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Khan MRUZ, Trivedi V. Molecular modelling, docking and network analysis of phytochemicals from Haritaki churna: role of protein cross-talks for their action. J Biomol Struct Dyn 2024; 42:4297-4312. [PMID: 37288779 DOI: 10.1080/07391102.2023.2220036] [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: 04/09/2023] [Accepted: 05/26/2023] [Indexed: 06/09/2023]
Abstract
Phytochemicals are bioactive agents present in medicinal plants with therapeutic values. Phytochemicals isolated from plants target multiple cellular processes. In the current work, we have used fractionation techniques to identify 13 bioactive polyphenols in ayurvedic medicine Haritaki Churna. Employing the advanced spectroscopic and fractionation, structure of bioactive polyphenols was determined. Blasting the phytochemical structure allow us to identify a total of 469 protein targets from Drug bank and Binding DB. Phytochemicals with their protein targets from Drug bank was used to create a phytochemical-protein network comprising of 394 nodes and 1023 edges. It highlights the extensive cross-talk between protein target corresponding to different phytochemicals. Analysis of protein targets from Binding data bank gives a network comprised of 143 nodes and 275 edges. Taking the data together from Drug bank and binding data, seven most prominent drug targets (HSP90AA1, c-Src kinase, EGFR, Akt1, EGFR, AR, and ESR-α) were found to be target of the phytochemicals. Molecular modelling and docking experiment indicate that phytochemicals are fitting nicely into active site of the target proteins. The binding energy of the phytochemicals were better than the inhibitors of these protein targets. The strength and stability of the protein ligand complexes were further confirmed using molecular dynamic simulation studies. Further, the ADMET profiles of phytochemicals extracted from HCAE suggests that they can be potential drug targets. The phytochemical cross-talk was further proven by choosing c-Src as a model. HCAE down regulated c-Src and its downstream protein targets such as Akt1, cyclin D1 and vimentin. Hence, network analysis followed by molecular docking, molecular dynamics simulation and in-vitro studies clearly highlight the role of protein network and subsequent selection of drug candidate based on network pharmacology.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Rafi Uz Zama Khan
- Malaria Research Group, Department of Biosciences and Bioengineering, Indian Institute of Technology-Guwahati, Guwahati, Assam, India
| | - Vishal Trivedi
- Malaria Research Group, Department of Biosciences and Bioengineering, Indian Institute of Technology-Guwahati, Guwahati, Assam, India
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Chen C, Yurtsever A, Li P, Sun L. Two-Dimensional Layered Nanomaterials Steering Self-Assembly of Dodecapeptides with Three Building Blocks. ACS Appl Mater Interfaces 2024; 16:19699-19710. [PMID: 38588069 DOI: 10.1021/acsami.3c18851] [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: 04/10/2024]
Abstract
Self-assembly of peptides on layered nanomaterials such as graphite and MoS2 in the formation of long-range ordered two-dimensional nanocrystal patterns leading to its potential applications for biosensing and bioelectronics has attracted significant interest in nanoscience and nanotechnology. However, controlling the self-assembly of peptides on nanomaterials is still challenging due to the unclear role of nanomaterials in steering self-assembly. Here, we used the in-situ AFM technique to capture different changes of peptide coverage as well as lengthening and widening rates depending on peptide concentrations, show the distinct boundary dynamics of two stabilized peptide domains, and resolve the molecular resolution structural differences and specific orientation of peptide on both nanomaterials. Moreover, ex-situ results showed that the nanomaterial layers tuned the opposite changes of nanowire heights and densities and displayed the different water-resistance stabilities on both nanomaterials. This work provides a basis for understanding nanomaterials steering peptide self-assembly and using hybrid bionanomaterials as a scaffold, enabling for potential biosensing and bioelectronics applications.
