Research Institute of Power Engineering, Bauman Moscow State Technical University, Baumanskaya 2-ya str. 5, 105005 Moscow, Russia
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninskii Prospect, 31, Build. 4, 119071 Moscow, Russia
| | - Ilya E. Men’shchikov
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninskii Prospect, 31, Build. 4, 119071 Moscow, Russia
| | - Viktoriia V. Gaidamavichute
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninskii Prospect, 31, Build. 4, 119071 Moscow, Russia
| | - Alexander E. Grinchenko
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninskii Prospect, 31, Build. 4, 119071 Moscow, Russia
| | - Anatoly A. Zherdev
- Research Institute of Power Engineering, Bauman Moscow State Technical University, Baumanskaya 2-ya str. 5, 105005 Moscow, Russia
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Acar Çevik U, Işık A, Evren AE, Kapusız Ö, Gül ÜD, Özkay Y, Kaplancıklı ZA. Synthesis of new benzimidazole derivatives containing 1,3,4-thiadiazole: their in vitro antimicrobial, in silico molecular docking and molecular dynamic simulations studies. SAR QSAR Environ Res 2022; 33:899-914. [PMID: 36420624 DOI: 10.1080/1062936x.2022.2149620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
A series of some new benzimidazole-1,3,4-thiadiazoles was synthesized. The structures of target substances were confirmed by using 1H-NMR and 13С-NMR spectroscopy, mass spectrometry and elemental analysis. The synthesized compounds were evaluated for antimicrobial activity against six bacterial strains namely Escherichia coli (ATCC 25922), Klebsiella pneumoniae (ATCC 13883), Pseudomonas aeruginosa (ATCC 27853), Enterococcus faecalis (ATCC 2942), Bacillus subtilis (ATCC 6633), Staphylococcus aureus (ATCC 29213)and four fungal strains namely Candida albicans (ATCC 24433), Candida krusei (ATCC 6258), Candida parapsilosis (ATCC 22019) and Candida glabrata (ATCC 9). Antimicrobial data revealed that compounds 4f and 4i with MIC of < 0.97 µg/mL were found to be most effective against E. coli. Among the studied molecules, compounds 4f and 4i showed the best antifungal activity with MIC value of 1.95 µg/mL. Additionally, docking studies were performed towards the most promising compounds 4f and 4i, in the active site of DNA gyrase revealing strong interactions. A molecular dynamics (MD) simulation analysis was also used to investigate the dynamic nature, binding interaction, and protein-ligand stability.
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Affiliation(s)
- U Acar Çevik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
| | - A Işık
- Department of Biochemistry, Faculty of Science, Selçuk University, Konya, Turkey
| | - A E Evren
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
- Department of Pharmacy Services, Bilecik Şeyh Edebali University, Vocational School of Health Services, Bilecik, Turkey
| | - Ö Kapusız
- Bioengineering, Bilecik Şeyh Edebali University, Graduate Education Institute, Bilecik, Turkey
| | - Ü D Gül
- Department of Bioengineering, Faculty of Engineering, Bilecik Seyh Edebali University, Bilecik, Turkey
| | - Y Özkay
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
| | - Z A Kaplancıklı
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
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Rani I, Goyal A, Sharma M. Computational Design of Phosphatidylinositol 3-Kinase Inhibitors. Assay Drug Dev Technol 2022; 20:317-337. [PMID: 36269231 DOI: 10.1089/adt.2022.057] [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] [Indexed: 06/16/2023] Open
Abstract
One of the most sought-after therapeutic targets for treating human cancers is the phosphoinositide 3-kinase; PI3k is an integral part of the PI3K/protein kinase B signaling arcade. This pathway is frequently activated in malignancies. Drug resistance and dose-limiting adverse effects are currently associated challenges with the existing anticancer chemotherapy. Therefore, in this research, a series of pyrimidine derivatives were designed and evaluated against human PI3K by using molecular docking analysis. The docking results were further verified by molecular dynamic simulation, which analyzed the strength of the macromolecular complex with respect to time. Compounds IV and XIV were found to be the most potent inhibitors of the human PI3K receptor with a high degree of stability within the active site of the target receptor for a timeframe of 50 ns. Thus, both of these compounds could be important drug candidates for the development of PI3K inhibitors as a prospective anticancer agent.
