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Ma CH, Zhao JF, Zhang XG, Ding CH, Hao HH, Ji YH, Li LP, Guo ZT, Liu WS. Discovery of ellagic acid as a competitive inhibitor of Src homology phosphotyrosyl phosphatase 2 (SHP2) for cancer treatment: In vitro and in silico study. Int J Biol Macromol 2024; 254:127845. [PMID: 37935292 DOI: 10.1016/j.ijbiomac.2023.127845] [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: 09/25/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 11/09/2023]
Abstract
Targeting SHP2 has become a potential cancer treatment strategy. In this study, ellagic acid was first reported as a competitive inhibitor of SHP2, with an IC50 value of 0.69 ± 0.07 μM, and its inhibitory potency was 34.86 times higher that of the positive control NSC87877. Ellagic acid also had high inhibitory activity on the SHP2-E76K and SHP2-E76A mutants, with the IC50 values of 1.55 ± 0.17 μM and 0.39 ± 0.05 μM, respectively. Besides, the IC50 values of ellagic acid on homologous proteins SHP1, PTP1B, and TCPTP were 0.93 ± 0.08 μM, 2.04 ± 0.28 μM, and 11.79 ± 0.83 μM, with selectivity of 1.35, 2.96, and 17.09 times, respectively. The CCK8 proliferation experiment exhibited that ellagic acid would inhibit the proliferation of various cancer cells. It was worth noting that the combination of ellagic acid and KRASG12C inhibitor AMG510 would produce a strong synergistic effect in inhibiting NCI-H358 cells. Western blot experiment exhibited that ellagic acid would downregulate the phosphorylation levels of Erk and Akt in NCI-H358 and MDA-MB-468 cells. Molecular docking and molecular dynamics studies revealed the binding information between SHP2 and ellagic acid. In summary, this study provides new ideas for the development of SHP2 inhibitors.
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Affiliation(s)
- Chun-Hui Ma
- Department of Clinical Laboratory, Affiliated Hospital of Weifang Medical University, Weifang 261041, Shandong, China; Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang 261041, Shandong Province, China
| | - Ji-Feng Zhao
- Shandong Key Laboratory of Medicine and Health (Clinical Applied Pharmacology), Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261041, Shandong Province, China; Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang 261041, Shandong Province, China
| | - Xu-Guang Zhang
- Department of Clinical Laboratory, Affiliated Hospital of Weifang Medical University, Weifang 261041, Shandong, China
| | - Chuan-Hua Ding
- Shandong Key Laboratory of Medicine and Health (Clinical Applied Pharmacology), Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261041, Shandong Province, China
| | - Hui-Hui Hao
- Shandong Key Laboratory of Medicine and Health (Clinical Applied Pharmacology), Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261041, Shandong Province, China
| | - Ying-Hui Ji
- Shandong Key Laboratory of Medicine and Health (Clinical Applied Pharmacology), Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261041, Shandong Province, China
| | - Li-Peng Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Zhen-Tao Guo
- Department of Nephrology, Affiliated Hospital of Weifang Medical University, Weifang 261041, Shandong, China.
| | - Wen-Shan Liu
- Shandong Key Laboratory of Medicine and Health (Clinical Applied Pharmacology), Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261041, Shandong Province, China; Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang 261041, Shandong Province, China.