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Affiliation(s)
- Chen Chen
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Ayhan Yurtsever
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Peiying Li
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Linhao Sun
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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Yu Z, Lv H, Zhou M, Fu P, Zhao W. Identification and molecular docking of tyrosinase inhibitory peptides from allophycocyanin in Spirulina platensis. J Sci Food Agric 2024; 104:3648-3653. [PMID: 38224494 DOI: 10.1002/jsfa.13249] [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] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/22/2023] [Accepted: 01/15/2023] [Indexed: 01/17/2024]
Abstract
BACKGROUND Tyrosinase, a copper-containing metalloenzyme with catalytic activity, is widely found in mammals. It is the key rate-limiting enzyme that catalyzes melanin synthesis. For humans, tyrosinase is beneficial to the darkening of eyes and hair. However, excessive deposition of melanin in the skin can lead to dull skin color and lead to pigmentation. Therefore, many skin-whitening compounds have been developed to decrease tyrosinase activity. This study aimed to identify a new tyrosinase inhibitory peptide through enzymatic hydrolysis, in vitro activity verification, molecular docking, and molecular dynamics (MD) simulation. RESULTS A tripeptide Asp-Glu-Arg (DER) was identified, with a '-CDOCKER_Energy' value of 121.26 Kcal mol-1 . DER has effective tyrosinase inhibitory activity. Research shows that its half maximal inhibitory concentration value is 1.04 ± 0.01 mmol L-1 . In addition, DER binds to tyrosinase residues His85, His244, His259, and Asn260, which are key residues that drive the interaction between the peptide and tyrosinase. Finally, through MD simulation, the conformational changes and structural stability of the complexes were further explored to verify and supplement the results of molecular docking. CONCLUSION This experiment shows that DER can effectively inhibit tyrosinase activity. His244, His259, His260, and Asn260 are the critical residues that drive the interaction between the peptide and tyrosinase, and hydrogen bonding is an important force. DER from Spirulina has the potential to develop functional products with tyrosinase inhibition. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Zhipeng Yu
- School of Food Science and Engineering, Hainan University, Haikou, P. R. China
| | - Hong Lv
- School of Food Science and Engineering, Hainan University, Haikou, P. R. China
| | - Mingjie Zhou
- School of Food Science and Engineering, Bohai University, Jinzhou, P. R. China
| | - Pengcheng Fu
- School of Food Science and Engineering, Hainan University, Haikou, P. R. China
| | - Wenzhu Zhao
- School of Food Science and Engineering, Hainan University, Haikou, P. R. China
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Zhou Y, Bie C, van Zijl PC, Yadav NN. The relayed nuclear Overhauser effect in magnetization transfer and chemical exchange saturation transfer MRI. NMR Biomed 2023; 36:e4778. [PMID: 35642102 PMCID: PMC9708952 DOI: 10.1002/nbm.4778] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/19/2022] [Accepted: 05/29/2022] [Indexed: 05/23/2023]
Abstract
Magnetic resonance (MR) is a powerful technique for noninvasively probing molecular species in vivo but suffers from low signal sensitivity. Saturation transfer (ST) MRI approaches, including chemical exchange saturation transfer (CEST) and conventional magnetization transfer contrast (MTC), allow imaging of low-concentration molecular components with enhanced sensitivity using indirect detection via the abundant water proton pool. Several recent studies have shown the utility of chemical exchange relayed nuclear Overhauser effect (rNOE) contrast originating from nonexchangeable carbon-bound protons in mobile macromolecules in solution. In this review, we describe the mechanisms leading to the occurrence of rNOE-based signals in the water saturation spectrum (Z-spectrum), including those from mobile and immobile molecular sources and from molecular binding. While it is becoming clear that MTC is mainly an rNOE-based signal, we continue to use the classical MTC nomenclature to separate it from the rNOE signals of mobile macromolecules, which we will refer to as rNOEs. Some emerging applications of the use of rNOEs for probing macromolecular solution components such as proteins and carbohydrates in vivo or studying the binding of small substrates are discussed.
