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Naik S, Soumya V, Mamledesai SN, Manickavasagam M, Choudhari P, Rathod S. Discovery of Substituted 2-oxoquinolinylthiazolidin-4-one Analogues as Potential EGFRK Inhibitors in Lung Cancer Treatment. Drug Res (Stuttg) 2024; 74:227-240. [PMID: 38830371 DOI: 10.1055/a-2305-2789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
PURPOSE Cancer is the second leading cause of death globally and is responsible for an estimated 9.6 million deaths in 2018. Globally, about 1 in 6 deaths is due to cancer and the chemotherapeutic drugs available have high toxicity and have reported side effects hence, there is a need for the synthesis of novel drugs in the treatment of cancer. METHODS The current research work dealt with the synthesis of a series of 3-(3-acetyl-2-oxoquinolin-1-(2H)-yl-2-(substitutedphenyl)thiazolidin-4-one (Va-j) derivatives and evaluation of their in-vitro anticancer activity. All the synthesized compounds were satisfactorily characterized by IR and NMR data. Compounds were further evaluated for their in-vitro anticancer activity against A-549 (lung cancer) cell lines. The in-vitro anticancer activity was based upon the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide (MTT) assay method. RESULTS The synthesized compounds exhibited satisfactory anticancer properties against the A-549 cell line. The compound (VH): showed the highest potency amongst the tested derivatives against the A-549 cell line with IC50 values of 100 µg/ml respectively and was also found to be more potent than Imatinib (150 µg/ml) which was used as a standard drug. Molecular docking studies of the titled compounds (Va-j) were carried out using AutoDock Vina/PyRx software. The synthesized compounds exhibited well-conserved hydrogen bonds with one or more amino acid residues in the active pocket of the EGFRK tyrosine kinase domain (PDB 1m17). CONCLUSION Among all the synthesized analogues, the binding affinity of the compound (Vh) was found to be higher than other synthesized derivatives and a molecular dynamics simulation study explored the stability of the docked complex system.
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Affiliation(s)
- Soniya Naik
- Department of Pharmaceutical Chemistry, Sri Ramachandra Faculty of Pharmacy, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, India
- Department of Pharmaceutical Chemistry, P.E.S's Rajaram and Tarabai Bandekar College of Pharmacy, Farmagudi, Ponda, Goa, India
| | - Vasu Soumya
- Department of Pharmaceutical Chemistry, Sri Ramachandra Faculty of Pharmacy, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, India
| | - Shivlingrao N Mamledesai
- Department of Pharmaceutical Chemistry, P.E.S's Rajaram and Tarabai Bandekar College of Pharmacy, Farmagudi, Ponda, Goa, India
| | - M Manickavasagam
- Department of Oncology, SRMC & RI, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, India
| | - Prafulla Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, Maharashtra, India
| | - Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, Maharashtra, India
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Ali S, Ahmad K, Shaikh S, Chun HJ, Choi I, Lee EJ. Mss51 protein inhibition serves as a novel target for type 2 diabetes: a molecular docking and simulation study. J Biomol Struct Dyn 2024; 42:4862-4869. [PMID: 37338036 DOI: 10.1080/07391102.2023.2223652] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Myostatin is a widely recognized inhibitory factor of skeletal muscle growth and significantly influences muscle development and metabolism. In mice, myostatin inhibition improves insulin sensitivity, increases glucose uptake by skeletal muscle, and reduces body fat. Furthermore, Mss51 is downregulated in response to myostatin inhibition, and its deletion appears to improve the metabolic state of skeletal muscle and reduce adipose tissue, which makes Mss51 a potential target for the treatment of obesity and type 2 diabetes. Here, we report a computationally predicted and validated three-dimensional structure of Mss51. Computational screening was used to identify naturally occurring compounds from the Herbal and Specs chemical database that might inhibit Mss51, based on binding affinities and physiochemical and ADMET properties. ZINC00338371, ZINC95099599 and ZINC08214878 were found to bind to Mss51 with high binding affinity and specificity. In addition, 100 ns molecular dynamics simulations were conducted to assess the stabilities of the interactions between the three compounds and Mss51. MD simulation demonstrated that all three compounds bind to the active pocket site of Mss51 stably and cause conformation changes. ZINC00338371 was found to bind most stably with binding free energy -229.022 ± 13.776 kJ/mol to Mss51, suggesting that it has therapeutic potential as a treatment option for obesity and type 2 diabetes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shahid Ali
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea
| | - Khurshid Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea
| | - Sibhghatulla Shaikh
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea
| | - Hee Jin Chun
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea
| | - Eun Ju Lee
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea
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Loganathan T, Fletcher J, Abraham P, Kannangai R, Chakraborty C, El Allali A, Alsamman AM, Zayed H, C GPD. Expression analysis and mapping of Viral-Host Protein interactions of Poxviridae suggests a lead candidate molecule targeting Mpox. BMC Infect Dis 2024; 24:483. [PMID: 38730352 PMCID: PMC11088078 DOI: 10.1186/s12879-024-09332-x] [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: 09/18/2023] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Monkeypox (Mpox) is an important human pathogen without etiological treatment. A viral-host interactome study may advance our understanding of molecular pathogenesis and lead to the discovery of suitable therapeutic targets. METHODS GEO Expression datasets characterizing mRNA profile changes in different host responses to poxviruses were analyzed for shared pathway identification, and then, the Protein-protein interaction (PPI) maps were built. The viral gene expression datasets of Monkeypox virus (MPXV) and Vaccinia virus (VACV) were used to identify the significant viral genes and further investigated for their binding to the library of targeting molecules. RESULTS Infection with MPXV interferes with various cellular pathways, including interleukin and MAPK signaling. While most host differentially expressed genes (DEGs) are predominantly downregulated upon infection, marked enrichments in histone modifiers and immune-related genes were observed. PPI analysis revealed a set of novel virus-specific protein interactions for the genes in the above functional clusters. The viral DEGs exhibited variable expression patterns in three studied cell types: primary human monocytes, primary human fibroblast, and HeLa, resulting in 118 commonly deregulated proteins. Poxvirus proteins C6R derived protein K7 and K7R of MPXV and VACV were prioritized as targets for potential therapeutic interventions based on their histone-regulating and immunosuppressive properties. In the computational docking and Molecular Dynamics (MD) experiments, these proteins were shown to bind the candidate small molecule S3I-201, which was further prioritized for lead development. RESULTS MPXV circumvents cellular antiviral defenses by engaging histone modification and immune evasion strategies. C6R-derived protein K7 binding candidate molecule S3I-201 is a priority promising candidate for treating Mpox.
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Affiliation(s)
- Tamizhini Loganathan
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore-632014, Tamil Nadu, India
| | - John Fletcher
- Department of Clinical Virology, Christian Medical College, Tamil Nadu, Vellore, 632004, India
| | - Priya Abraham
- Department of Clinical Virology, Christian Medical College, Tamil Nadu, Vellore, 632004, India
| | - Rajesh Kannangai
- Department of Clinical Virology, Christian Medical College, Tamil Nadu, Vellore, 632004, India
| | | | - Achraf El Allali
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Mohammed, Morocco.
| | - Alsamman M Alsamman
- Department of Genome Mapping, Molecular Genetics, and Genome Mapping Laboratory, Agricultural Genetic Engineering Research Institute, Giza, Egypt
| | - Hatem Zayed
- Department of Biomedical Sciences College of Health Sciences, QU. Health, Qatar University, Doha, Qatar
| | - George Priya Doss C
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore-632014, Tamil Nadu, India.