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Affiliation(s)
- Isha Rani
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
- Department of Pharmaceutical Chemistry, M.M. College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Ambala, India
| | - Anju Goyal
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - M Sharma
- Institute of Advanced Research (IAR), Gandhinagar, India
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Shi S, Lin L, Hu Z, Gu L, Zhang Y. Study on the Stability of Bio-Oil Modified Prime Coat Oil Based on Molecular Dynamics. Materials (Basel) 2022; 15:6737. [PMID: 36234082 PMCID: PMC9571086 DOI: 10.3390/ma15196737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
To explore the effect of different emulsifier contents on the stability performance of biomass-emulsified asphalt, three types of emulsified asphalt with 1%, 3%, and 5% anionic emulsifiers were prepared and analyzed by molecular dynamics simulation and macroscopic experiments. Firstly, we used molecular simulation software (Material Studio, MS) to construct a model of biomass-emulsified asphalt with different emulsifier contents and analyzed the microscopic mechanism of the emulsifier to improve the stability of the emulsified asphalt by the radial distribution function, interaction energy, interfacial layer thickness, and solubility parameters of the emulsified asphalt system with different emulsifier contents. The results were validated by macro and micro tests including storage stability, particle size determination, and infrared spectroscopy. The results show that at low emulsifier contents, the emulsifier can reduce the interfacial tension between the oil-water interface and expand the transition region between the two phases (interfacial layer thickness), which will prevent interparticle agglomeration and reduce the emulsion particle size, thus reducing the settling rate and ensuring the stability of the emulsion. When the emulsifier content is further increased beyond the critical micelle concentration, the emulsifiers will agglomerate with each other and show larger peaks in the radial distribution function, and the phenomenon of emulsifier agglomeration will appear in the five-day storage stability test, resulting in a corresponding decrease in the proximity of the infrared absorption peak area ratio in the same wavelength band of the upper and lower layers of the biomass-emulsified asphalt, and the emulsion stability decreases instead.
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Affiliation(s)
- Shuang Shi
- School of Transportation, Southeast University, Southeast University Road #2, Nanjing 211189, China
| | - Lanqin Lin
- School of Transportation, Southeast University, Southeast University Road #2, Nanjing 211189, China
| | - Zhaoguang Hu
- China Road and Bridge Corporation, 88 Outer Andingmen Street, Beijing 100011, China
| | - Linhao Gu
- School of Transportation, Southeast University, Southeast University Road #2, Nanjing 211189, China
| | - Yanning Zhang
- School of Transportation, Southeast University, Southeast University Road #2, Nanjing 211189, China
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Dobrovskiy AY, Nazarychev VM, Volgin IV, Lyulin SV. The Transport Properties of Semi-Crystalline Polyetherimide BPDA-P3 in Amorphous and Ordered States: Computer Simulations. Membranes (Basel) 2022; 12:856. [PMID: 36135875 PMCID: PMC9504751 DOI: 10.3390/membranes12090856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
The effect of polymer chain ordering on the transport properties of the polymer membrane was examined for the semi-crystalline heterocyclic polyetherimide (PEI) BPDA-P3 based on 3,3',4,4'-biphenyltetracarboxylic dianhydride (BPDA) and diamine 1,4-bis [4-(4-aminophenoxy)phenoxy]benzene (P3). All-atom Molecular Dynamics (MD) simulations were used to investigate the gas diffusion process carried through the pores of a free volume several nanometers in size. The long-term (~30 μs) MD simulations of BPDA-P3 were performed at T = 600 K, close to the experimental value of the melting temperature (Tm ≈ 577 K). It was found during the simulations that the transition of the PEI from an amorphous state to an ordered one occurred. We determined a decrease in solubility for both the gases examined (CO2 and CH4), caused by the redistribution of free volume elements occurring during the structural ordering of the polymer chains in glassy state (Tg ≈ 487 K). By analyzing the diffusion coefficients in the ordered state, the presence of gas diffusion anisotropy was found. However, the averaged values of the diffusion coefficients did not differ from each other in the amorphous and ordered states. Thus, permeability in the observed system is primarily determined by gas solubility, rather than by gas diffusion.