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Affiliation(s)
- Yang Zhou
- Key Laboratory for Magnetic Resonance and Multimodality Imaging of Guangdong Province, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, Guangdong 518055 (China)
| | - Chongxue Bie
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, 707 N. Broadway, Baltimore MD 21205 (USA)
- The Russell H. Morgan Department of Radiology, The Johns Hopkins University School of Medicine, 720 Rutland Ave, Baltimore, MD 21205 (USA)
- Department of Information Science and Technology, Northwest University, No.1 Xuefu Avenue, Xi’an, Shanxi 710127 (China)
| | - Peter C.M. van Zijl
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, 707 N. Broadway, Baltimore MD 21205 (USA)
- The Russell H. Morgan Department of Radiology, The Johns Hopkins University School of Medicine, 720 Rutland Ave, Baltimore, MD 21205 (USA)
| | - Nirbhay N. Yadav
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, 707 N. Broadway, Baltimore MD 21205 (USA)
- The Russell H. Morgan Department of Radiology, The Johns Hopkins University School of Medicine, 720 Rutland Ave, Baltimore, MD 21205 (USA)
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Zhou Y, Bie C, van Zijl PCM, Xu J, Zou C, Yadav NN. Detection of electrostatic molecular binding using the water proton signal. Magn Reson Med 2022; 88:901-915. [PMID: 35394084 PMCID: PMC9232913 DOI: 10.1002/mrm.29230] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/07/2022] [Accepted: 02/22/2022] [Indexed: 12/25/2022]
Abstract
PURPOSE Saturation transfer MRI has previously been used to probe molecular binding interactions with signal enhancement via the water signal. Here, we detail the relayed nuclear overhauser effect (rNOE) based mechanisms of this signal enhancement, develop a strategy of quantifying molecular binding affinity, i.e., the dissociation constant ( K D $$ {K}_D $$ ), and apply the method to detect electrostatic binding of several charged small biomolecules. Another goal was to estimate the detection limit for transient receptor-substrate binding. THEORY AND METHODS The signal enhancement mechanism was quantitatively described by a three-step magnetization transfer model, and numerical simulations were performed to verify this theory. The binding equilibria of arginine, choline, and acetyl-choline to anionic resin were studied as a function of ligand concentration, pH, and salt content. Equilibrium dissociation constants ( K D $$ {K}_D $$ ) were determined by fitting the multiple concentration data. RESULTS The numerical simulations indicate that the signal enhancement is sufficient to detect the molecular binding of sub-millimolar (∼100 μM) concentration ligands to low micromolar levels of molecular targets. The measured rNOE signals from arginine, choline, and acetyl-choline binding experiments show that several magnetization transfer pathways (intra-ligand rNOEs and intermolecular rNOEs) can contribute. The rNOEs that arise from molecular ionic binding were influenced by pH and salt concentration. The molecular binding strengths in terms of K D $$ {K}_{\mathrm{D}} $$ ranged from 70-160 mM for the three cations studied. CONCLUSION The capability to use MRI to detect the transient binding of small substrates paves a pathway towards the detection of micromolar level receptor-substrate binding in vivo.
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Affiliation(s)
- Yang Zhou
- F.M. Kirby Research Center for Functional Brain ImagingKennedy Krieger InstituteBaltimoreMDUSA
- The Russell H. Morgan Department of RadiologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
- Key Laboratory for Magnetic Resonance and Multimodality Imaging of Guangdong ProvinceShenzhen Institute of Advanced Technology, Chinese Academy of SciencesShenzhenGuangdongChina
| | - Chongxue Bie
- F.M. Kirby Research Center for Functional Brain ImagingKennedy Krieger InstituteBaltimoreMDUSA
- The Russell H. Morgan Department of RadiologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
- Department of Information Science and TechnologyNorthwest UniversityXi'anChina
| | - Peter C. M. van Zijl
- F.M. Kirby Research Center for Functional Brain ImagingKennedy Krieger InstituteBaltimoreMDUSA
- The Russell H. Morgan Department of RadiologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
| | - Jiadi Xu
- F.M. Kirby Research Center for Functional Brain ImagingKennedy Krieger InstituteBaltimoreMDUSA
- The Russell H. Morgan Department of RadiologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
| | - Chao Zou
- Key Laboratory for Magnetic Resonance and Multimodality Imaging of Guangdong ProvinceShenzhen Institute of Advanced Technology, Chinese Academy of SciencesShenzhenGuangdongChina