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2
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Faisal S, Badshah SL, Sharaf M, Abdalla M. Insight into the Hantaan virus RNA-dependent RNA polymerase inhibition using in-silico approaches. Mol Divers 2023; 27:2505-2522. [PMID: 36376718 PMCID: PMC9663193 DOI: 10.1007/s11030-022-10567-6] [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: 02/14/2022] [Accepted: 11/01/2022] [Indexed: 11/16/2022]
Abstract
The Hantaan virus (HTN) is a member of the hantaviridae family. It is a segmented type, negative-strand virus (sNSVs). It causes hemorrhagic fever with renal syndrome, which includes fever, vascular hemorrhage, and renal failure. This illness is one of the most serious hemorrhagic diseases in the world, and it is a major public health concern due to its high mortality rate. The Hantaan virus RNA-dependent RNA polymerase complex (RdRp) is involved in viral RNA transcription and replication for the survival and transmission of this virus. Therefore, it is a primary target for antiviral drug development. Interference with the endonucleolytic "cap-snatching" reaction by the HTN virus RdRp endonuclease domain is a particularly appealing approach for drug discovery against this virus. This RdRp endonuclease domain of the HTN virus has a metal-dependent catalytic activity. We targeted this metal-dependent enzymatic activity to identify inhibitors that can bind and disrupt this endonuclease enzyme activity using in-silico approaches i.e., molecular docking, molecular dynamics simulation, predicted absorption, distribution, metabolism, excretion, toxicity (ADMET) and drug-likeness studies. The docking studies showed that peramivir, and ingavirin compounds can effectively bind with the manganese ions and engage with other active site residues of this protein. Molecular simulations also showed stable binding of these ligands with the active site of HTN RdRp. Simulation analysis showed that they were in constant contact with the active site manganese ions and amino acid residues of the HTN virus endonuclease domain. This study will help in better understanding the HTN and related viruses.
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Affiliation(s)
- Shah Faisal
- Department of Chemistry, Islamia College University Peshawar, Peshawar, 25120, Pakistan
| | - Syed Lal Badshah
- Department of Chemistry, Islamia College University Peshawar, Peshawar, 25120, Pakistan.
| | - Mohamed Sharaf
- Department of Biochemistry, Faculty of Agriculture, AL-Azhar University, Nasr City, Cairo, 11751, Egypt
- Department of Biochemistry and Molecular Biology, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, People's Republic of China
| | - Mohnad Abdalla
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, 250022, China.
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3
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Pant R, Kumar R, Sharma S, Karuppasamy R, Veerappapillai S. Exploring the potential of Halalkalibacterium halodurans laccase for endosulfan and chlorophacinone degradation: insights from molecular docking and molecular dynamics simulations. J Biomol Struct Dyn 2023:1-15. [PMID: 37990551 DOI: 10.1080/07391102.2023.2283165] [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: 03/27/2023] [Accepted: 11/06/2023] [Indexed: 11/23/2023]
Abstract
Pesticides are widely used in agriculture but at the same time, a majority of them are known to cause serious harm to health and the environment. In the recent past, laccases have been reported as key enzymes having the ability to degrade pollutants by converting them into less toxic forms. In this investigation, laccase from polyextremophilic bacterium Halalkalibacterium halodurans C-125 was analyzed for its structural, physicochemical, and functional characterization using in silico approaches. The 3D model of the said enzyme is unknown; therefore, the model was generated by template-independent modeling using ROBETTA, I-TASSER, and Alphafold server. The best-generated model from Alphafold with a confidence of 0.95 was validated from ERRAT and Verify 3D scores of 89.95 and 91.80%, respectively. The Ramachandran plot generated using the PROCHECK server further predicted the accuracy of the model with 93.7% and 5.9% of residues present in most favored and additional allowed regions of the plot respectively. The active sites, ion binding sites, and subcellular localization of laccase were also predicted. The generated model was docked with 121 pollutants (pesticides, insecticides, herbicides, fungicides, and rodenticides) for its degradation potential towards these pollutants. Two ligands chlorophacinone (based on the highest binding energy) and endosulfan (based on agricultural uses) were selected for molecular dynamic simulation studies. Endosulfan as a pesticide is banned but in some countries governments allow its use for special purposes which need serious consideration on developing bioremediation approaches for endosulfan degradation. MD simulation studies revealed that both chlorophacinone and endosulfan form hydrogen bonds and hydrophobic bonds with the active site of laccase and chlorophacinone-laccase complex were more stable in comparison to endosulfan. The present investigation provides insight into the structural features of laccase and its potential for the degradation of pesticides which can be further validated by experimental data.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rajat Pant