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Windah ALL, Tallei TE, AlShehail BM, Suoth EJ, Fatimawali, Alhashem YN, Halwani MA, AlShakhal MM, Aljeldah M, Alissa M, Alsuwat MA, Almanaa TN, Alshehri AA, Rabaan AA. Immunoinformatics-Driven Strategies for Advancing Epitope-Based Vaccine Design for West Nile Virus. J Pharm Sci 2024; 113:906-917. [PMID: 38042341 DOI: 10.1016/j.xphs.2023.11.025] [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: 09/04/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023]
Abstract
The West Nile virus (WNV) is the causative agent of West Nile disease (WND), which poses a potential risk of meningitis or encephalitis. The aim of the study was to design an epitope-based vaccine for WNV by utilizing computational analyses. The epitope-based vaccine design process encompassed WNV sequence collection, phylogenetic tree construction, and sequence alignment. Computational models identified B-cell and T-cell epitopes, followed by immunological property analysis. Epitopes were then modeled and docked with B-cell receptors, MHC I, and MHC II. Molecular dynamics simulations further explored dynamic interactions between epitopes and receptors. The findings indicated that the B-cell epitope QINHHWHKSGSSIG, along with three T-cell epitopes (FLVHREWFM for MHC I, NPFVSVATANAKVLI for MHC II, and NAYYVMTVGTKTFLV for MHC II), successfully passed the immunological evaluations. These four epitopes were further subjected to docking and molecular dynamics simulation studies. Although each demonstrated favorable affinities with their respective receptors, only NAYYVMTVGTKTFLV displayed a stable interaction with MHC II during MDS analysis, hence emerging as a potential candidate for a WNV epitope-based vaccine. This study demonstrates a comprehensive approach to epitope vaccine design, combining computational analyses, molecular modeling, and simulation techniques to identify potential vaccine candidates for WNV.
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Affiliation(s)
- Axl Laurens Lukas Windah
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, East Java, Indonesia
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia.
| | - Bashayer M AlShehail
- Pharmacy Practice Department, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Elly Juliana Suoth
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Mana-do 95115, North Sulawesi, Indonesia
| | - Fatimawali
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Mana-do 95115, North Sulawesi, Indonesia
| | - Yousef N Alhashem
- Clinical Laboratory Science Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia
| | - Muhammad A Halwani
- Department of Medical Microbiology, Faculty of Medicine, Al Baha University. Al Baha 4781, Saudi Arabia
| | - Mouayd M AlShakhal
- Internal Medicine Department, Qatif Central Hospital, Qatif 32654, Saudi Arabia
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Meshari A Alsuwat
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, Taif University, Al-Taif 21974, Saudi Arabia
| | - Taghreed N Almanaa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmad A Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
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Majrashi TA, Sabt A, Almahli H, El Hassab MA, Noamaan MA, Elkaeed EB, Hamissa MF, Maslamani AN, Shaldam MA, Eldehna WM. DFT and molecular simulation validation of the binding activity of PDEδ inhibitors for repression of oncogenic k-Ras. PLoS One 2024; 19:e0300035. [PMID: 38457483 PMCID: PMC10923412 DOI: 10.1371/journal.pone.0300035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/20/2024] [Indexed: 03/10/2024] Open
Abstract
The development of effective drugs targeting the K-Ras oncogene product is a significant focus in anticancer drug development. Despite the lack of successful Ras signaling inhibitors, recent research has identified PDEδ, a KRAS transporter, as a potential target for inhibiting the oncogenic KRAS signaling pathway. This study aims to investigate the interactions between eight K-Ras inhibitors (deltarazine, deltaflexin 1 and 2, and its analogues) and PDEδ to understand their binding modes. The research will utilize computational techniques such as density functional theory (DFT) and molecular electrostatic surface potential (MESP), molecular docking, binding site analyses, molecular dynamic (MD) simulations, electronic structure computations, and predictions of the binding free energy. Molecular dynamic simulations (MD) will be used to predict the binding conformations and pharmacophoric features in the active site of PDEδ for the examined structures. The binding free energies determined using the MMPB(GB)SA method will be compared with the observed potency values of the tested compounds. This computational approach aims to enhance understanding of the PDEδ selective mechanism, which could contribute to the development of novel selective inhibitors for K-Ras signaling.
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Affiliation(s)
- Taghreed A. Majrashi
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Asir, Saudi Arabia
| | - Ahmed Sabt
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo, Egypt
| | - Hadia Almahli
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Mahmoud A. El Hassab
- Faculty of Pharmacy, Department of Medicinal Chemistry, King Salman International University (KSIU), South Sinai, Egypt
| | - Mahmoud A. Noamaan
- Faculty of Science, Mathematics Department, Cairo University, Giza, Egypt
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Ad Diriyah, Riyadh, Saudi Arabia
| | - Mohamed Farouk Hamissa
- Medicinal and Pharmaceutical Chemistry Department, Pharmaceutical and Drug Industries Research Division, National Research Centre, Dokki, Giza, Egypt
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague, Czech Republic
| | | | - Moataz A. Shaldam
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Wagdy M. Eldehna
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Kafrelsheikh University, Kafrelsheikh, Egypt
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Ahmad K, Lee EJ, Ali S, Han KS, Hur SJ, Lim JH, Choi I. Licochalcone A and B enhance muscle proliferation and differentiation by regulating Myostatin. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 125:155350. [PMID: 38237512 DOI: 10.1016/j.phymed.2024.155350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND Myostatin (MSTN) inhibition has demonstrated promise for the treatment of diseases associated with muscle loss. In a previous study, we discovered that Glycyrrhiza uralensis (G. uralensis) crude water extract (CWE) inhibits MSTN expression while promoting myogenesis. Furthermore, three specific compounds of G. uralensis, namely liquiritigenin, tetrahydroxymethoxychalcone, and Licochalcone B (Lic B), were found to promote myoblast proliferation and differentiation, as well as accelerate the regeneration of injured muscle tissue. PURPOSE The purpose of this study was to build on our previous findings on G. uralensis and demonstrate the potential of its two components, Licochalcone A (Lic A) and Lic B, in muscle mass regulation (by inhibiting MSTN), aging and muscle formation. METHODS G. uralensis, Lic A, and Lic B were evaluated thoroughly using in silico, in vitro and in vivo approaches. In silico analyses included molecular docking, and dynamics simulations of these compounds with MSTN. Protein-protein docking was carried out for MSTN, as well as for the docked complex of MSTN-Lic with its receptor, activin type IIB receptor (ACVRIIB). Subsequent in vitro studies used C2C12 cell lines and primary mouse muscle stem cells to acess the cell proliferation and differentiation of normal and aged cells, levels of MSTN, Atrogin 1, and MuRF1, and plasma MSTN concentrations, employing techniques such as western blotting, immunohistochemistry, immunocytochemistry, cell proliferation and differentiation assays, and real-time RT-PCR. Furthermore, in vivo experiments using mouse models focused on measuring muscle fiber diameters. RESULTS CWE of G. uralensis and two of its components, namely Lic A and B, promote myoblast proliferation and differentiation by inhibiting MSTN and reducing Atrogin1 and MuRF1 expressions and MSTN protein concentration in serum. In silico interaction analysis revealed that Lic A (binding energy -6.9 Kcal/mol) and B (binding energy -5.9 Kcal/mol) bind to MSTN and reduce binding between it and ACVRIIB, thereby inhibiting downstream signaling. The experimental analysis, which involved both in vitro and in vivo studies, demonstrated that the levels of MSTN, Atrogin 1, and MuRF1 were decreased when G. uralensis CWE, Lic A, or Lic B were administered into mice or treated in the mouse primary muscle satellite cells (MSCs) and C2C12 myoblasts. The diameters of muscle fibers increased in orally treated mice, and the differentiation and proliferation of C2C12 cells were enhanced. G. uralensis CWE, Lic A, and Lic B also promoted cell proliferation in aged cells, suggesting that they may have anti-muslce aging properties. They also reduced the expression and phosphorylation of SMAD2 and SMAD3 (MSTN downstream effectors), adding to the evidence that MSTN is inhibited. CONCLUSION These findings suggest that CWE and its active constituents Lic A and Lic B have anti-mauscle aging potential. They also have the potential to be used as natural inhibitors of MSTN and as therapeutic options for disorders associated with muscle atrophy.