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Affiliation(s)
| | | | | | - Sergey V. Lyulin
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoj pr. 31 (V.O.), 199004 St. Petersburg, Russia
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Jabraoui H, Esteve A, Schoenitz M, Dreizin EL, Rossi C. Atomic Scale Insights into the First Reaction Stages Prior to Al/CuO Nanothermite Ignition: Influence of Porosity. ACS Appl Mater Interfaces 2022; 14:29451-29461. [PMID: 35699731 DOI: 10.1021/acsami.2c07069] [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] [Indexed: 06/15/2023]
Abstract
This theoretical work aims to understand the influence of nanopores at CuO-Al nanothermite interfaces on the initial stage of thermite reaction. ReaxFF molecular dynamics simulations were run to investigate the chemical and structural evolution of the reacting interface between the fuel, Al, and oxidizer, CuO, between 400 and 900 K and considering interfaces with and without a pore. Results show that the initial alumina layer becomes enriched with Al and grows primarily into the Al metal at higher temperatures. The modification of alumina is driven by simultaneous Al and O migration between metallic Al and the native amorphous Al2O3 layer. However, the presence of a pore significantly affects the growth kinetics and the composition of this alumina layer at temperatures exceeding 600 K, which impacts the initiation properties of the nanothermite. In the system without a pore, where Al is in direct contact with CuO, a ternary aluminate layer, a mixture of Al, O, and Cu, is formed at 800 K, which slows Al and O diffusion, thus compromising the nanothermite reactivity in fully dense Al/CuO composites. Conversely, the presence of a pore between Al and CuO promotes Al enrichment of the alumina layer above 600 K. At that temperature, any free oxygen molecules in the pore become attached to the reactive alumina surface resulting in a rapid oxygen pressure drop in the pore. This is expected to accelerate the reduction of the adjacent CuO as observed in experiments with Al/CuO composites with porosity at the CuO-Al interfaces.
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Affiliation(s)
| | - Alain Esteve
- LAAS-CNRS, University of Toulouse, 31077 Toulouse, France
| | - Mirko Schoenitz
- New Jersey Institute of Technology, Newark, New Jersey 07103, United States
| | - Edward L Dreizin
- New Jersey Institute of Technology, Newark, New Jersey 07103, United States
| | - Carole Rossi
- LAAS-CNRS, University of Toulouse, 31077 Toulouse, France
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Syaifie PH, Harisna AH, Nasution MAF, Arda AG, Nugroho DW, Jauhar MM, Mardliyati E, Maulana NN, Rochman NT, Noviyanto A, Banegas-Luna AJ, Pérez-Sánchez H. Computational Study of Asian Propolis Compounds as Potential Anti-Type 2 Diabetes Mellitus Agents by Using Inverse Virtual Screening with the DIA-DB Web Server, Tanimoto Similarity Analysis, and Molecular Dynamic Simulation. Molecules 2022; 27. [PMID: 35807241 DOI: 10.3390/molecules27133972] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/10/2022] [Accepted: 06/15/2022] [Indexed: 02/01/2023] Open
Abstract
Propolis contains a wide range of pharmacological activities because of their various bioactive compounds. The beneficial effect of propolis is interesting for treating type-2 diabetes mellitus (T2DM) owing to dysregulation of multiple metabolic processes. In this study, 275 of 658 Asian propolis compounds were evaluated as potential anti-T2DM agents using the DIA-DB web server towards 18 known anti-diabetes protein targets. More than 20% of all compounds could bind to more than five diabetes targets with high binding affinity (<−9.0 kcal/mol). Filtering with physicochemical and pharmacokinetic properties, including ADMET parameters, 12 compounds were identified as potential anti-T2DM with favorable ADMET properties. Six of those compounds, (2R)-7,4′-dihydroxy-5-methoxy-8-methylflavone; (RR)-(+)-3′-senecioylkhellactone; 2′,4′,6′-trihydroxy chalcone; alpinetin; pinobanksin-3-O-butyrate; and pinocembrin-5-methyl ether were first reported as anti-T2DM agents. We identified the significant T2DM targets of Asian propolis, namely retinol-binding protein-4 (RBP4) and aldose reductase (AKR1B1) that have important roles in insulin sensitivity and diabetes complication, respectively. Molecular dynamic simulations showed stable interaction of selected propolis compounds in the active site of RBP4 and AKR1B1. These findings suggest that Asian propolis compound may be effective for treatment of T2DM by targeting RBP4 and AKR1B1.