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
| | - Ravi Kumar
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
- Department of Biological Sciences and Engineering, Netaji Subhas Institute of Technology (University of Delhi), New Delhi, India
| | - Shilpa Sharma
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
| | - Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Shanthi Veerappapillai
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Kubra B, Badshah SL, Faisal S, Sharaf M, Emwas AH, Jaremko M, Abdalla M. Inhibition of the predicted allosteric site of the SARS-CoV-2 main protease through flavonoids. J Biomol Struct Dyn 2023; 41:9103-9120. [PMID: 36404610 DOI: 10.1080/07391102.2022.2140201] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/19/2022] [Indexed: 11/22/2022]
Abstract
Since its emergence in 2019, coronavirus infection (COVID-19) has become a global pandemic and killed several million people worldwide. Even though several types of vaccines are available against the COVID-19 virus, SARS-CoV-2, new strains are emerging that pose a constant danger to vaccine effectiveness. In this computational study, we identified and predicted potent allosteric inhibitors of the SARS-CoV-2 main protease (Mpro). Via molecular docking and simulations, more than 100 distinct flavonoids were docked with the allosteric site of Mpro. Docking experiments revealed four top hit compounds (Hesperidin, Schaftoside, Brickellin, and Marein) that bound strongly to the Mpro predicted allosteric site. Simulation analyses further revealed that these continually interacted with the enzyme's allosteric region throughout the simulation time. ADMET and Lipinski drug likenesses were calculated to indicate the therapeutic value of the top four hits: They were non-toxic and exhibited high human intestinal absorption concentrations. These novel allosteric site inhibitors provide a higher chance of drugging SARS-CoV2 Mpro due to the rapid mutation rate of the viral enzyme's active sites. Our findings provide a new avenue for developing novel allosteric inhibitors of SARS-CoV-2 Mpro.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bibi Kubra
- Department of Chemistry, Islamia College University Peshawar, Peshawar, Pakistan
| | - Syed Lal Badshah
- Department of Chemistry, Islamia College University Peshawar, Peshawar, Pakistan
| | - Shah Faisal
- Department of Chemistry, Islamia College University Peshawar, Peshawar, Pakistan
| | - Mohamed Sharaf
- Department of Biochemistry and Molecular Biology, College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| | - Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohnad Abdalla
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, Shandong, China
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Faisal S, Badshah SL, Kubra B, Emwas AH, Jaremko M. Alkaloids as potential antivirals. A comprehensive review. NATURAL PRODUCTS AND BIOPROSPECTING 2023; 13:4. [PMID: 36598588 PMCID: PMC9812014 DOI: 10.1007/s13659-022-00366-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/01/2022] [Indexed: 05/26/2023]
Abstract
Alkaloids are a diverse group of natural phytochemicals. These phytochemicals in plants provide them protection against pests, and herbivorous organisms and also control their development. Numerous of these alkaloids have a variety of biological effects, and some have even been developed into medications with different medicinal properties. This review aims to provide a broad overview of the numerous naturally occurring alkaloids (isolated from both terrestrial and aquatic species) along with synthetically produced alkaloid compounds having prominent antiviral properties. Previous reviews on this subject have focused on the biological actions of both natural and synthetic alkaloids, but they have not gone into comprehensive detail about their antiviral properties. We reviewed here several antiviral alkaloids that have been described in the literature in different investigational environments i.e. (in-vivo, in-ovo, in-vitro, and in-silico), and found that these alkaloid compounds have significant antiviral properties against several infectious viruses. These alkaloids repressed and targeted various important stages of viral infection at non-toxic doses while some of the alkaloids reported here also exhibited comparable inhibitory activities to commercially used drugs. Overall, these anti-viral effects of alkaloids point to a high degree of specificity, implying that they could serve as effective and safe antiviral medicines if further pursued in medicinal and pharmacological investigations.