| | - Nirbhay N. Yadav
- F.M. Kirby Research Center for Functional Brain ImagingKennedy Krieger InstituteBaltimoreMDUSA
- The Russell H. Morgan Department of RadiologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
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Georgiou N, Cheilari A, Karta D, Chontzopoulou E, Plavec J, Tzeli D, Vassiliou S, Mavromoustakos T. Conformational Properties and Putative Bioactive Targets for Novel Thiosemicarbazone Derivatives. Molecules 2022; 27:molecules27144548. [PMID: 35889421 PMCID: PMC9324535 DOI: 10.3390/molecules27144548] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/07/2022] [Accepted: 07/14/2022] [Indexed: 12/04/2022] Open
Abstract
The structure assignment and conformational analysis of the thiosemicarbazones, DKI21 and DKI24, were performed through homonuclear and heteronuclear 2D Nuclear Magnetic Resonance (NMR) spectroscopy (2D-COSY, 2D-NOESY, 2D-ROESY, 2D-HSQC, and 2D-HMBC) and quantum mechanics (QM) calculations, using Functional Density Theory (DFT). In addition, utilizing a combination of 2D-NOESY and 2D-ROESY spectra an exo structure was established for both of the analogs. This experimental results were confirmed by theoretical mechanistic studies, as the lowest minima conformations derived through DFT calculations were compatible with the spatial correlations observed in the 2D-NOESY and 2D-ROESY spectra. Finally, molecular binding experiments were performed to detect the potential targets for DKI21 and DKI24, derived from SwissAdme. In silico molecular binding experiments showed favorable binding energy values for the most of the enzymes studied. The ADMET calculations, using the preADMET and pKCSm software, showed that the two molecules appear as possible drug leads.
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Affiliation(s)
- Nikitas Georgiou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 11571 Athens, Greece; (N.G.); (D.K.); (E.C.)
| | - Antigoni Cheilari
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece;
| | - Danai Karta
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 11571 Athens, Greece; (N.G.); (D.K.); (E.C.)
| | - Eleni Chontzopoulou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 11571 Athens, Greece; (N.G.); (D.K.); (E.C.)
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, SI-1001 Ljubljana, Slovenia;
| | - Demeter Tzeli
- Laboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 11571 Athens, Greece;
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 11635 Athens, Greece
| | - Stamatia Vassiliou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 11571 Athens, Greece; (N.G.); (D.K.); (E.C.)
- Correspondence: (S.V.); (T.M.)
| | - Thomas Mavromoustakos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 11571 Athens, Greece; (N.G.); (D.K.); (E.C.)
- Correspondence: (S.V.); (T.M.)
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Georgiou N, Katsogiannou A, Skourtis D, Iatrou H, Tzeli D, Vassiliou S, Javornik U, Plavec J, Mavromoustakos T. Conformational Properties of New Thiosemicarbazone and Thiocarbohydrazone Derivatives and Their Possible Targets. Molecules 2022; 27:2537. [PMID: 35458736 DOI: 10.3390/molecules27082537] [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] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/23/2022] [Accepted: 04/11/2022] [Indexed: 11/16/2022]
Abstract
The structure assignment and conformational analysis of thiosemicarbazone KKI15 and thiocarbohydrazone KKI18 were performed through homonuclear and heteronuclear 2D Nuclear Magnetic Resonance (NMR) spectroscopy (2D-COSY, 2D-NOESY, 2D-HSQC, and 2D-HMBC) and quantum mechanics (QM) calculations using Functional Density Theory (DFT). After the structure identification of the compounds, various conformations of the two compounds were calculated using DFT. The two molecules showed the most energy-favorable values when their two double bonds adopted the E configuration. These configurations were compatible with the spatial correlations observed in the 2D-NOESY spectrum. In addition, due to the various isomers that occurred, the energy of the transition states from one isomer to another was calculated. Finally, molecular binding experiments were performed to detect potential targets for KKI15 and KKI18 derived from SwissAdme. In silico molecular binding experiments showed favorable binding energy values for all four enzymes studied. The strongest binding energy was observed in the enzyme butyrylcholinesterase. ADMET calculations using the preADMET and pKCSm software showed that the two molecules appear as possible drug leads.