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Liu Y, An C, Liu N, Wang M, Ye B, Liao D. Noncovalent Interactions and Crystal Structure Prediction of Energetic Materials. Molecules 2022; 27:3755. [PMID: 35744882 DOI: 10.3390/molecules27123755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022]
Abstract
The crystal and molecular structures, intermolecular interactions, and energy of CL-20, HATO, and FOX-7 were comparatively predicted based on molecular dynamic (MD) simulations. By comparison, the 2D fingerprint plot, Hirshfeld surface, reduced density gradient isosurface, and electrostatic potential surface were studied to detect the intermolecular interactions. Meanwhile, the effects of vacuum and different solvents on the crystal habit of CL-20, HATO, and FOX-7 were studied by AE and MAE model, respectively. The energy calculation was also analysed based on the equilibrium structures of these crystal models by MD simulations. Our results would provide fundamental insights for the crystal engineering of energetic materials.
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Kumer A, Chakma U, Rana MM, Chandro A, Akash S, Elseehy MM, Albogami S, El-Shehawi AM. Investigation of the New Inhibitors by Sulfadiazine and Modified Derivatives of α-D-glucopyranoside for White Spot Syndrome Virus Disease of Shrimp by In Silico: Quantum Calculations, Molecular Docking, ADMET and Molecular Dynamics Study. Molecules 2022; 27:3694. [PMID: 35744817 DOI: 10.3390/molecules27123694] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/02/2022] [Accepted: 06/06/2022] [Indexed: 12/03/2022]
Abstract
The α-D-glucopyranoside and its derivatives were as the cardinal investigation for developing an effective medication to treat the highest deadly white spot syndrome virus (WSSV) diseases in Shrimp. In our forthcoming work, both computational tools, such as molecular docking, quantum calculations, pharmaceutical kinetics, ADMET, and their molecular dynamics, as well as the experimental trial against WSSV, were executed to develop novel inhibitors. In the beginning, molecular docking was carried out to determine inhibitors of the four targeted proteins of WSSV (PDB ID: 2ED6, 2GJ2, 2GJI, and 2EDM), and to determine the binding energies and interactions of ligands and proteins after docking. The range of binding affinity was found to be between −5.40 and −7.00 kcal/mol for the protein 2DEM, from −5.10 to 6.90 kcal/mol for the protein 2GJ2, from −4.70 to −6.2 kcal/mol against 2GJI, and from −5.5 kcal/mol to −6.6 kcal/mol for the evolved protein 2ED6 whereas the L01 and L03 display the highest binding energy in the protein 2EDM. After that, the top-ranked compounds (L01, L02, L03, L04, and L05), based on their high binding energies, were tested for molecular dynamics (MD) simulations of 100 ns to verify the docking validation and stability of the docked complex by calculating the root mean square deviation (RMSD) and root mean square fluctuation (RMSF). The molecules with the highest binding energy were then picked and compared to the standard drugs that were been applied to fish experimentally to evaluate the treatment at various doses. Consequently, approximately 40–45% cure rate was obtained by applying the dose of oxytetracycline (OTC) 50% with vitamin C with the 10.0 g/kg feed for 10 days. These drugs (L09 to L12) have also been executed for molecular docking to compare with α-D-glucopyranoside and its derivatives (L01 to L08). Next, the evaluation of pharmacokinetic parameters, such as drug-likeness and Lipinski’s principles; absorption; distribution; metabolism; excretion; and toxicity (ADMET) factors, were employed gradually to further evaluate their suitability as inhibitors. It was discovered that all ligands (L01 to L12) were devoid of hepatotoxicity, and the AMES toxicity excluded L05. Additionally, all of the compounds convey a significant aqueous solubility and cannot permeate the blood-brain barrier. Moreover, quantum calculations based on density functional theory (DFT) provide the most solid evidence and testimony regarding their chemical stability, chemical reactivity, biological relevance, reactive nature and specific part of reactivity. The computational and virtual screenings for in silico study reveals that these chosen compounds (L01 to L08) have conducted the inhibitory effect to convey as a possible medication against the WSSV than existing drugs (L09, L10, L11 and L12) in the market. Next the drugs (L09, L10, L11 and L12) have been used in trials.