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Affiliation(s)
- Khurshid Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, South Korea
| | - Eun Ju Lee
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, South Korea
| | - Shahid Ali
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, South Korea
| | - Ki Soo Han
- Neo Cremar Co., Ltd., Seoul 05702, South Korea
| | - Sun Jin Hur
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, South Korea
| | - Jeong Ho Lim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, South Korea
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, South Korea.
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Dixit B, Vranken W, Ghysels A. Conformational dynamics of α-1 acid glycoprotein (AGP) in cancer: A comparative study of glycosylated and unglycosylated AGP. Proteins 2024; 92:246-264. [PMID: 37837263 DOI: 10.1002/prot.26607] [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: 03/24/2023] [Revised: 09/01/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023]
Abstract
α-1 acid glycoprotein (AGP) is one of the most abundant plasma proteins. It fulfills two important functions: immunomodulation, and binding to various drugs and receptors. These different functions are closely associated and modulated via changes in glycosylation and cancer missense mutations. From a structural point of view, glycans alter the local biophysical properties of the protein leading to a diverse ligand-binding spectrum. However, glycans can typically not be observed in the resolved X-ray crystallography structure of AGP due to their high flexibility and microheterogeneity, so limiting our understanding of AGP's conformational dynamics 70 years after its discovery. We here investigate how mutations and glycosylation interfere with AGP's conformational dynamics changing its biophysical behavior, by using molecular dynamics (MD) simulations and sequence-based dynamics predictions. The MD trajectories show that glycosylation decreases the local backbone flexibility of AGP and increases the flexibility of distant regions through allosteric effects. We observe that mutations near the glycosylation site affect glycan's conformational preferences. Thus, we conclude that mutations control glycan dynamics which modulates the protein's backbone flexibility directly affecting its accessibility. These findings may assist in the drug design targeting AGP's glycosylation and mutations in cancer.
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Affiliation(s)
- Bhawna Dixit
- IBiTech-BioMMeda Group, Ghent University, Ghent, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Wim Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - An Ghysels
- IBiTech-BioMMeda Group, Ghent University, Ghent, Belgium
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Ahmad SS, Lim JH, Ahmad K, Chun HJ, Hur SJ, Lee EJ, Choi I. Targeting myostatin using quercetin as a media supplement to improve myogenesis for cultured meat production: An in silico and in vitro study. Curr Res Food Sci 2024; 8:100678. [PMID: 38298827 PMCID: PMC10828575 DOI: 10.1016/j.crfs.2024.100678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 02/02/2024] Open
Abstract
Cultured meat (CM) is an alternative protein food and is produced by cultivating muscle satellite (stem) cells (MSCs) derived from livestock animals (bovine, chickens, and porcine) through myogenesis leading to generate muscle mass. Myostatin (MSTN) is well well-known negative regulator of myogenesis, and in the present study, in silico screening of natural compounds was performed to identify MSTN inhibitors. Interestingly, quercetin was found to inhibit MSTN (binding energy -7.40 kcal/mol), and this was further validated by a 100 ns molecular dynamics simulation. Quercetin was added to culture media to boost myogenesis, and its potent antioxidant property helped maintain media pH. Furthermore, quercetin increased the myotube thickness and length, increased MSC differentiation, and upregulated the gene and protein expressions of myoblast determination protein 1 (MYOD), Myogenin (MYOG), and Myosin heavy chains (MYH) in vitro. In addition, quercetin inhibited the activities of MSTN, activin receptor type-2B (ACVR2B), and SMAD2 and 3, and thus significantly enhanced MSC differentiation and myotube formation. Overall, this study shows that quercetin might be useful for enhancing large-scale CM production. It is hoped that this study provides a starting point for research in the CM area aimed to enhancing product quality, nutritional values, and the efficacy of large-scale production.