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Affiliation(s)
- Shah Faisal
- Department of Chemistry, Islamia College University Peshawar, Peshawar, 25120, Pakistan
| | - Syed Lal Badshah
- Department of Chemistry, Islamia College University Peshawar, Peshawar, 25120, Pakistan.
| | - Bibi Kubra
- Department of Chemistry, Islamia College University Peshawar, Peshawar, 25120, Pakistan
| | - Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Mariusz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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6
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Durgam L, Guruprasad L. Molecular mechanism of ATP and RNA binding to Zika virus NS3 helicase and identification of repurposed drugs using molecular dynamics simulations. J Biomol Struct Dyn 2022; 40:12642-12659. [PMID: 34516356 DOI: 10.1080/07391102.2021.1973909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Congenital Zika virus syndrome has caused a public health emergency of international concern. So far, there are no drugs available to prevent or treat the infection caused by Zika virus. The Zika virus NS3 helicase is a potential protein target for drug discovery due to its vital role in viral genome replication. NS3 helicase unwinds the viral RNA to enable the reproduction of the viral genome by the NS5 protein. NS3 helicase has two crucial binding sites; the ATP binding site and the RNA binding site. We used molecular docking and molecular dynamics (MD) simulations to study the structural behavior of Zika virus NS3 helicase in its apo form and in the presence of ATP, single-stranded RNA, and both ATP-RNA to understand their potential implications in NS3 helicase activity. Further, we have carried out virtual screening of FDA approved drugs, followed by molecular docking to identify the ATP-competitive hit molecules as probable Zika virus NS3 helicase inhibitors. The MD simulations trajectories were analyzed using normal mode analysis and principal component analysis that reveals fluctuations in the R-loop. These findings aid in understanding the molecular mechanisms of the simultaneous binding of ATP and RNA, and guide the design and discovery of new inhibitors of the Zika virus NS3 helicase as a promising drug target to treat the Zika virus infection. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Laxman Durgam
- School of Chemistry, University of Hyderabad, Hyderabad, India
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Identification and Inhibition of the Druggable Allosteric Site of SARS-CoV-2 NSP10/NSP16 Methyltransferase through Computational Approaches. Molecules 2022; 27:molecules27165241. [PMID: 36014480 PMCID: PMC9416396 DOI: 10.3390/molecules27165241] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/24/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022] Open
Abstract
Since its emergence in early 2019, the respiratory infectious virus, SARS-CoV-2, has ravaged the health of millions of people globally and has affected almost every sphere of life. Many efforts are being made to combat the COVID-19 pandemic’s emerging and recurrent waves caused by its evolving and more infectious variants. As a result, novel and unexpected targets for SARS-CoV-2 have been considered for drug discovery. 2′-O-Methyltransferase (nsp10/nsp16) is a significant and appealing target in the SARS-CoV-2 life cycle because it protects viral RNA from the host degradative enzymes via a cap formation process. In this work, we propose prospective allosteric inhibitors that target the allosteric site, SARS-CoV-2 MTase. Four drug libraries containing ~119,483 compounds were screened against the allosteric site of SARS-CoV-2 MTase identified in our research. The identified best compounds exhibited robust molecular interactions and alloscore-score rankings with the allosteric site of SARS-CoV-2 MTase. Moreover, to further assess the dynamic stability of these compounds (CHEMBL2229121, ZINC000009464451, SPECS AK-91811684151, NCI-ID = 715319), a 100 ns molecular dynamics simulation, along with its holo-form, was performed to provide insights on the dynamic nature of these allosteric inhibitors at the allosteric site of the SARS-CoV-2 MTase. Additionally, investigations of MM-GBSA binding free energies revealed a good perspective for these allosteric inhibitor–enzyme complexes, indicating their robust antagonistic action on SARS-CoV-2 (nsp10/nsp16) methyltransferase. We conclude that these allosteric repressive agents should be further evaluated through investigational assessments in order to combat the proliferation of SARS-CoV-2.