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Pandya N, Kumar A. A multi-epitope vaccine candidate developed from unique immunogenic epitopes against Cryptosporidium hominis by utilizing an immunoinformatics-driven approach. J Biomol Struct Dyn 2022:1-18. [PMID: 35510602 DOI: 10.1080/07391102.2022.2070284] [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] [Indexed: 10/18/2022]
Abstract
An immunoinformatics-based strategy is being investigated to identify prospective multi-subunit vaccine candidates against Cryptosporidium hominis (C. hominis). We used a systematic technique based on protein structure to create a competent multi-subunit vaccine candidate against C. hominis, with the likelihood of antigenicity, allergenicity, and transmembrane helices as the screening criteria. Using the suitable linkers, the best-screened epitopes such as B-cell epitopes (BCL), Helper T-lymphocytes (HTL), and cytotoxic T-lymphocytes (CTL) were linked together to intensify and develop the presentation and processing of the antigenic molecules. The greatest 3 D model of the component protein was created with the help of modeling software called Raptorax. The validation of the modeled protein was accomplished via the use of PROCHECK. Furthermore, using the ClusPro web server, the projected modeled structure was docked with known receptor TLR-4 to determine their interactions. A molecular dynamics (MD) simulation was used to investigate the stability of the multi-subunit vaccine bound with TLR-4 based on the docking score. Aside from that, the codon optimization and in silico expression demonstrate the possibility of high expression and simple purification of the vaccine product resulting from codon optimization. The overall findings indicated that the multi-subunit vaccine might be a viable vaccination candidate against C. hominis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nirali Pandya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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Wansri R, Lin ACK, Pengon J, Kamchonwongpaisan S, Srimongkolpithak N, Rattanajak R, Wilasluck P, Deetanya P, Wangkanont K, Hengphasatporn K, Shigeta Y, Liangsakul J, Suroengrit A, Boonyasuppayakorn S, Chuanasa T, De-Eknamkul W, Hannongbua S, Rungrotmongkol T, Chamni S. Semi-Synthesis of N-Aryl Amide Analogs of Piperine from Piper nigrum and Evaluation of Their Antitrypanosomal, Antimalarial, and Anti-SARS-CoV-2 Main Protease Activities. Molecules 2022; 27:2841. [PMID: 35566194 DOI: 10.3390/molecules27092841] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 02/01/2023] Open
Abstract
Piper nigrum, or black pepper, produces piperine, an alkaloid that has diverse pharmacological activities. In this study, N-aryl amide piperine analogs were prepared by semi-synthesis involving the saponification of piperine (1) to yield piperic acid (2) followed by esterification to obtain compounds 3, 4, and 5. The compounds were examined for their antitrypanosomal, antimalarial, and anti-SARS-CoV-2 main protease activities. The new 2,5-dimethoxy-substituted phenyl piperamide 5 exhibited the most robust biological activities with no cytotoxicity against mammalian cell lines, Vero and Vero E6, as compared to the other compounds in this series. Its half-maximal inhibitory concentration (IC50) for antitrypanosomal activity against Trypanosoma brucei rhodesiense was 15.46 ± 3.09 μM, and its antimalarial activity against the 3D7 strain of Plasmodium falciparum was 24.55 ± 1.91 μM, which were fourfold and fivefold more potent, respectively, than the activities of piperine. Interestingly, compound 5 inhibited the activity of 3C-like main protease (3CLPro) toward anti-SARS-CoV-2 activity at the IC50 of 106.9 ± 1.2 μM, which was threefold more potent than the activity of rutin. Docking and molecular dynamic simulation indicated that the potential binding of 5 in the 3CLpro active site had the improved binding interaction and stability. Therefore, new aryl amide analogs of piperine 5 should be investigated further as a promising anti-infective agent against human African trypanosomiasis, malaria, and COVID-19.
