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Emirdağ S, Ulusoy NG, Aksel M. Design, Synthesis and Biological Evaluation of Novel Gypsogenin Derivatives as Potential Anticancer and Antimicrobial Agents. Chem Biodivers 2024; 21:e202400471. [PMID: 38594210 DOI: 10.1002/cbdv.202400471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/11/2024]
Abstract
Natural compounds are important sources for the treatment of chronic disorders such as cancer and microbial infectious disorders. In this research, Gypsogenin and its derivatives (2 a-2 f) have been tested against different cancer cell lines (MCF-7, HeLa, Jurkat and K562 cell lines) and further analyzed for cell proliferation, cell death type, and for act of the mechanism. Cell proliferation was determined by the MTT method and cell death types were analyzed with HO/PI staining. Fibroblast Growth Factor 1 (FGF-1), Interleukin 1 (IL-1), Interleukin 6 (IL-6), and Tumor Necrosis Factor Alpha (TNF-α), key players in breast cancer development and progression, were determined by Elisa kits. Results showed that compound 2 e inhibited the MCF-7 cell line proliferation with an IC50 value of 0.66±0.17 μM with 93.38 % apoptosis rate. Compound 2 e also decreased FGF-1, IL-1, IL-6, and TNF-α levels. Molecular docking studies performed in the binding site of FGFR-1 indicated that compound 2 e formed key hydrogen bonding with Arg627 and Asn568. Besides, compounds 2 a-2 f were evaluated for their antimicrobial activities against gram-negative and gram-positive bacteria and C. albicans via the microdilution method. Overall, compound 2 e stands out as a potential anticancer agent for future studies.
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Affiliation(s)
- Safiye Emirdağ
- Faculty of Science Dean's Department of Chemistry, Ege University, 35040, İzmir, Turkey
| | - Nafia Gökçe Ulusoy
- Faculty of Science Dean's Department of Chemistry, Ege University, 35040, İzmir, Turkey
| | - Mehran Aksel
- Department of Biophysics, Faculty of Medicine, Aydın Adnan Menderes University, 09010, Aydin, Turkey
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Ralte L, Sailo H, Kumar R, Khiangte L, Kumar NS, Singh YT. Identification of novel AKT1 inhibitors from Sapria himalayana bioactive compounds using structure-based virtual screening and molecular dynamics simulations. BMC Complement Med Ther 2024; 24:116. [PMID: 38454426 PMCID: PMC10921764 DOI: 10.1186/s12906-024-04415-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
Through the experimental and computational analyses, the present study sought to elucidate the chemical composition and anticancer potential of Sapria himalayana plant extract (SHPE). An in vitro analysis of the plant extract was carried out to determine the anticancer potential. Further, network pharmacology, molecular docking, and molecular dynamic simulation were employed to evaluate the potential phytochemical compounds for cervical cancer (CC) drug formulations. The SHPE exhibited anti-cancerous potential through inhibition properties against cancer cell lines. The LC-MS profiling showed the presence of 14 compounds in SHPE. Using network pharmacology analysis, AKT1 (AKT serine/threonine kinase 1) is identified as the possible potential target, and EGFR (Epidermal Growth Factor Receptor) is identified as the possible key signal pathway. The major targets were determined to be AKT1, EGFR by topological analysis and molecular docking. An in silico interaction of phytoconstituents employing molecular docking demonstrated a high binding inclination of ergoloid mesylate and Ergosta-5,7,9(11),22-tetraen-3-ol, (3.beta.,22E)- with binding affinities of -15.5 kcal/mol, and -11.3 kcal/mol respectively. Further, MD simulation and PCA analyses showed that the phytochemicals possessed significant binding efficacy with CC protein. These results point the way for more investigation into SHPE compound's potential as CC treatment.