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Affiliation(s)
- Syed Sayeed Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 38541, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, 38541, South Korea
| | - Jeong Ho Lim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 38541, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, 38541, South Korea
| | - Khurshid Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 38541, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, 38541, South Korea
| | - Hee Jin Chun
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 38541, South Korea
| | - Sun Jin Hur
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, South Korea
| | - Eun Ju Lee
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 38541, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, 38541, South Korea
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 38541, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, 38541, South Korea
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Thakur A, Sharma B, Parashar A, Sharma V, Kumar A, Mehta V. 2D-QSAR, molecular docking and MD simulation based virtual screening of the herbal molecules against Alzheimer's disorder: an approach to predict CNS activity. J Biomol Struct Dyn 2024; 42:148-162. [PMID: 36970779 DOI: 10.1080/07391102.2023.2192805] [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: 10/10/2022] [Accepted: 03/10/2023] [Indexed: 03/29/2023]
Abstract
Acetylcholinesterase (AChE) is one of the key enzyme targets that have been used clinically for the management of Alzheimer's Disorder (AD). Numerous reports in the literature predict and demonstrate in-vitro, and in-silico anticholinergic activity of herbal molecules, however, majority of them failed to find clinical application. To address these issues, we developed a 2D-QSAR model that could efficiently predict the AChE inhibitory activity of herbal molecules along with predicting their potential to cross the blood-brain-barrier (BBB) to exert their beneficial effects during AD. Virtual screening of the herbal molecules was performed and amentoflavone, asiaticoside, astaxanthin, bahouside, biapigenin, glycyrrhizin, hyperforin, hypericin, and tocopherol were predicted as the most promising herbal molecules for inhibiting AChE. Results were validated through molecular docking, atomistic molecular dynamics simulations and Molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) studies against human AChE (PDB ID: 4EY7). To determine whether or not these molecules can cross BBB to inhibit AChE within the central nervous system (CNS) for being beneficial for the management of AD, we determined a CNS Multi-parameter Optimization (MPO) score, which was found in the range of 1 to 3.76. Overall, the best results were observed for amentoflavone and our results demonstrated a PIC50 value of 7.377 nM, molecular docking score of -11.5 kcal/mol, and CNS MPO score of 3.76. In conclusion, we successfully developed a reliable and efficient 2D-QSAR model and predicted amentoflavone to be the most promising molecule that could inhibit human AChE enzyme within the CNS and could prove beneficial for the management of AD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aman Thakur
- DCO, Govt. of Rajasthan, Bharatpur, Rajasthan, India
| | - Bhanu Sharma
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India
- Biotechnology Division, CSIR-IHBT, Palampur, Himachal Pradesh, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Arun Parashar
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India
| | - Vivek Sharma
- Department of Pharmacology, Govt. College of Pharmacy, Shimla, Himachal Pradesh, India
| | - Ajay Kumar
- Institute of Pharmaceutical Sciences, Kurukshetra University, Kurukshetra, Haryana, India
| | - Vineet Mehta
- Department of Pharmacology, Govt. College of Pharmacy, Shimla, Himachal Pradesh, India
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10
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Shaikh S, Ali S, Lim JH, Ahmad K, Han KS, Lee EJ, Choi I. Virtual Insights into Natural Compounds as Potential 5α-Reductase Type II Inhibitors: A Structure-Based Screening and Molecular Dynamics Simulation Study. Life (Basel) 2023; 13:2152. [PMID: 38004292 PMCID: PMC10671996 DOI: 10.3390/life13112152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
Androgenic alopecia (AGA) is a dermatological disease with psychosocial consequences for those who experience hair loss. AGA is linked to an increase in androgen levels caused by an excess of dihydrotestosterone in blood capillaries produced from testosterone by 5α-reductase type II (5αR2), which is expressed in scalp hair follicles; 5αR2 activity and dihydrotestosterone levels are elevated in balding scalps. The diverse health benefits of flavonoids have been widely reported in epidemiological studies, and research interest continues to increase. In this study, a virtual screening approach was used to identify compounds that interact with active site residues of 5αR2 by screening a library containing 241 flavonoid compounds. Here, we report two potent flavonoid compounds, eriocitrin and silymarin, that interacted strongly with 5αR2, with binding energies of -12.1 and -11.7 kcal/mol, respectively, which were more significant than those of the control, finasteride (-11.2 kcal/mol). Molecular dynamic simulations (200 ns) were used to optimize the interactions between compounds and 5αR2 and revealed that the interaction of eriocitrin and silymarin with 5αR2 was stable. The study shows that eriocitrin and silymarin provide developmental bases for novel 5αR2 inhibitors for the management of AGA.
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Affiliation(s)
- Sibhghatulla Shaikh
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (S.S.); (S.A.); (J.H.L.); (K.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Shahid Ali
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (S.S.); (S.A.); (J.H.L.); (K.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Jeong Ho Lim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (S.S.); (S.A.); (J.H.L.); (K.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Khurshid Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (S.S.); (S.A.); (J.H.L.); (K.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Ki Soo Han
- Neo Cremar Co., Ltd., Seoul 05702, Republic of Korea;
| | - Eun Ju Lee
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (S.S.); (S.A.); (J.H.L.); (K.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (S.S.); (S.A.); (J.H.L.); (K.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Republic of Korea
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11
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Sakthivel P, Sakthivel I, Paramasivam S, Perumal SS, Ekambaram SP. Underpinning Endogeneous Damp EDA-Fibronectin in the Activation of Molecular Targets of Rheumatoid Arthritis and Identifcation of its Effective Inhibitors by Computational Methods. Appl Biochem Biotechnol 2023; 195:7037-7059. [PMID: 36976508 DOI: 10.1007/s12010-023-04451-8] [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] [Accepted: 03/15/2023] [Indexed: 03/29/2023]
Abstract
Rheumatoid arthritis (RA) is one of the most severe inflammatory diseases that cause swelling, stiffness and pain in the joints, which pose a significant threat worldwide. Damage-associated molecular patterns (DAMPs) are danger molecules of endogenous origin, released during cell injury or cell death, interacts with various Pattern recognition receptors (PRRs) and activates various inflammatory diseases. One of the DAMP molecules, so-called EDA-fibronectin (Fn) is also responsible for causing RA. EDA-Fn triggers RA through its interaction with TLR4. Apart from TLR4, it is divulged that certain other PRR's are also responsible for RA, but the identity and mechanism of those PRRs remain unknown until now. Hence, for the first time, we tried to reveal those PRR's interaction with EDA-Fn in RA through computational methods. Protein-protein interaction (PPI) was checked using ClusPro between EDA-Fn and certain Pattern recognition receptors (PRRs) to explore the binding affinities of the potential PRRs. Protein-protein docking unveiled that TLR5, TLR2 and RAGE has good interaction with EDA-Fn than the well-reported TLR4. Macromolecular simulation was performed for TLR5, TLR2 and RAGE complexes along with the control group TLR4 for 50 ns to further investigate the stability, leading to the identification of TLR2, TLR5 and RAGE as the stable complexes. Hence, TLR2, TLR5 and RAGE on interaction with EDA-Fn may lead to the progression of RA that may need additional validations through in vitro and in vivo animal models. Molecular docking was used to analyse the binding force of the top 33 active anti-arthritic compounds with the target protein EDA-Fn. Molecular docking study showed that withaferin A has a good binding activity with EDA-fibronectin target. Hence, it is emphasized that guggulsterone and berberine could modulate the EDA-Fn-mediated TLR5/TLR2/RAGE pathways, thereby it could inhibit the deteriorating effects of RA which needs further in vitro and in vivo experimental validations.
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Affiliation(s)
- Premnath Sakthivel
- Department of Pharmaceutical Technology, University College of Engineering, Bharathidasan Institute of Technology Campus, Anna University, Tiruchirappalli, 620 024, Tamil Nadu, India
| | - Indrajith Sakthivel
- Department of Pharmaceutical Technology, University College of Engineering, Bharathidasan Institute of Technology Campus, Anna University, Tiruchirappalli, 620 024, Tamil Nadu, India
| | - Sivasakthi Paramasivam
- Department of Pharmaceutical Technology, University College of Engineering, Bharathidasan Institute of Technology Campus, Anna University, Tiruchirappalli, 620 024, Tamil Nadu, India
| | - Senthamil Selvan Perumal
- Department of Pharmaceutical Technology, University College of Engineering, Bharathidasan Institute of Technology Campus, Anna University, Tiruchirappalli, 620 024, Tamil Nadu, India
| | - Sanmuga Priya Ekambaram
- Department of Pharmaceutical Technology, University College of Engineering, Bharathidasan Institute of Technology Campus, Anna University, Tiruchirappalli, 620 024, Tamil Nadu, India.