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8
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Sundar S, Piramanayagam S, Natarajan J. A review on structural genomics approach applied for drug discovery against three vector-borne viral diseases: Dengue, Chikungunya and Zika. Virus Genes 2022; 58:151-171. [PMID: 35394596 DOI: 10.1007/s11262-022-01898-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/22/2022] [Indexed: 12/22/2022]
Abstract
Structural genomics involves the advent of three-dimensional structures of the genome encoded proteins through various techniques available. Numerous structural genomics research groups have been developed across the globe and they contribute enormously to the identification of three-dimensional structures of various proteins. In this review, we have discussed the applications of the structural genomics approach towards the discovery of potential lead-like molecules against the genomic drug targets of three vector-borne diseases, namely, Dengue, Chikungunya and Zika. Currently, all these three diseases are associated with the most important global public health problems and significant economic burden in tropical countries. Structural genomics has accelerated the identification of novel drug targets and inhibitors for the treatment of these diseases. We start with the current development status of the drug targets and antiviral drugs against these three diseases and conclude by describing challenges that need to be addressed to overcome the shortcomings in the process of drug discovery.
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Affiliation(s)
- Shobana Sundar
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, India
| | | | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India.
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9
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de Lima Menezes G, Vogel Saivish M, Lacerda Nogueira M, Alves da Silva R. Virtual screening of small natural compounds against NS1 protein of DENV, YFV and ZIKV. J Biomol Struct Dyn 2022; 41:2981-2991. [PMID: 35188085 DOI: 10.1080/07391102.2022.2042390] [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
Diseases caused by viruses of the genus Flavivirus are among the main diseases that affect the world and they are a serious public health problem. Three of them stand out: Dengue, Yellow fever and Zika viruses. The non-structural protein 1 (NS1), encoded by this viral genus, in its dimeric form, plays important roles in the pathogenesis and RNA replication of these viruses. Therefore, the identification of chemicals with the potential to inhibit the formation of the NS1 protein dimer of DENV, YFV and ZIKV would enable them to act as a multi-target drug. For this, we selected conformations of the NS1 protein monomer with similar β-roll domain structure among the three virus species from conformations obtained from molecular dynamics simulations performed in GROMACS in 5 replicates of 150 ns for each species. After selecting the protein structures, a virtual screening of compounds from the natural products catalog of the ZINC database was performed using AutoDock Vina. The 100 best compounds were classified according efficiency criteria. Two compounds were observed in common to the species, with energy scores ranging from -9.2 kcal/mol to -10.1 kcal/mol. The results obtained here demonstrate the high similarity of NS1 proteins in the Flavivirus genus and high affinity for the same compounds; thus justifying the potential of these small molecules act in multitarget therapy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Marielena Vogel Saivish
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil.,Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
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10
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Lafridi H, Almalki FA, Ben Hadda T, Berredjem M, Kawsar SMA, Alqahtani AM, Esharkawy ER, Lakhrissi B, Zgou H. In silico evaluation of molecular interactions between macrocyclic inhibitors with the HCV NS3 protease. Docking and identification of antiviral pharmacophore site. J Biomol Struct Dyn 2022; 41:2260-2273. [PMID: 35075979 DOI: 10.1080/07391102.2022.2029571] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An array of computational approaches DFT/QSAR/POM methods has been used for a better understanding of drug properties regarding 13 inhibitor derivatives containing either P2 cyclopentane P1 carboxylic acid moiety (1-9) or a P1 cyclopropyl acyl sulfonamide (10-13). To further recognize binding interactions and their activity trends, molecular docking studies were carried out with the use of HCV, which can be used to accurately predict the interactions of ligands with the receptor. The QSAR models are developed through the use of Multiple Linear Regression (MLR) together with Principal Component Analysis (PCA) methods. The statistical results indicate the multiple correlation coefficient R2 = 0.840, which shows favorable estimation stability, as well as showing a significant correlation between the HCV NS3 protease of the studied compounds and their electron-accepting ability. The POM analysis of the Physico-chemical properties of compounds 1-13, shows that they are bearing (O1, O2) and/or (O1, O2, O3) antiviral pockets, whereby all oxygen atoms are Osp2 and bearing negative charges. Similar to the reference ligand (F9K), the most active compound 10 was bound deeply into the binding cavity of NS3 protease making interactions with the residues Gly137, His57, Ala157, and His528. The anti-hepatitis pharmacophore site is similar to the anti-HIV pharmacophore site.