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Affiliation(s)
- Laldinfeli Ralte
- Department of Botany, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Hmingremhlua Sailo
- Department of Botany, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Rakesh Kumar
- Department of Botany, Mizoram University, Aizawl, Mizoram, 796004, India
| | | | | | - Yengkhom Tunginba Singh
- Department of Botany, Mizoram University, Aizawl, Mizoram, 796004, India.
- Department of Life Sciences (Botany), Manipur University, Imphal, Manipur, 795003, India.
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Gao HX, Chen N, He Q, Shi B, Zeng WC. Effects of structural characteristics of phenolic compounds on oxidation of glycerol trioleate: Action rule and mechanism. Food Chem 2024; 433:137361. [PMID: 37688816 DOI: 10.1016/j.foodchem.2023.137361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/11/2023]
Abstract
Effects of structural characteristics of phenolic compounds on the oxidation of glycerol trioleate were investigated, and the action rule and mechanism were further explored. By using thermal and multispectral analyses, all tested phenolic compounds significantly inhibited the oxidation of glycerol trioleate, and reduced the decomposition of CC and ester bonds of glycerol trioleate, which were attributed to their capability to inhibit the production of free radicals. Quercetin and gallic acid were the most effective among the condensed and hydrolyzable phenolic compounds in present study, respectively. For condensed phenolic compounds, the hydroxyl groups in B ring, substitution in C ring, and the structure of C ring played a crucial role in their inhibitory action. For hydrolyzable phenolic compounds, the amount of hydroxyl groups and their molecular weight had obvious effects on their inhibitory action. According to the measurement of molecular electrostatic potential and frontier molecular orbitals by density functional theory, the large maximum electrostatic potential and the small energy gap value were beneficial to enhance the inhibitory capability of phenolic compounds on the oxidation of glycerol trioleate. All present results suggested the potential action rule and molecular mechanism about the inhibitory effects of phenolic compounds on the oxidation of glycerol trioleate.
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Affiliation(s)
- Hao-Xiang Gao
- Antioxidant Polyphenols Team, Department of Food Engineering, Sichuan University, Chengdu 610065, PR China
| | - Nan Chen
- Antioxidant Polyphenols Team, Department of Food Engineering, Sichuan University, Chengdu 610065, PR China
| | - Qiang He
- The Key Laboratory of Food Science and Technology of Sichuan Province of Education, Sichuan University, Chengdu 610065, PR China
| | - Bi Shi
- Department of Biomass and Leather Engineering, Sichuan University, Chengdu 610065, PR China
| | - Wei-Cai Zeng
- Antioxidant Polyphenols Team, Department of Food Engineering, Sichuan University, Chengdu 610065, PR China; The Key Laboratory of Food Science and Technology of Sichuan Province of Education, Sichuan University, Chengdu 610065, PR China.
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Umar AB, Uzairu A. New flavone-based arylamides as potential V600E-BRAF inhibitors: Molecular docking, DFT, and pharmacokinetic properties. J Taibah Univ Med Sci 2023; 18:1000-1010. [PMID: 36950455 PMCID: PMC10025095 DOI: 10.1016/j.jtumed.2023.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/21/2022] [Accepted: 02/21/2023] [Indexed: 03/06/2023] Open
Abstract
Objectives The V600E-BRAF protein kinase is an attractive and essential therapeutic target in melanoma and other tumors. However, because of its resistance to the known inhibitors and side effects of some identified inhibitors, new potent inhibitors need to be identified. Methods In the present work, in silico strategies such as the molecular docking simulation, DFT (Density-Functional-Theory) computations, and pharmacokinetic evaluation were used to determine potential V600E-BRAF inhibitors from a set of 31 synthesized novel flavone-based arylamides. Results The docking result demonstrated that four compounds (10, 11, 28, and 31) had acceptable docking scores (MolDock score of -167.523 kcal mol-1, -158.168 kcal mol-1, -160.581 kcal mol-1,-162.302 kcal mol-1, and a Rerank score of -124.365, -129.365, -135.878 and -117.081, respectively) appeared as most active and potent V600E-BRAF inhibitors that topped vemurafenib (-158.139 and -118.607 kcal mol-1). The appearance of H-bonds and hydrophobic interactions with essential residues for V600E-BRAF proved the high stability of these complexes. The energy for the frontier molecular orbitals such as HOMO, LUMO, energy gap, and other reactivity parameters was computed using DFT. The frontier molecular-orbital surfaces and electrostatic potentials (EPs) were investigated to demonstrate the charge-density distributions that might be linked to anticancer activity. Similarly, the chosen compounds revealed superior pharmacological properties according to the drug-likeness rules (bioavailability) and pharmacokinetic properties. Conclusion The chosen compounds were recognized as potent V600E-BRAF inhibitors with superior pharmacokinetic properties and could be promising cancer drug candidates.