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Baammi S, Daoud R, El Allali A. Assessing the effect of a series of mutations on the dynamic behavior of phosphite dehydrogenase using molecular docking, molecular dynamics and quantum mechanics/molecular mechanics simulations. J Biomol Struct Dyn 2022; 41:4154-4166. [PMID: 35442169 DOI: 10.1080/07391102.2022.2064912] [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] [Indexed: 10/18/2022]
Abstract
Discovered in Pseudomonas stutzeri, phosphite dehydrogenase (PTDH) is an enzyme that catalyzes the oxidation of phosphite to phosphate while simultaneously reducing NAD+ to NADH. Despite several investigations into the mechanism of reaction and cofactor regeneration, only a few studies have focused on improving the activity and stability of PTDH. In this study, we combine molecular docking, molecular dynamics (MD) simulation, and Quantum Mechanics/Molecular Mechanics (QM/MM) to identify the impact of 30 mutations on the activity and stability of PTDH. Molecular docking results suggest that E266Q, K76A, K76M, K76R, K76C, and R237K can act on the NAD+ binding site through relatively weak bond development due to their high free binding energy. Moreover, Mulliken population analysis and potential energy barrier indicate that T101A, E175A, E175A/A176R, A176R, and E266Q act on phosphite oxidation. The mutants M53N, M53A, K76R, D79N, D79A, T101A, W134A, W134F Y139F, A146S, E175A, F198I, F198M, E266Q, H292K, S295A, R301K, and R301A were found to act on the structural dynamic of PTDH. The remaining mutants cause the loss of the nitrogen atom of R237 and H292, respectively, inactivating the enzyme. This study provides specific explanations of how mutations affect weak interactions of PTDH. The results should allow researchers to conduct experimental studies to improve PTDH activity and stability.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soukayna Baammi
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Rachid Daoud
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Achraf El Allali
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
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Luo T, Ma Y, Yao S, Wang J, Liu W. Experimental and Molecular Dynamics Simulation Study on Sol-Gel Conversion Process of Aluminum Carboxylate System. Materials (Basel) 2022; 15:2704. [PMID: 35408036 DOI: 10.3390/ma15072704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/24/2022] [Accepted: 04/04/2022] [Indexed: 02/04/2023]
Abstract
Due to the lack of relevant in situ characterization techniques, the investigation of aluminum sol–gel progress is lacking. In this study, combined with molecular dynamics simulation and conventional experimental methods, the microstructures, rheological properties, and gelation process of the carboxylic aluminum sol system were studied. The experimental results showed that, with the increase in solid content, the microstructure of the colloid developed from a loose and porous framework to a homogeneous and compact structure. The viscosity of aluminum sol decreased significantly with the increase in temperature, and a temperature above 318 k was more conducive to improving the fluidity. The simulation results show that the increase in free volume and the connectivity of pores in colloidal framework structure were the key factors to improve fluidity. In addition, free water molecules had a higher migration rate, which could assist the rotation and rearrangement of macromolecular chains and also played an essential role in improving fluidity. The Molecular dynamics simulation (MD) results were consistent with experimental results and broaden the scope of experimental research, providing necessary theoretical guidance for enhancing the spinning properties of aluminum sol.
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Cai B, Li J, Lai W, Liu J, Liu B. Construction of Al-Mg-Zn Interatomic Potential and the Prediction of Favored Glass Formation Compositions and Associated Driving Forces. Materials (Basel) 2022; 15:ma15062062. [PMID: 35329514 PMCID: PMC8952002 DOI: 10.3390/ma15062062] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 02/01/2023]
Abstract
An interatomic potential is constructed for the ternary Al-Mg-Zn system under a proposed modified tight-binding scheme, and it is verified to be realistic. Applying this ternary potential, atomistic simulations predict an intrinsic glass formation region in the composition triangle, within which the glassy alloys are more energetically favored in comparison with their solid solution counterparts. Kinetically, the amorphization driving force of each disordered state is derived to correlate the readiness of its glass-forming ability in practice; thus, an optimal stoichiometry region is pinpointed around Al35Mg35Zn30. Furthermore, by monitoring the structural evolution for various (Al50Mg50)1−xZnx (x = 30, 50, and 70 at.%) compositions, the optimized-glass-former Al35Mg35Zn30 is characterized by both the highest degree of icosahedral ordering and the highest phase stability among the investigated compositions. In addition, the icosahedral network in Al35Mg35Zn30 exhibits a much higher cross-linking degree than that in Al25Mg25Zn50. This suggests that there is a certain correlation between the icosahedral ordering and the larger glass-forming ability of Al35Mg35Zn30. Our results have significant implications in clarifying glass formation and hierarchical atomic structures, and in designing new ternary Al-Mg-Zn glassy alloys with high GFA.