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Affiliation(s)
- Hind Lafridi
- Material Sciences, Processes, Environment and Modeling, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco.,Polydisciplinary Faculty, Ibn Zohr University, Ouarzazate, Morocco
| | - Faisal A Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm AlQura University, Makkah, Saudi Arabia
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm AlQura University, Makkah, Saudi Arabia.,Laboratory of Applied Chemistry and Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Malika Berredjem
- Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar - Annaba University, Annaba, Algeria
| | - Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
| | - Ali M Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Kingdom of Saudi Arabia
| | - Eman R Esharkawy
- Department of Plant Ecology and Range Management, Ecology and Dry Lands Agriculture Division, Desert Research Center, Mathef El-Mataria, Egypt.,Department of Chemistry, Science Faculty for Girls, Northern Border University ARAR, North Region, Saudi Arabia
| | - Brahim Lakhrissi
- Laboratory of Organic Chemistry, Catalysis, and Environment, Department of Chemistry, Faculty of Sciences, Ibn Tofaïl University, Kenitra, Morocco
| | - Hsaine Zgou
- Polydisciplinary Faculty, Ibn Zohr University, Ouarzazate, Morocco
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11
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Wu Y, Wang Z, Du Q, Zhu Z, Chen T, Xue Y, Wang Y, Zeng Q, Shen C, Jiang C, Liu L, Zhu H, Liu Q. Pharmacological Effects and Underlying Mechanisms of Licorice-Derived Flavonoids. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:9523071. [PMID: 35082907 PMCID: PMC8786487 DOI: 10.1155/2022/9523071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 12/17/2021] [Indexed: 12/12/2022]
Abstract
Glycyrrhizae Radix et Rhizoma is the most frequently prescribed natural medicine in China and has been used for more than 2,000 years. The flavonoids of licorice have garnered considerable attention in recent decades due to their structural diversity and myriad pharmacological effects, especially as novel therapeutic agents against inflammation and cancer. Although many articles have been published to summarize different pharmacological activities of licorice in recent years, the systematic summary for flavonoid components is not comprehensive. Therefore, in this review, we summarized the pharmacological and mechanistic data from recent researches on licorice flavonoids and their bioactive components.
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Affiliation(s)
- Yufan Wu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Zhuxian Wang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Qunqun Du
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Zhaoming Zhu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Tingting Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Yaqi Xue
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Yuan Wang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Quanfu Zeng
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Chunyan Shen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Cuiping Jiang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Li Liu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Hongxia Zhu
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510315, China
| | - Qiang Liu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
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Faisal S, Badshah SL, Kubra B, Sharaf M, Emwas AH, Jaremko M, Abdalla M. Computational Study of SARS-CoV-2 RNA Dependent RNA Polymerase Allosteric Site Inhibition. Molecules 2021; 27:223. [PMID: 35011458 PMCID: PMC8746673 DOI: 10.3390/molecules27010223] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 12/25/2021] [Accepted: 12/26/2021] [Indexed: 01/12/2023] Open
Abstract
The COVID-19 pandemic has caused millions of fatalities since 2019. Despite the availability of vaccines for this disease, new strains are causing rapid ailment and are a continuous threat to vaccine efficacy. Here, molecular docking and simulations identify strong inhibitors of the allosteric site of the SARS-CoV-2 virus RNA dependent RNA polymerase (RdRp). More than one hundred different flavonoids were docked with the SARS-CoV-2 RdRp allosteric site through computational screening. The three top hits were Naringoside, Myricetin and Aureusidin 4,6-diglucoside. Simulation analyses confirmed that they are in constant contact during the simulation time course and have strong association with the enzyme's allosteric site. Absorption, distribution, metabolism, excretion and toxicity (ADMET) data provided medicinal information of these top three hits. They had good human intestinal absorption (HIA) concentrations and were non-toxic. Due to high mutation rates in the active sites of the viral enzyme, these new allosteric site inhibitors offer opportunities to drug SARS-CoV-2 RdRp. These results provide new information for the design of novel allosteric inhibitors against SARS-CoV-2 RdRp.