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Affiliation(s)
- Abdullahi B. Umar
- Department of Chemistry, Faculty of Physical Sciences, Ahmad Bello University, Zaria, Kaduna State, Nigeria
| | - Adamu Uzairu
- Department of Chemistry, Faculty of Physical Sciences, Ahmad Bello University, Zaria, Kaduna State, Nigeria
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Refaat Fahim J, Darwish AG, El Zawily A, Wells J, Abourehab MA, Yehia Desoukey S, Zekry Attia E. Exploring the volatile metabolites of three Chorisia species: Comparative headspace GC–MS, multivariate chemometrics, chemotaxonomic significance, and anti-SARS-CoV-2 potential. Saudi Pharm J 2023; 31:706-726. [PMID: 37181141 PMCID: PMC10172601 DOI: 10.1016/j.jsps.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/15/2023] [Indexed: 03/31/2023] Open
Abstract
Chorisia (syn. Ceiba) species are important ornamental, economic, and medicinal plants that are endowed with a diversity of secondary metabolites; however, their volatile organic compounds (VOCs) have been scarcely studied. Therefore, this work explores and compares the headspace floral volatiles of three common Chorisia species, namely Chorisia chodatii Hassl., Chorisia speciosa A. St.-Hil, and Chorisia insignis H.B.K. for the first time. A total of 112 VOCs of varied biosynthetic origins were identified at different qualitative and quantitative ratios, encompassing isoprenoids, fatty acid derivatives, phenylpropanoids, and others. Flowers of the investigated species showed perceptibly differentiated volatile profiles, with those emitted by C. insignis being dominated by non-oxygenated compounds (56.69 %), whereas oxygenated derivatives prevailed among the volatiles of C. chodatii (66.04 %) and C. speciosa (71.53 %). The variable importance in the projection (VIP) in the partial least-squares-discriminant (PLS-DA) analysis described 25 key compounds among the studied species, of which linalool was verified as the most important aroma compound based on VIP values and significance analysis, and it could represent the most typical VOC among these Chorisia species. Furthermore, molecular docking and dynamics analyses of both the major and the key VOCs displayed their moderate to promising binding interactions with four main proteins of SARS-CoV-2, including Mpro, PLpro, RdRp, and spike S1 subunit RBD. The current results collectively cast new light on the chemical diversity of the VOCs of Chorisia plants as well as their chemotaxonomic and biological relevance.