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Higo J, Takashima H, Fukunishi Y, Yoshimori A. Generalized-ensemble method study: A helix-mimetic compound inhibits protein-protein interaction by long-range and short-range intermolecular interactions. J Comput Chem 2021; 42:956-969. [PMID: 33755222 DOI: 10.1002/jcc.26516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 12/30/2022]
Abstract
A heterocyclic compound mS-11 is a helix-mimetic designed to inhibit binding of an intrinsic disordered protein neural restrictive silence factor/repressor element 1 silencing factor (NRSF/REST) to a receptor protein mSin3B. We apply a generalized ensemble method, multi-dimensional virtual-system coupled molecular dynamics developed by ourselves recently, to a system consisting of mS-11 and mSin3B, and obtain a thermally equilibrated distribution, which is comprised of the bound and unbound states extensively. The lowest free-energy position of mS-11 coincides with the NRSF/REST position in the experimentally-determined NRSF/REST-mSin3B complex. Importantly, the molecular orientation of mS-11 is ordering in a wide region around mSin3B. The resultant binding scenario is: When mS-11 is distant from the binding site of mSin3B, mS-11 descends the free-energy slope toward the binding site maintaining the molecular orientation to be advantageous for binding. Then, finally a long and flexible hydrophobic sidechain of mS-11 fits into the binding site, which is the lowest-free-energy complex structure inhibiting NRSF/REST binding to mSin3B.
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Affiliation(s)
- Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Japan
| | - Hajime Takashima
- Department of Research and Development, PRISM BioLab Co., Ltd., Fujisawa, Japan
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Atsushi Yoshimori
- Chemoinformatics & AI Research Group, Institute for Theoretical Medicine, Inc., Fujisawa, Japan
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Vetrivel P, Murugesan R, Bhosale PB, Ha SE, Kim HH, Heo JD, Kim GS. A Network Pharmacological Approach to Reveal the Pharmacological Targets and Its Associated Biological Mechanisms of Prunetin-5-O-Glucoside against Gastric Cancer. Cancers (Basel) 2021; 13:1918. [PMID: 33921173 DOI: 10.3390/cancers13081918] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 03/30/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Identification of pharmacological targets in cancer provides a major walkthrough toward treatment strategies. The present research adopted a network pharmacology approach utilizing a flavonoid glucoside prunetin-5-O-glucoside (PG) compound against gastric cancer. The correlative targets were analyzed using Swiss target prediction and DiGeNET databases. Functional enrichment and significant pathways enriched were predicted for the targets to associate its biological mechanisms with cancer. Protein interaction network and cluster analysis was performed using Search Tool for the Retrieval of Interacting Genes/Proteins (STRING). Our analysis revealed three core targets among the clustered modules that plays a crucial role in relation with cancer. With this information, the core targets were examined for the binding affinity with PG using molecular docking analysis and validations on the protein targets was performed using western blot analysis and Human Protein Atlas. Our analysis through comprehensive network pharmacology resulted in the prediction of three core targets of PG that can be significant biomarkers against gastric cancer. Abstract Gastric cancer (GC) is an aggressive malignancy with increased mortality rate and low treatment options. Increasing evidence suggests that network pharmacology will be a novel method for identifying the systemic mechanism of therapeutic compounds in diseases like cancer. The current study aimed to use a network pharmacology approach to establish the predictive targets of prunetin-5-O-glucoside (PG) against gastric cancer and elucidate its biological mechanisms. Primarily, genes associated with the pathogenesis of GC was identified from the DiGeNET database and targets of PG was obtained from the Swiss target prediction database. In total, 65 correlative hits were identified as anti-gastric cancer targets of PG. Functional enrichment and pathway analysis revealed significant biological mechanisms of the targets. Interaction of protein network and cluster analysis using STRING resulted in three crucial interacting hub targets namely, HSP90AA1, CDK2, and MMP1. Additionally, the in vitro cytotoxic potential of PG was assessed on three gastric cancer cells (AGS, MKN-28, and SNU-484). Furthermore, the crucial targets were validated using molecular docking, followed by their expressions being evaluated by western blot and Human Protein Atlas. The findings indicate that the pharmacological action of PG against GC might be associated with the regulation of three core targets: HSP90AA1, CDK2, and MMP1. Thus, the network pharmacology undertaken in the current study established the core active targets of PG, which may be extensively applied with further validations for treatment in GC.