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Affiliation(s)
- Shah Faisal
- Department of Chemistry, Islamia College University Peshawar, Peshawar 25120, Pakistan; (S.F.); (B.K.)
| | - Syed Lal Badshah
- Department of Chemistry, Islamia College University Peshawar, Peshawar 25120, Pakistan; (S.F.); (B.K.)
| | - Bibi Kubra
- Department of Chemistry, Islamia College University Peshawar, Peshawar 25120, Pakistan; (S.F.); (B.K.)
| | - Mohamed Sharaf
- Department of Biochemistry and Molecular Biology, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China;
- Department of Biochemistry, Faculty of Agriculture, AL-Azhar University, Nasr City, Cairo 11751, Egypt
| | - Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Jinan 250012, China
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Badshah SL, Naeem A. Computational Simulation of Conjugated Cholera Toxin Protein. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2021. [DOI: 10.3103/s0891416821050049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Badshah SL, Faisal S, Muhammad A, Poulson BG, Emwas AH, Jaremko M. Antiviral activities of flavonoids. Biomed Pharmacother 2021; 140:111596. [PMID: 34126315 PMCID: PMC8192980 DOI: 10.1016/j.biopha.2021.111596] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 12/16/2022] Open
Abstract
Flavonoids are natural phytochemicals known for their antiviral activity. The flavonoids acts at different stages of viral infection, such as viral entrance, replication and translation of proteins. Viruses cause various diseases such as SARS, Hepatitis, AIDS, Flu, Herpes, etc. These, and many more viral diseases, are prevalent in the world, and some (i.e. SARS-CoV-2) are causing global chaos. Despite much struggle, effective treatments for these viral diseases are not available. The flavonoid class of phytochemicals has a vast number of medicinally active compounds, many of which are studied for their potential antiviral activity against different DNA and RNA viruses. Here, we reviewed many flavonoids that showed antiviral activities in different testing environments such as in vitro, in vivo (mice model) and in silico. Some flavonoids had stronger inhibitory activities, showed no toxicity & the cell proliferation at the tested doses are not affected. Some of the flavonoids used in the in vivo studies also protected the tested mice prophylactically from lethal doses of virus, and effectively prevented viral infection. The glycosides of some of the flavonoids increased the solubility of some flavonoids, and therefore showed increased antiviral activity as compared to the non-glycoside form of that flavonoid. These phytochemicals are active against different disease-causing viruses, and inhibited the viruses by targeting the viral infections at multiple stages. Some of the flavonoids showed more potent antiviral activity than the market available drugs used to treat viral infections.
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Affiliation(s)
- Syed Lal Badshah
- Department of Chemistry, Islamia College University Peshawar, Peshawar 25120, Khyber Pakhtunkhwa, Pakistan.