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Reja S, Sarkar K, Mukherjee D, Fayaz T, Kumar P, Das P, Sanphui P, Das RK. 3, 3′-[succinylbis(diazaneyl)]bis(N,N,N-trimethylpropan-1-ammonium) perchlorate: Synthesis, characterization, computational studies and in vitro anticancer activity against the human colon carcinoma cell line (HT-29). J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Degfie T, Ombito JO, Demissie TB, Eswaramoorthy R, Dekebo A, Endale M. Antibacterial and Antioxidant Activities, in silico Molecular Docking, ADMET and DFT Analysis of Compounds from Roots of Cyphostemma cyphopetalum. Adv Appl Bioinform Chem 2022; 15:79-97. [PMID: 36330228 PMCID: PMC9624657 DOI: 10.2147/aabc.s377336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022] Open
Abstract
Background Cyphostemma cyphopetalum is a medicinal plant traditionally used to treat various ailments. Limited studies on C. cyphopetalum inspired us to investigate the chemical nature and therapeutic potential of the plant. Methods Silica gel column chromatographic separation was used for isolation. 1D and 2D NMR spectroscopic analysis and literature data were used for structural elucidation. Agar well diffusion assay was used for evaluation of antibacterial activity against E. coli, P. aeruginosa, and S. aureus. DPPH assay was used to evaluate radical scavenging activities. Molecular docking was done by AutoDock Vina 4.2 open-source program. DFT calculations were performed using the Gaussian 16 program package. Results Dichloromethane/methanol (1:1) roots extract afforded a new hydroxyl-spongiane diterpenoid lactone derivative, 3-hydroxyisoagatholactone (1), along with β-sitosterol (2) and ε-viniferin (3) whereas methanol extract afforded trans-resveratrol (4), gnetin H (5), tricuspidatol A (6), ε-viniferin-diol (7) and parthenostilbenin B (8). At 50 μg/mL, compound 3 recorded the highest inhibition against E. coli (8.55 ± 0.45 mm) and S. aureus (9.30 ±1.39 mm). Against P. aeruginosa, compound 5 consistently outperformed chloramphenicol (11.76 ± 0.77 mm, at 30 g/mL). Maximum binding affinity were observed by compound 3 against DNA gyrase B (-7.6 kcal/mol) where as compound 5 displayed maximum binding against PqsA (-8.8 kcal/mol) and S. aureus PK (-5.8 kcal/mol). Compounds 1, 3 and 4 satisfy Lipinski's rule of five. Trans-resveratrol (4) demonstrated strong DPPH scavenging activity at 12.5 g/mL, with IC50 values of 0.052 µg/mL, compared to ascorbic acid (IC50 value of 0.0012 µg/mL). Conclusion In this work, eight compounds were identified from the roots extracts of C. cyphopetalum including a new hydroxyl-spongiane diterpenoid lactone, 3-hydroxyisoagatholactone (1). Compounds 3 and 5 exhibited good antibacterial activity and binding affinities. The docking result is in agreement with the in vitro antibacterial study. Overall, the study result suggests that the isolated compounds have the potential to be used as therapeutic agents, which supports the traditional uses of C. cyphpetalum roots.
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Affiliation(s)
- Teshome Degfie
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Japheth O Ombito
- Department of Chemistry, University of Botswana, Gaborone, Botswana
| | - Taye B Demissie
- Department of Chemistry, University of Botswana, Gaborone, Botswana
| | - Rajalakshmanan Eswaramoorthy
- Department of Biomaterials, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Aman Dekebo
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
- Institute of Pharmaceutical Sciences, Adama Science and Technology University, Adama, Ethiopia
| | - Milkyas Endale
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
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8
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Vergoten G, Bailly C. Interaction of panduratin A and derivatives with the SARS-CoV-2 main protease (m pro): a molecular docking study. J Biomol Struct Dyn 2022:1-11. [PMID: 35975613 DOI: 10.1080/07391102.2022.2112618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Panduratin A (Pa-A) is a prenylated cyclohexenyl chalcone isolated from the rhizomes of the medicinal and culinary plant Boesenbergia rotunda (L.) Mansf., commonly called fingerroots. Both an ethanolic plant extract and Pa-A have shown a marked antiviral activity against the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for the COVID-19 pandemic disease. Pa-A functions as a protease inhibitor inhibiting