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Wnętrzak A, Chachaj-Brekiesz A, Stępniak A, Kobierski J, Dynarowicz-Latka P. Different effects of oxysterols on a model lipid raft - Langmuir monolayer study complemented with theoretical calculations. Chem Phys Lipids 2022; 244:105182. [PMID: 35182569 DOI: 10.1016/j.chemphyslip.2022.105182] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 01/11/2022] [Revised: 02/09/2022] [Accepted: 02/13/2022] [Indexed: 11/18/2022]
Abstract
Three oxysterols (7β-hydroxycholesterol; 7β-OH, 7-ketocholesterol; 7-K and 25-hydroxycholesterol, 25-OH) differing in the site of oxidation (ring system versus chain) and kind of polar group (hydroxyl versus carbonyl) were studied in lipid raft environment using the Langmuir monolayer technique complemented with theoretical calculations. Experiments were performed for the unmodified raft system, composed of sphingomyelin (SM) and cholesterol (Chol), and in the next step the raft was modified by the incorporation of oxysterol in different proportions. In the examined three-component system (Chol:SM:oxysterol), apart from interactions between the lipid raft components, the affinity of Chol to its oxidized derivatives also plays an important role. 25-OH was found to enhance interactions between SM and Chol and thus stabilize the raft, contrary to 7β-OH and 7-K, which exterted the fluidizing effect as well as the destabilization of the raft. Different action of oxysterols on model raft was observed. 7β-OH and 7-K, which are highly potent inducers of cell dath caused raft destabilization, while 25-OH, which is the least toxic of the investigated oxysterols, was found to stabilize the raft.
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Affiliation(s)
- Anita Wnętrzak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland.
| | - Anna Chachaj-Brekiesz
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Alicja Stępniak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Jan Kobierski
- Department of Pharmaceutical Biophysics, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland
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Sun Y, Wang B, Pei J, Luo Y, Yuan N, Xiao Z, Wu H, Luo C, Wang J, Wei S, Pei Y, Fu S, Wang D. Molecular dynamic and pharmacological studies on protein-engineered hirudin variants of Hirudinaria manillensis and Hirudo medicinalis. Br J Pharmacol 2022; 179:3740-3753. [PMID: 35135035 DOI: 10.1111/bph.15816] [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: 09/23/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND AND PURPOSE Hirudin variants are the most powerful thrombin inhibitors discovered to date, with a lower risk of bleeding than heparin. For anticoagulation, the C-termini of hirudins bind to the exocite I of thrombin. Anticoagulant effects of gene-recombinant hirudin are weaker than natural hirudin for the reason of lacking tyrosine-O-sulfation at C terminus. EXPERIMENTAL APPROACH The integrative pharmacological study applied molecular dynamic, molecular biological, and in vivo and in vitro experiments to elucidate the anticoagulant effects of protein-engineered hirudins. KEY RESULTS Molecular dynamic (MD) analysis showed that modifications of the C-termini of hirudin variant 1 of Hirudo medicinalis (HV1) and hirudin variant 2 of Hirudinaria manillensis (HM2) changed the binding energy of the C-termini to human thrombin. The study indicated Asp61 of HM2 that corresponds to sulfated Tyr63 of HV1 is critical for inhibiting thrombin activities, and the anticoagulant effects of HV1 and HM2 were improved when the amino acid residues adjacent to Asp61 were mutated to Asp, such as the prolongation of the activated partial thromboplastin time (APTT), prothrombin time (PT) and thrombin time (TT) of human blood, and decreased Ki and IC50 values. In the in vivo experiments, mutations at C-termini of HV1 and HM2 significantly changed APTT, PT and TT. CONCLUSION AND IMPLICATIONS The study indicated that the anticoagulant effects of gene-engineered HM2 are stronger than gene-engineered HV1, and HM2-E60D-I62D has the strongest effects and could be an antithrombotic medicine with better therapeutic effects.
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Affiliation(s)
- Yan Sun
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China
| | - Baochun Wang
- The First Department of Gastrointestinal Surgery, Hainan General Hospital, Haikou, Hainan, China
| | - Jinli Pei
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China.,Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Ying Luo
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China
| | - Nan Yuan
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China
| | - Zhengpan Xiao
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China
| | - Hao Wu
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China.,Central Laboratory, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, China
| | - Chenghui Luo
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China
| | - Jiaxuan Wang
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China
| | - Shuangshuang Wei
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China
| | - Yechun Pei
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China
| | - Shengmiao Fu
- Department of Medical Laboratory Science, Hainan General Hospital, Haikou, Hainan, China
| | - Dayong Wang
- Laboratory of Biopharmaceutics and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China.,Key laboratory of Tropical Biological Resources of the Ministry of Education of China, Hainan University, Haikou, Hainan, China
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