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12
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Choudhari S, Patil SK, Rathod S. Identification of hits as anti-obesity agents against human pancreatic lipase via docking, drug-likeness, in-silico ADME(T), pharmacophore, DFT, molecular dynamics, and MM/PB(GB)SA analysis. J Biomol Struct Dyn 2023:1-23. [PMID: 37735906 DOI: 10.1080/07391102.2023.2258407] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023]
Abstract
Obesity, characterized by excessive fat accumulation, is a major health concern. Inhibition of human pancreatic lipase, an enzyme involved in fat digestion, offers a potential strategy for weight loss and obesity treatment. This study aimed to identify polyphenols capable of forming stable complexes with human pancreatic lipase to block its activity. Molecular docking, density functional theory (DFT), molecular dynamics (MD) simulations, and MMPBGBSA calculations were employed to evaluate ligand binding, stability, and energy profiles. Pharmacophore modeling was also performed to identify key structural features for effective inhibition. Virtual screening identified ZINC000015120539, ZINC000000899200, ZINC000001531702, and ZINC000013340267 as potential candidates, exhibiting favorable binding and stable interactions over 100 ns MD simulations. These findings provide insights into the inhibitory potential of selected polyphenols on human pancreatic lipase and support further experimental investigations for obesity treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sujata Choudhari
- Department of Pharmaceutical Chemistry, Sarojini College of Pharmacy, Kolhapur, MS, India
- Department of Pharmaceutics, Ashokrao Mane College of Pharmacy, Peth Vadgaon, MS, India
| | - Sachin Kumar Patil
- Department of Pharmaceutics, Ashokrao Mane College of Pharmacy, Peth Vadgaon, MS, India
| | - Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
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13
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Kant R, Jha P, Saluja D, Chopra M. Identification of novel inhibitors of Neisseria gonorrhoeae MurI using homology modeling, structure-based pharmacophore, molecular docking, and molecular dynamics simulation-based approach. J Biomol Struct Dyn 2023; 41:7433-7446. [PMID: 36106953 DOI: 10.1080/07391102.2022.2121943] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 09/01/2022] [Indexed: 10/14/2022]
Abstract
MurI is one of the most significant role players in the biosynthesis of the peptidoglycan layer in Neisseria gonorrhoeae (Ng). We attempted to highlight the structural and functional relationship between Ng-MurI and D-glutamate to design novel molecules targeting this interaction. The three-dimensional (3D) model of the protein was constructed by homology modeling and the quality and consistency of generated model were assessed. The binding site of the protein was identified by molecular docking studies and a pharmacophore was identified using the interactions of the control ligand. The structure-based pharmacophore model was validated and employed for high-throughput virtual screening and molecular docking to identify novel Ng-MurI inhibitors. Finally, the model was optimized by molecular dynamics (MD) simulations and the optimized model complex with the substrate glutamate and novel molecules facilitated us to confirm the stability of the protein-ligand docked complexes. The 100 ns MD simulations of the potential lead compounds with protein confirmed that the modeled complexes were stable. This study identifies novel potential compounds with good fitness and docking scores, which made the interactions of biological significance within the protein active site. Hence, the identified compounds may act as new leads to design and develop Ng-MurI inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ravi Kant
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research & Delhi School of Public Health, IoE, University of Delhi, Delhi, India
| | - Prakash Jha
- Laboratory of Molecular Modeling and Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Daman Saluja
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research & Delhi School of Public Health, IoE, University of Delhi, Delhi, India
| | - Madhu Chopra
- Laboratory of Molecular Modeling and Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
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14
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Zahraee H, Mohammadi F, Parvaee E, Khoshbin Z, Arab SS. Reducing the assemblies of amyloid-beta multimers by sodium dodecyl sulfate surfactant at concentrations lower than critical micelle concentration: molecular dynamics simulation exploration. J Biomol Struct Dyn 2023:1-15. [PMID: 37599504 DOI: 10.1080/07391102.2023.2247086] [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: 03/09/2023] [Accepted: 08/05/2023] [Indexed: 08/22/2023]
Abstract
Amyloid-β peptide, the predominant proteinaceous component of senile plaques, is responsible for the incidence of Alzheimer's disease (AD), an age-associated neurodegenerative disorder. Specifically, the amyloid-β(1-42) (Aβ1-42) isoform, known for its high toxicity, is the predominant biomarker for the preliminary diagnosis of AD. The aggregation of the Aβ1-42 peptides can be affected by the components of the cellular medium through changing their structures and molecular interactions. In this study, we investigated the effect of sodium dodecyl sulfate (SDS) at much lower concentrations than the critical micelle concentration (CMC) on Aβ1-42 aggregation. For this purpose, we studied mono-, di-, tri- and tetramers of Aβ1-42 peptide in two different concentrations of SDS molecules (10 and 40 molecules) using a 300 ns molecular dynamics simulation for each system. The distance between the center of mass (COM) of Aβ1-42 peptides confirms that an increase in the number of SDS molecules decreases their aggregation probability due to greater interaction with SDS molecules. Besides, the less compactness parameter reveals the reduced aggregation probability of Aβ1-42 peptides. Based on the energetic FEL landscapes, SDS molecules with the concentration closer to the CMC are an effective inhibitory agent to prevent the formation of Aβ1-42 fibrils. Also, the aggregation direction of the peptide pairs can be predicted by determining the direction of the accumulation-deterrent forces.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hamed Zahraee
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Mohammadi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elahe Parvaee
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Zahra Khoshbin
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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15
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Liu WS, Zhao JF, Guo XJ, Lu SZ, Li W, Li WZ. Design, synthesis, activity and molecular dynamics studies of 1,3,4-thiadiazole derivatives as selective allosteric inhibitors of SHP2 for the treatment of cancer. Eur J Med Chem 2023; 258:115585. [PMID: 37390510 DOI: 10.1016/j.ejmech.2023.115585] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/25/2023] [Accepted: 06/18/2023] [Indexed: 07/02/2023]
Abstract
Overexpression or gene mutation of SHP2 is closely linked with a variety of cancers and has been identified as a crucial anticancer target. In the study, we took SHP2 allosteric inhibitor SHP099 as the lead compound, and 32 1,3,4-thiadiazole derivatives were identified as selective allosteric inhibitors of SHP2. In vitro enzyme activity test showed that some compounds had high inhibition on full length SHP2, and almost no activity on homologous protein SHP1, exhibiting high selectivity. Compound YF704 (4w) had the best inhibition activity, with IC50 value of 0.25 ± 0.02 μM, and also showed strong inhibitory activity on SHP2-E76K and SHP2-E76A, with IC50 values of 6.88 ± 0.69 μM and 1.38 ± 0.12 μM, respectively. CCK8 proliferation test found that multiple compounds would effectively inhibit the proliferation of a variety of cancer cells. Among them, the IC50 values of compound YF704 on MV4-11 and NCI-H358 cells were 3.85 ± 0.34 μM and 12.01 ± 0.62 μM, respectively. Specially, these compounds were sensitive to NCI-H358 cells containing KRASG12C mutation, thus overcoming the problem that SHP099 was insensitive to such cells. Apoptosis experiment showed that compound YF704 would effectively induce apoptosis of MV4-11 cells. Western blot showed that compound YF704 would downregulate the phosphorylation levels of Erk1/2 and Akt in MV4-11 and NCI-H358 cells. Molecular docking study show that compound YF704 would effectively bind to the allosteric region of SHP2 and form hydrogen bond interactions with key residues Thr108, Arg111 and Phe113. Molecular dynamics study further revealed the binding mechanism of SHP2 and compound YF704. In conclusion, we hope to provide potential SHP2 selective inhibitors and provide valuable clues for cancer treatment.