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Bò L, Miotto M, Di Rienzo L, Milanetti E, Ruocco G. Exploring the Association Between Sialic Acid and SARS-CoV-2 Spike Protein Through a Molecular Dynamics-Based Approach. Front Med Technol 2021; 2:614652. [PMID: 35047894 PMCID: PMC8757799 DOI: 10.3389/fmedt.2020.614652] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/03/2020] [Indexed: 12/19/2022] Open
Abstract
Recent experimental evidence demonstrated the capability of SARS-CoV-2 Spike protein to bind sialic acid molecules, which was a trait not present in SARS-CoV and could shed light on the molecular mechanism used by the virus for the cell invasion. This peculiar feature has been successfully predicted by in-silico studies comparing the sequence and structural characteristics that SARS-CoV-2 shares with other sialic acid-binding viruses, like MERS-CoV. Even if the region of the binding has been identified in the N-terminal domain of Spike protein, so far no comprehensive analyses have been carried out on the spike-sialic acid conformations once in the complex. Here, we addressed this aspect performing an extensive molecular dynamics simulation of a system composed of the N-terminal domain of the spike protein and a sialic acid molecule. We observed several short-lived binding events, reconnecting to the avidic nature of the binding, interestingly occurring in the surface Spike region where several insertions are present with respect to the SARS-CoV sequence. Characterizing the bound configurations via a clustering analysis on the Principal Component of the motion, we identified different possible binding conformations and discussed their dynamic and structural properties. In particular, we analyze the correlated motion between the binding residues and the binding effect on the stability of atomic fluctuation, thus proposing regions with high binding propensity with sialic acid.
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Affiliation(s)
- Leonardo Bò
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
| | - Mattia Miotto
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
- Department of Physics, Sapienza University, Rome, Italy
| | - Lorenzo Di Rienzo
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
| | - Edoardo Milanetti
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
- Department of Physics, Sapienza University, Rome, Italy
| | - Giancarlo Ruocco
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
- Department of Physics, Sapienza University, Rome, Italy
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Xi J, Hu Q, Zhao L, Si XA. Molecular Binding Contributes to Concentration Dependent Acrolein Deposition in Rat Upper Airways: CFD and Molecular Dynamics Analyses. Int J Mol Sci 2018; 19:E997. [PMID: 29584651 DOI: 10.3390/ijms19040997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 12/30/2017] [Revised: 03/18/2018] [Accepted: 03/23/2018] [Indexed: 01/28/2023] Open
Abstract
Existing in vivo experiments show significantly decreased acrolein uptake in rats with increasing inhaled acrolein concentrations. Considering that high-polarity chemicals are prone to bond with each other, it is hypothesized that molecular binding between acrolein and water will contribute to the experimentally observed deposition decrease by decreasing the effective diffusivity. The objective of this study is to quantify the probability of molecular binding for acrolein, as well as its effects on acrolein deposition, using multiscale simulations. An image-based rat airway geometry was used to predict the transport and deposition of acrolein using the chemical species model. The low Reynolds number turbulence model was used to simulate the airflows. Molecular dynamic (MD) simulations were used to study the molecular binding of acrolein in different media and at different acrolein concentrations. MD results show that significant molecular binding can happen between acrolein and water molecules in human and rat airways. With 72 acrolein embedded in 800 water molecules, about 48% of acrolein compounds contain one hydrogen bond and 10% contain two hydrogen bonds, which agreed favorably with previous MD results. The percentage of hydrogen-bonded acrolein compounds is higher at higher acrolein concentrations or in a medium with higher polarity. Computational dosimetry results show that the size increase caused by the molecular binding reduces the effective diffusivity of acrolein and lowers the chemical deposition onto the airway surfaces. This result is consistent with the experimentally observed deposition decrease at higher concentrations. However, this size increase can only explain part of the concentration-dependent variation of the acrolein uptake and acts as a concurrent mechanism with the uptake-limiting tissue ration rate. Intermolecular interactions and associated variation in diffusivity should be considered in future dosimetry modeling of high-polarity chemicals such as acrolein.