infection of human cells by the virus. We have modeled the interaction of Pa-A, and 26 panduratin analogues with the main protease (Mpro) of SARS-CoV-2 using molecular docking. The natural product 4-hydroxypanduratin showed a higher Mpro binding capacity than Pa-A and isopanduratin A. The interaction with MPro of all known panduratin derivatives (Pa-A to Pa-Y) have been compared, together with more than 60 reference products. Three compounds emerged as potential robust MPro binders: Pa-R, Pa-V, Pa-S, with a binding capacity significantly higher than 4-OH-Pa-A and Pa-A. The empirical energy of interaction (ΔE) calculated with the best compound in the panduratin series, Pa-R bound to Mpro, surpassed that measured with the top reference protease inhibitors such a ruprintrivir, lufotrelvir, and glecaprevir. Structure-binding relationships are discussed. Compounds with a flavanone moiety (PA-R/S) are the best binders, better than those with a chromene unit (Pa-F/G). The extended molecules (such as Pa-V) exhibit good Mpro binding, but the dimeric compound Pa-Y is too long and protrudes outside the binding cavity. The work provides novel ideas to guide the design of new molecules interacting with Mpro.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gérard Vergoten
- Inserm, INFINITE - U1286, Institut de Chimie Pharmaceutique Albert Lespagnol (ICPAL), Faculté de Pharmacie, University of Lille, France, Lille
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Abdizadeh R, Hadizadeh F, Abdizadeh T. Evaluation of apigenin-based biflavonoid derivatives as potential therapeutic agents against viral protease (3CLpro) of SARS-CoV-2 via molecular docking, molecular dynamics and quantum mechanics studies. J Biomol Struct Dyn 2022:1-31. [PMID: 35848354 DOI: 10.1080/07391102.2022.2098821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of the pandemic COVID-19 disease that affects human respiratory function. Despite the scientific progression made in the development of the vaccine, there is an urgent need for the discovery of antiviral drugs for better performance at different stages of SARS-CoV-2 reproduction. The main protease (Mpro or 3CLpro) plays a pivotal role in the life cycle of the virus, making it an attractive target for the development of antiviral agents effective against the new strains of coronaviruses (CoVs). In this study, a series of apigenin-based natural biflavonoid derivatives as potential inhibitors of coronaviruses 3CLpro was investigated by in silico approaches. For this purpose, the molecular docking was performed to analyze the interaction of the natural biflavonoids with SARS-Cov-2 main protease and for further investigation, docking to the 3CLpro of SARS-CoV and MERS-CoV. Based on docking scores and comparison with the reference inhibitors (ritonavir and lopinavir), more than half of the biflavonoids had strong interactions with the residues of the binding pocket of the coronaviruses 3CLpro and exhibited better binding affinities toward the main protease than ritonavir and lopinavir. The top biflavonoids were further explored through molecular dynamics simulation, binding free energy calculation and residual energy contributions estimated by the MM-PBSA. Also, drug likeness property investigation by Swiss ADME tools and density functional theory (DFT) calculations were performed. The results confirmed that the 3CLpro-amentoflavone, 3CLpro-bilobetin, 3CLpro-ginkgetin, and 3CLpro-sotetsuflavone complexes possess a large amount of dynamic properties such as high stability, significant binding energy and fewer conformation fluctuations. Also, the pharmacokinetics and drug-likeness studies and HOMO-LUMO and DFT descriptor values indicated a promising result of the selected natural biflavonoids. Overall findings indicate that the apigenin-based biflavonoids may inhibit COVID-19 by significant interactions in the binding pocket and those results can pave the way in drug discovery although the effectiveness of these bioactive compounds should be further validated by in-vitro and in-vivo investigations. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rahman Abdizadeh
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Farzin Hadizadeh
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tooba Abdizadeh
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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11