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Affiliation(s)
- 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.
| | - 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
| | - Xiao-Jing Guo
- Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, 261041, Shandong Province, China
| | - Sheng-Ze Lu
- School of Pharmacy, Weifang Medical University, Weifang, 261053, Shandong Province, China
| | - Wei Li
- School of Pharmacy, Weifang Medical University, Weifang, 261053, Shandong Province, China
| | - Wan-Zhong Li
- School of Pharmacy, Weifang Medical University, Weifang, 261053, Shandong Province, China.
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16
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Sendri N, Singh S, Sharma B, Purohit R, Bhandari P. Effect of co-pigments on anthocyanins of Rhododendron arboreum and insights into interaction mechanism. Food Chem 2023; 426:136571. [PMID: 37331145 DOI: 10.1016/j.foodchem.2023.136571] [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: 02/07/2023] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 06/20/2023]
Abstract
The impact of intermolecular copigmentation between five phenolic acids, two flavonoid and three amino acids with R. arboreum anthocyanins (ANS) and its isolated cyanidin-3-O-monoglycosides were investigated through experimental and theoretical approach. On addition of different copigments, phenolic acid induced strong hyperchromic (0.26-0.55 nm) and bathochromic shift (6.6-14.2 nm). The color intensity and stability of ANS with, storage at 4 °C & 25 °C, sunlight, oxidation and heat were evaluated by chromaticity, anthocyanin content, kinetic and structural simulation analysis. The strongest copigmentation reaction was observed with narningin (NA) and also showed high thermostability and highest half-life i.e. 3.39 h-1.24 h at 90-160 °C. The cyanidin-3-O-monoglycosides were analysed for their copigmentation effect and observations revealed that NA displayed best copigmentation effect to cyanidin-3-O-arabinoside (B) followed by cyanidin-3-O-galactoside (A), and cyanidin-3-O-rhamnoside (C). Additionally, structural simulation and steered molecular dynamics insights NA is the most favourable co-pigment involving π-π stacking and H-bonding.
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Affiliation(s)
- Nitisha Sendri
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sarvpreet Singh
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bhanu Sharma
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rituraj Purohit
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Pamita Bhandari
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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17
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Manzoor H, Zahid H, Emerling CA, Kumar KR, Hussain HMJ, Seo GH, Wajid M, Naz S. A biallelic variant of DCAF13 implicated in a neuromuscular disorder in humans. Eur J Hum Genet 2023; 31:629-637. [PMID: 36797467 PMCID: PMC10250411 DOI: 10.1038/s41431-023-01319-7] [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: 08/29/2022] [Revised: 02/05/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
Neuromuscular disorders encompass a broad range of phenotypes and genetic causes. We investigated a consanguineous family in which multiple patients had a neuromuscular disorder characterized by a waddling gait, limb deformities, muscular weakness and facial palsy. Exome sequencing was completed on the DNA of three of the four patients. We identified a novel missense variant in DCAF13, ENST00000612750.5, NM_015420.7, c.907 G > A;p.(Asp303Asn), ENST00000616836.4, NM_015420.6, c.1363 G > A:p.(Asp455Asn) (rs1209794872) segregating with this phenotype; being homozygous in all four affected patients and heterozygous in the unaffected individuals. The variant was extremely rare in the public databases (gnomAD allele frequency 0.000007081); was absent from the DNA of 300 ethnically matched controls and affected an amino acid which has been conserved across 1-2 billion years of evolution in eukaryotes. DCAF13 contains three WD40 domains and is hypothesized to have roles in both rRNA processing and in ubiquitination of proteins. Analysis of DCAF13 with the p.(Asp455Asn) variant predicted that the amino acid change is deleterious and affects a β-hairpin turn, within a WD40 domain of the protein which may decrease protein stability. Previously, a heterozygous variant of DCAF13 NM_015420.6, c.20 G > C:p.(Trp7Ser) with or without a heterozygous missense variant in CCN3, was suggested to cause inherited cortical myoclonic tremor with epilepsy. In addition, a heterozygous DCAF13 variant has been associated with autism spectrum disorder. Our study indicates a potential role of biallelic DCAF13 variants in neuromuscular disorders. Screening of additional patients with similar phenotype may broaden the allelic and phenotypic spectrum due to DCAF13 variants.
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Affiliation(s)
- Humera Manzoor
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore, Pakistan
| | - Hafsa Zahid
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | | | - Kishore R Kumar
- Molecular Medicine Laboratory and Department of Neurology, Concord Repatriation General Hospital, Concord Clinical School Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | | | | | - Muhammad Wajid
- Department of Zoology, University of Okara, Punjab, Pakistan
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan.
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18
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Hua L, Anjum F, Shafie A, Ashour AA, Almalki AA, Alqarni AA, Banjer HJ, Almaghrabi SA, He S, Xu N. Identifying promising GSK3β inhibitors for cancer management: a computational pipeline combining virtual screening and molecular dynamics simulations. Front Chem 2023; 11:1200490. [PMID: 37284581 PMCID: PMC10239944 DOI: 10.3389/fchem.2023.1200490] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/05/2023] [Indexed: 06/08/2023] Open
Abstract
Glycogen synthase kinase-3 (GSK3β), a serine/threonine protein kinase, has been discovered as a novel target for anticancer drugs. Although GSK3β is involved in multiple pathways linked to the etiology of various cancers, no specific GSK3β inhibitor has been authorized for cancer therapy. Most of its inhibitors have toxicity effects therefore, there is a need to develop safe and more potent inhibitors. In this study, a library of 4,222 anti-cancer compounds underwent rigorous computational screening to identify potential candidates for targeting the binding pocket of GSK3β. The screening process involved various stages, including docking-based virtual screening, physicochemical and ADMET analysis, and molecular dynamics simulations. Ultimately, two hit compounds, BMS-754807 and GSK429286A, were identified as having high binding affinities to GSK3β. BMS-754807 and GSK429286A exhibited binding affinities of -11.9, and -9.8 kcal/mol, respectively, which were greater than that of the positive control (-7.6 kcal/mol). Further, molecular dynamics simulations for 100 ns were employed to optimize the interaction between the compounds and GSK3β, and the simulations demonstrated that the interaction was stable and consistent throughout the study. These hits were also anticipated to have good drug-like properties. Finally, this study suggests that BMS-754807 and GSK429286A may undergo experimental validation to evaluate their potential as cancer treatments in clinical settings.