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Rhinehardt KL, Vance SA, Mohan RV, Sandros M, Srinivas G. Molecular modeling and SPRi investigations of interleukin 6 (IL6) protein and DNA aptamers. J Biomol Struct Dyn 2017; 36:1934-1947. [PMID: 28592206 DOI: 10.1080/07391102.2017.1338619] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Interleukin 6 (IL6), an inflammatory response protein has major implications in immune-related inflammatory diseases. Identification of aptamers for the IL6 protein aids in diagnostic, therapeutic, and theranostic applications. Three different DNA aptamers and their interactions with IL6 protein were extensively investigated in a phosphate buffed saline (PBS) solution. Molecular-level modeling through molecular dynamics provided insights of structural, conformational changes and specific binding domains of these protein-aptamer complexes. Multiple simulations reveal consistent binding region for all protein-aptamer complexes. Conformational changes coupled with quantitative analysis of center of mass (COM) distance, radius of gyration (Rg), and number of intermolecular hydrogen bonds in each IL6 protein-aptamer complex was used to determine their binding performance strength and obtain molecular configurations with strong binding. A similarity comparison of the molecular configurations with strong binding from molecular-level modeling concurred with Surface Plasmon Resonance imaging (SPRi) for these three aptamer complexes, thus corroborating molecular modeling analysis findings. Insights from the natural progression of IL6 protein-aptamer binding modeled in this work has identified key features such as the orientation and location of the aptamer in the binding event. These key features are not readily feasible from wet lab experiments and impact the efficacy of the aptamers in diagnostic and theranostic applications.
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Affiliation(s)
- Kristen L Rhinehardt
- a Department of Nanoengineering , Joint School of Nanoscience and Nanoengineering (JSNN), North Carolina A & T State University , 2907 East Gate City Blvd., Greensboro , NC 27401 , USA
| | - Stephen A Vance
- b Department of Nanoscience , Joint School of Nanoscience and Nanoengineering (JSNN), North Carolina A & T State University , 2907 East Gate City Blvd., Greensboro , NC 27401 , USA
| | - Ram V Mohan
- a Department of Nanoengineering , Joint School of Nanoscience and Nanoengineering (JSNN), North Carolina A & T State University , 2907 East Gate City Blvd., Greensboro , NC 27401 , USA
| | - Marinella Sandros
- b Department of Nanoscience , Joint School of Nanoscience and Nanoengineering (JSNN), North Carolina A & T State University , 2907 East Gate City Blvd., Greensboro , NC 27401 , USA
| | - Goundla Srinivas
- a Department of Nanoengineering , Joint School of Nanoscience and Nanoengineering (JSNN), North Carolina A & T State University , 2907 East Gate City Blvd., Greensboro , NC 27401 , USA
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Iida S, Nakamura H, Higo J. Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation. Biochem J 2016; 473:1651-62. [PMID: 27288028 DOI: 10.1042/BCJ20160053] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/29/2016] [Indexed: 01/23/2023]
Abstract
We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein-protein or protein-ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks.
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Saegusa Y, Ishizuka T, Kojima T, Mori S, Kawano M, Kojima T. Supramolecular interaction of fullerenes with a curved π-surface of a monomeric quadruply ring-fused porphyrin. Chemistry 2015; 21:5302-6. [PMID: 25736095 DOI: 10.1002/chem.201500389] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Indexed: 11/06/2022]
Abstract
Molecular binding of fullerenes, C60 and C70, with the Zn(II) complex of a monomeric ring-fused porphyrin derivative (2-py) as a host molecule, which has a concave π-conjugated surface, has been confirmed spectroscopically. The structures of associated complexes composed of fullerenes and 2-py were explicitly established by X-ray diffraction analysis. The fullerenes in the 2:1 complexes, which consist of two 2-py molecules and one fullerene molecule, are fully covered by the concave surfaces of the two 2-py molecules in the crystal structure. In contrast, in the crystal structure of the 1:1 complex consisting of one 2-py molecule and one C60 molecule, the C60 molecule formed a π-π stacked pair with a C60 molecule in the neighboring complex using a partial surface, which was uncovered by the 2-py molecule. Additionally, the molecular size of fullerene adopted significantly affects the (1)H NMR spectral changes and the redox properties of 2-py upon the molecular binding.
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Affiliation(s)
- Yuta Saegusa
- Department of Chemistry, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571 (Japan)
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