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Ghosh R, Badavath VN, Chowdhuri S, Sen A. Identification of Alkaloids from Terminalia chebula as Potent SARS- CoV-2 Main Protease Inhibitors: An In Silico Perspective. ChemistrySelect 2022; 7:e202200055. [PMID: 35600910 PMCID: PMC9111116 DOI: 10.1002/slct.202200055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/28/2022] [Indexed: 11/12/2022]
Abstract
Natural compounds in medicinal plants are best remedies for different diseases and are important to develop new drugs. This work was dedicated to understand the role of different natural compounds of Terminalia Chebula, a well-known herbal plant, in the treating of Covid 19. In this article, we have investigated interactions of such natural compounds from Terminalia Chebula with the main protease (Mpro) of the SARS-CoV-2, which is a key component for cleavage of viral polyprotein, and an important target for the development of drugs towards COVID-19. We have performed molecular docking study on 22 different molecules of Terminalia Chebula and proposed that 7 of the natural compounds (triterpenoids and sterols) interacts with a comparable or stronger interactions than the inhibitor N3. Molecular dynamics simulations (100 ns) revealed that 7 Mpro-Terminalia Chebula complexes are stable, conformationally less fluctuated, slightly less compact, and marginally expanded than ligand-free conformation of Mpro. The intermolecular H-bonding and detailed MM/PBSA and MM-GBSA analysis showed Daucosterol interaction to be the most strong, whereas comparable interactions were observed for Arjunetin, Maslinic acid, and Bellericoside. Our study suggested that these natural compounds can act as potent Mpro inhibitors for SARS-CoV-2, and may evolve as promising anti-COVID-19 drugs in the near future.
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Affiliation(s)
- Rajesh Ghosh
- School of Basic SciencesIndian Institute of Technology BhubaneswarBhubaneswarIndia
| | | | - Snehasis Chowdhuri
- School of Basic SciencesIndian Institute of Technology BhubaneswarBhubaneswarIndia
| | - Anik Sen
- Department of ChemistryInstitute of ScienceGITAM (Deemed to be University)Visakhapatnam530045Andhra PradeshIndia
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12
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Discovery of novel 3-butyl-6-benzyloxyphthalide Mannich base derivatives as multifunctional agents against Alzheimer's disease. Bioorg Med Chem 2022; 58:116660. [DOI: 10.1016/j.bmc.2022.116660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/18/2022] [Accepted: 02/08/2022] [Indexed: 12/21/2022]
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Erdogan T. In-silico investigation of some recent natural compounds for their potential use against SARS-CoV-2: a DFT, molecular docking and molecular dynamics study. J Biomol Struct Dyn 2022; 41:2448-2465. [PMID: 35088655 DOI: 10.1080/07391102.2022.2033136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Since its first appearance in December 2019, SARS-CoV-2 has infected many people all over the world, causing serious health problems in many people and causing many deaths, but no specific drug has been developed yet. SARS-CoV-2 main protease (SARS-CoV-2 Mpro) has an important role in viral replication and transcription, so inhibition of this enzyme is proposed to be an attractive route for the treatment of COVID-19. Natural compounds have been used in the treatment of many diseases throughout the history. In this study, it was aimed to investigate SARS-CoV-2 Mpro inhibition abilities, thus the therapeutic potentials of some novel phytochemicals which have recently been entered the literature. For this purpose, eleven novel phytochemicals obtained from various natural resources have been investigated for their potential antiviral activity against SARS-CoV-2 with the use of in silico methods. In the first part of the study, DFT (density functional theory) calculations were performed on the investigated compounds. In this part, geometry optimizations, vibrational analyses, and MEP (molecular electrostatic potential) map calculations were performed. In the second part, molecular docking calculations and then molecular dynamics (MD) simulations were performed to investigate how these natural compounds interact with SARS-CoV-2 Mpro which is a promising target for COVID-19 treatments. In this part, MM-PBSA (molecular mechanics with Poisson-Boltzmann surface area) calculations were also performed to determine the binding free energies of the investigated compounds. Results showed that most of the investigated compounds interacted with SARS-CoV-2 Mpro effectively and can be promising structures for drug development studies for COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Taner Erdogan