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Affiliation(s)
- Libo Hua
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acupuncture Moxibustion and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Amal Adnan Ashour
- Department of Oral and Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry, Taif University, Taif, Saudi Arabia
| | - Abdulraheem Ali Almalki
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Ali Abdullah Alqarni
- Department of Oral and Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry, Taif University, Taif, Saudi Arabia
| | - Hamsa Jameel Banjer
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Sarah Abdullah Almaghrabi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Center for Innovations in Personalized Medicine (CIPM), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shan He
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, China
- Institute for Nano Scale and Technology, College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
- College of Engineering, Information Technology and Environment, Charles Darwin University, Darwin, NT, Australia
| | - Nenggui Xu
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acupuncture Moxibustion and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
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Barry A, McNulty MT, Jia X, Gupta Y, Debiec H, Luo Y, Nagano C, Horinouchi T, Jung S, Colucci M, Ahram DF, Mitrotti A, Sinha A, Teeninga N, Jin G, Shril S, Caridi G, Bodria M, Lim TY, Westland R, Zanoni F, Marasa M, Turudic D, Giordano M, Gesualdo L, Magistroni R, Pisani I, Fiaccadori E, Reiterova J, Maringhini S, Morello W, Montini G, Weng PL, Scolari F, Saraga M, Tasic V, Santoro D, van Wijk JAE, Milošević D, Kawai Y, Kiryluk K, Pollak MR, Gharavi A, Lin F, Simœs E Silva AC, Loos RJF, Kenny EE, Schreuder MF, Zurowska A, Dossier C, Ariceta G, Drozynska-Duklas M, Hogan J, Jankauskiene A, Hildebrandt F, Prikhodina L, Song K, Bagga A, Cheong H, Ghiggeri GM, Vachvanichsanong P, Nozu K, Lee D, Vivarelli M, Raychaudhuri S, Tokunaga K, Sanna-Cherchi S, Ronco P, Iijima K, Sampson MG. Multi-population genome-wide association study implicates immune and non-immune factors in pediatric steroid-sensitive nephrotic syndrome. Nat Commun 2023; 14:2481. [PMID: 37120605 PMCID: PMC10148875 DOI: 10.1038/s41467-023-37985-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 04/10/2023] [Indexed: 05/01/2023] Open
Abstract
Pediatric steroid-sensitive nephrotic syndrome (pSSNS) is the most common childhood glomerular disease. Previous genome-wide association studies (GWAS) identified a risk locus in the HLA Class II region and three additional independent risk loci. But the genetic architecture of pSSNS, and its genetically driven pathobiology, is largely unknown. Here, we conduct a multi-population GWAS meta-analysis in 38,463 participants (2440 cases). We then conduct conditional analyses and population specific GWAS. We discover twelve significant associations-eight from the multi-population meta-analysis (four novel), two from the multi-population conditional analysis (one novel), and two additional novel loci from the European meta-analysis. Fine-mapping implicates specific amino acid haplotypes in HLA-DQA1 and HLA-DQB1 driving the HLA Class II risk locus. Non-HLA loci colocalize with eQTLs of monocytes and numerous T-cell subsets in independent datasets. Colocalization with kidney eQTLs is lacking but overlap with kidney cell open chromatin suggests an uncharacterized disease mechanism in kidney cells. A polygenic risk score (PRS) associates with earlier disease onset. Altogether, these discoveries expand our knowledge of pSSNS genetic architecture across populations and provide cell-specific insights into its molecular drivers. Evaluating these associations in additional cohorts will refine our understanding of population specificity, heterogeneity, and clinical and molecular associations.
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Affiliation(s)
- Alexandra Barry
- Division of Nephrology, Boston Children's Hospital, Boston, MA, USA
- Kidney Disease Initiative & Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michelle T McNulty
- Division of Nephrology, Boston Children's Hospital, Boston, MA, USA
- Kidney Disease Initiative & Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaoyuan Jia
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine (NCGM), Tokyo, Japan
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yask Gupta
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Hanna Debiec
- Sorbonne Université, UPMC Paris 06, Institut National de la Santé et de la Recherde Médicale, Unité Mixte de Rechereche, S 1155, Paris, France
| | - Yang Luo
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FY, United Kingdom
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - China Nagano
- Division of Nephrology, Boston Children's Hospital, Boston, MA, USA
- Kidney Disease Initiative & Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Seulgi Jung
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Songpa-gu, Seoul, Korea
| | - Manuela Colucci
- Renal Diseases Research Unit, Genetics and Rare Diseases Research Division, Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Dina F Ahram
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Adele Mitrotti
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy
| | - Aditi Sinha
- Department of Pediatrics, AIIMS, New Delhi, India
| | - Nynke Teeninga
- Department of Pediatric Nephrology, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gina Jin
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Gianluca Caridi
- Laboratory on Molecular Nephrology, IRCCS Instituto Giannina Gaslini, Genoa, Italy
| | - Monica Bodria
- Department of Nephrology and Renal Transplantation, IRCCS Instituto Giannina Gaslini, Genoa, Italy
| | - Tze Y Lim
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Rik Westland
- Department of Pediatric Nephrology, VU University Medical Center, Amsterdam, The Netherlands
| | - Francesca Zanoni
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Division of Transplantation, Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Maddalena Marasa
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Daniel Turudic
- Department of Pediatric Nephrology, Dialysis and Transplantation, Clinical Hospital Hospital Center Zagreb, University of Zagreb Medical School, Zagreb, Croatia
| | - Mario Giordano
- Division of Nephrology and Pediatric Dialysis, Bari Polyclinic Giovanni XXIII Children's Hospital, Bari, Italy
| | - Loreto Gesualdo
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy
| | - Riccardo Magistroni
- Department of Nephrology, Dialysis and Transplant Unit, University Hospital of Modena, Modena, Italy
- Surgical, Medical and Dental Department of Morphological Sciences, Section of Nephrology, University of Modena and Reggio Emilia, Modena, Italy
| | - Isabella Pisani
- Unità Operativa Nefrologia, Azienda Ospedaliero-Universitaria di Parma, Dipartimento di Medicina e Chirurgia, Università di Parma, Parma, Italy
| | - Enrico Fiaccadori
- Unità Operativa Nefrologia, Azienda Ospedaliero-Universitaria di Parma, Dipartimento di Medicina e Chirurgia, Università di Parma, Parma, Italy
| | - Jana Reiterova
- Department of Nephrology, Medicine and General University Hospital, Charles University, Prague, Czech Republic
| | | | - William Morello
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milano, Italy
| | - Giovanni Montini
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milano, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Patricia L Weng
- Department of Pediatric Nephrology, UCLA Medical Center and UCLA Medical Center-Santa Monica, Los Angeles, CA, USA
| | - Francesco Scolari
- Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, Division of Nephrology and Dialysis, University of Brescia and ASST Spedali Civili of Brescia, Brescia, Italy
| | - Marijan Saraga
- Department of Pediatrics, University of Split, Split, Croatia
| | - Velibor Tasic
- Department of Pediatric Nephrology, University Children's Hospital, Skopje, Macedonia