| | - Shah Faisal
- Department of Chemistry, Islamia College University Peshawar, Peshawar 25120, Khyber Pakhtunkhwa, Pakistan
| | - Akhtar Muhammad
- Department of Chemistry, Islamia College University Peshawar, Peshawar 25120, Khyber Pakhtunkhwa, Pakistan
| | - Benjamin Gabriel Poulson
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Abdul Hamid Emwas
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Mariusz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
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Noreen, Ali R, Badshah SL, Faheem M, Abbasi SW, Ullah R, Bari A, Jamal SB, Mahmood HM, Haider A, Haider S. Identification of potential inhibitors of Zika virus NS5 RNA-dependent RNA polymerase through virtual screening and molecular dynamic simulations. Saudi Pharm J 2020; 28:1580-1591. [PMID: 33424251 PMCID: PMC7783101 DOI: 10.1016/j.jsps.2020.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/15/2020] [Indexed: 01/11/2023] Open
Abstract
Zika virus (ZIKV) is one of the mosquito borne flavivirus with several outbreaks in past few years in tropical and subtropical regions. The non-structural proteins of flaviviruses are suitable active targets for inhibitory drugs due to their role in pathogenicity. In ZIKV, the non-structural protein 5 (NS5) RNA-Dependent RNA polymerase replicates its genome. Here we have performed virtual screening to identify suitable ligands that can potentially halt the ZIKV NS5 RNA dependent RNA polymerase (RdRp). During this process, we searched and screened a library of ligands against ZIKV NS5 RdRp. The selected ligands with significant binding energy and ligand-receptor interactions were further processed. Among the selected docked conformations, top five was further optimized at atomic level using molecular dynamic simulations followed by binding free energy calculations. The interactions of ligands with the target structure of ZIKV RdRp revealed that they form strong bonds within the active sites of the receptor molecule. The efficacy of these drugs against ZIKV can be further analyzed through in-vitro and in-vivo studies.
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Affiliation(s)
- Noreen
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
- Department of Chemistry, Islamia College University, Peshawar, Pakistan
| | - Roshan Ali
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Syed Lal Badshah
- Department of Chemistry, Islamia College University, Peshawar, Pakistan
| | - Muhammad Faheem
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Riaz Ullah
- Department of Pharmacognosy (MAPPRC), College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Bari
- Department of Pharmacuitcal Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Syed Babar Jamal
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Hafiz Majid Mahmood
- Department of Pharmacology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Adnan Haider
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Sajjad Haider
- Department of Chemical Engineering, College of Engineering, King Saud University, Riyadh, Saudi Arabia
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Tian Z, Tian L, Zhao S, Shi M, Guo S, Wang C, Tian Z, He X. Study on the interaction of polyamine transport (PAT) and 4-Chloro-naphthalimide-homospermidine conjugate (4-ClNAHSPD) by molecular docking and dynamics. J Biomol Struct Dyn 2020; 40:290-296. [PMID: 32856528 DOI: 10.1080/07391102.2020.1813199] [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: 10/23/2022]
Abstract
Polyamine transporter (PAT) is a protein that can deliver "drug-polyamine" conjugates to tumor cells. 4-Chloro-naphthalimide- homospermidine (4-ClNAHSPD) displayed good antitumor activity and excellent cell selectivity via PAT pathway. In this paper, 4-ClNAHSPD and spermidine (SPD) were docked against PAT. The results showed that 4-ClNAHSPD could bind to PAT through hydrogen bond, Van der Waals, salt bridge or attractive charge and hydrophobic interaction. The interaction of SPD and PAT, however, was hydrogen bond and Van der Waals interaction. Moreover, their binding sites were also different. The primary binding sites of 4-ClNAHSPD with PAT are the residues of VAL59, HIS222, ASP61, ASP179 and GLU64, while SPD interacts with PAT in the sites of ASP37, ASP244, APS275 and SER36. The docked ligand-protein complexes were simulated for 5000ps. In simulations, various binding sites further resulted in the diverse root-mean-square deviation (RMSD) and root-mean-square deviation fluctuation (RMSF) values. The RMSD and RMSF values of 4-ClNAHSPD-PAT indicated that 4-ClNAHSPD caused a weak conformational change of PAT in a different style from SPD. More importantly, the interaction force numbers of 4-ClNAHSPD-PAT were also changed after the simulation. These results supported that 4-ClNAHSPD harnesses PAT pathway for cellular entrance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zhiyong Tian
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Luyao Tian
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Sihan Zhao
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Man Shi
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Shudi Guo
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Chaojie Wang
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Zhihui Tian
- The Super Computer Center of Henan, Zhengzhou University, Zhengzhou, China
| | - Xiaohui He
- The Super Computer Center of Henan, Zhengzhou University, Zhengzhou, China
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