- Department of Chemistry and Chemical Processing Technologies, Kocaeli Vocational School, Kocaeli University, Kocaeli, Turkey
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González-Paz L, Hurtado-León ML, Lossada C, Fernández-Materán FV, Vera-Villalobos J, Loroño M, Paz JL, Jeffreys L, Alvarado YJ. Comparative study of the interaction of ivermectin with proteins of interest associated with SARS-CoV-2: A computational and biophysical approach. Biophys Chem 2021; 278:106677. [PMID: 34428682 PMCID: PMC8373590 DOI: 10.1016/j.bpc.2021.106677] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/13/2021] [Accepted: 08/15/2021] [Indexed: 01/18/2023]
Abstract
The SARS-CoV-2 pandemic has accelerated the study of existing drugs. The mixture of homologs called ivermectin (avermectin-B1a [HB1a] + avermectin-B1b [HB1b]) has shown antiviral activity against SARS-CoV-2 in vitro. However, there are few reports on the behavior of each homolog. We investigated the interaction of each homolog with promising targets of interest associated with SARS-CoV-2 infection from a biophysical and computational-chemistry perspective using docking and molecular dynamics. We observed a differential behavior for each homolog, with an affinity of HB1b for viral structures, and of HB1a for host structures considered. The induced disturbances were differential and influenced by the hydrophobicity of each homolog and of the binding pockets. We present the first comparative analysis of the potential theoretical inhibitory effect of both avermectins on biomolecules associated with COVID-19, and suggest that ivermectin through its homologs, has a multiobjective behavior.
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Affiliation(s)
- Lenin González-Paz
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), 4001 Maracaibo, Venezuela; Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Estudios Botánicos y Agroforestales (CEBA), Laboratorio de Protección Vegetal (LPV), 4001 Maracaibo, Venezuela.
| | - María Laura Hurtado-León
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), 4001 Maracaibo, Venezuela
| | - Carla Lossada
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Venezuela
| | - Francelys V Fernández-Materán
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Venezuela
| | - Joan Vera-Villalobos
- Facultad de Ciencias Naturales y Matemáticas, Departamento de Química y Ciencias Ambientales, Laboratorio de Análisis Químico Instrumental (LAQUINS), Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Marcos Loroño
- Departamento Académico de Química Analítica e Instrumental, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - J L Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Laura Jeffreys
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Ysaias J Alvarado
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Venezuela.
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(2E)-2-(4-ethoxybenzylidene)-3,4-dihydro-2H-naphthalen-1-one single crystal: Synthesis, growth, crystal structure, spectral characterization, biological evaluation and binding interactions with SARS-CoV-2 main protease. J Mol Struct 2021; 1244:130967. [PMID: 36373070 PMCID: PMC9637384 DOI: 10.1016/j.molstruc.2021.130967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/20/2021] [Accepted: 06/22/2021] [Indexed: 11/21/2022]
Abstract
A new α-Tetralone based chalcone compound, (2E)-2-(4-ethoxybenzylidene)-3,4-dihydro-2H-naphthalen-1-one (EBDN) has been synthesized by Claisen–Schmidt condensation reaction of α-Tetralone (1) with 4-Ethoxybenzaldehyde (2) in basic medium. Then it was allowed to grow through slow evaporation solution growth technique. The molecular structure of grown EBDN has been systematically characterized by SCXRD, FT-IR, 1H NMR and 13C NMR spectroscopic studies. The micro-hardness, thermal (TGA & DTA) and photoluminence studies of the synthesized EBDN were also examined. The EBDN was screened for its anti-inflammatory, antidiabetic and anti-oxidant activity. It has shown admirable anti-inflammatory and antidiabetic activity. Protein-Ligand interactions of EBDN with SARS-CoV-2 main protease (PDB code: 6yb7) also performed.
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