| | - Domenica Santoro
- Division of Nephrology and Dialysis Unit, University of Messina, Sicily, Italy
| | - Joanna A E van Wijk
- Department of Pediatric Nephrology, VU University Medical Center, Amsterdam, The Netherlands
| | - Danko Milošević
- Department of Pediatric Nephrology, Dialysis and Transplantation, Clinical Hospital Hospital Center Zagreb, University of Zagreb Medical School, Zagreb, Croatia
- Croatian Academy of Medical Sciences, Praska 2/III p.p. 27, 10000, Zagreb, Croatia
| | - Yosuke Kawai
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine (NCGM), Tokyo, Japan
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Martin R Pollak
- Division of Nephrology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Pediatric, Division of Pediatric Nephrology, Columbia University Irving Medical Center New York-Presbyterian Morgan Stanley Children's Hospital in New York, New York, NY, USA
| | - Ali Gharavi
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Fangmin Lin
- Department of Pediatric, Division of Pediatric Nephrology, Columbia University Irving Medical Center New York-Presbyterian Morgan Stanley Children's Hospital in New York, New York, NY, USA
| | - Ana Cristina Simœs E Silva
- Department of Pediatrics, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of General Internal Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michiel F Schreuder
- Department of Pediatric Nephrology, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Aleksandra Zurowska
- Department of Pediatrics, Nephrology and Hypertension, Medical University Gdansk, Gdansk, Poland
| | - Claire Dossier
- AP-HP, Pediatric Nephrology Department, Hôpital Robert-Debré, Paris, France
| | - Gema Ariceta
- Pediatric Nephrology, Hospital Universitari Vall d'Hebron, Universitat Autónoma de Barcelona, Barcelona, Spain
| | | | - Julien Hogan
- AP-HP, Pediatric Nephrology Department, Hôpital Robert-Debré, Paris, France
| | - Augustina Jankauskiene
- Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Friedhelm Hildebrandt
- Division of Nephrology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Larisa Prikhodina
- Research and Clinical Institute for Pediatrics, Pirogov Russian National Research Medical University, Taldomskava St, 2, Moscow, Russia
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Songpa-gu, Seoul, Korea
| | - Arvind Bagga
- Department of Pediatrics, AIIMS, New Delhi, India
| | - Hae Cheong
- Department of Pediatrics, Hallym University Sacred Heart Hospital, 22, Gwanpyeong-ro 170 beon-gil, Dongan-gu, Anyang-si, Gyeonggi-do, 14068, Korea
| | - Gian Marco Ghiggeri
- Department of Nephrology and Renal Transplantation, IRCCS Instituto Giannina Gaslini, Genoa, Italy
| | - Prayong Vachvanichsanong
- Department of Pediatrics, Faculty of Medicine, Prince of Songkla University, Hat-Yai, Songkhla, 90110, Thailand
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Dongwon Lee
- Division of Nephrology, Boston Children's Hospital, Boston, MA, USA
- Kidney Disease Initiative & Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Marina Vivarelli
- Division of Nephrology, and Dialysis, Department of Pediatric Subspecialities, Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Centre for Genetics and Genomics Versus Arthritis, University of Manchester, Manchester, UK
| | - Katsushi Tokunaga
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine (NCGM), Tokyo, Japan
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Pierre Ronco
- Sorbonne Université, UPMC Paris 06, Institut National de la Santé et de la Recherde Médicale, Unité Mixte de Rechereche, S 1155, Paris, France
- Department of Nephrology, Centre Hospitalier du Mans, Le Mans, France
| | - Kazumoto Iijima
- Hyogo Prefectural Kobe Children's Hospital, Kobe, Japan
- Department of Advanced Pediatric Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Matthew G Sampson
- Division of Nephrology, Boston Children's Hospital, Boston, MA, USA.
- Kidney Disease Initiative & Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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20
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Rathod S, Chavan P, Mahuli D, Rochlani S, Shinde S, Pawar S, Choudhari P, Dhavale R, Mudalkar P, Tamboli F. Exploring biogenic chalcones as DprE1 inhibitors for antitubercular activity via in silico approach. J Mol Model 2023; 29:113. [PMID: 36971900 DOI: 10.1007/s00894-023-05521-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/17/2023] [Indexed: 03/28/2023]
Abstract
Cases of drug-resistant tuberculosis (TB) have increased worldwide in the last few years, and it is a major threat to global TB control strategies and the human population. Mycobacterium tuberculosis is a common causative agent responsible for increasing cases of TB and as reported by WHO, approximately, 1.5 million death occurred from TB in 2020. Identification of new therapies against drug-resistant TB is an urgent need to be considered primarily. The current investigation aims to find the potential biogenic chalcone against the potential targets of drug-resistant TB via in silico approach. The ligand library of biogenic chalcones was screened against DprE1. Results of molecular docking and in silico ADMET prediction revealed that ZINC000005158606 has lead-like properties against the targeted protein. Pharmacophore modeling was done to identify the pharmacophoric features and their geometric distance present in ZINC000005158606. The binding stability study performed using molecular dynamics (MD) simulation of the DprE1-ZINC000005158606 complex revealed the conformational stability of the complex system over 100 ns with minimum deviation. Further, the in silico anti-TB sensitivity of ZINC000005158606 was found to be higher as compared to the standards against Mycobacterium tuberculosis. The overall in silico investigation indicated the potential of identified hit to act as a lead molecule against Mycobacterium tuberculosis.
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21
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In Silico Screening and Molecular Dynamics Simulation Studies in the Identification of Natural Compound Inhibitors Targeting the Human Norovirus RdRp Protein to Fight Gastroenteritis. Int J Mol Sci 2023; 24:ijms24055003. [PMID: 36902433 PMCID: PMC10002960 DOI: 10.3390/ijms24055003] [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: 12/22/2022] [Revised: 01/26/2023] [Accepted: 02/06/2023] [Indexed: 03/08/2023] Open
Abstract
Norovirus (HNoV) is a leading cause of gastroenteritis globally, and there are currently no treatment options or vaccines available to combat it. RNA-dependent RNA polymerase (RdRp), one of the viral proteins that direct viral replication, is a feasible target for therapeutic development. Despite the discovery of a small number of HNoV RdRp inhibitors, the majority of them have been found to possess a little effect on viral replication, owing to low cell penetrability and drug-likeness. Therefore, antiviral agents that target RdRp are in high demand. For this purpose, we used in silico screening of a library of 473 natural compounds targeting the RdRp active site. The top two compounds, ZINC66112069 and ZINC69481850, were chosen based on their binding energy (BE), physicochemical and drug-likeness properties, and molecular interactions. ZINC66112069 and ZINC69481850 interacted with key residues of RdRp with BEs of -9.7, and -9.4 kcal/mol, respectively, while the positive control had a BE of -9.0 kcal/mol with RdRp. In addition, hits interacted with key residues of RdRp and shared several residues with the PPNDS, the positive control. Furthermore, the docked complexes showed good stability during the molecular dynamic simulation of 100 ns. ZINC66112069 and ZINC69481850 could be proven as potential inhibitors of the HNoV RdRp in future antiviral medication development investigations.
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22
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Rathod S, Shinde K, Porlekar J, Choudhari P, Dhavale R, Mahuli D, Tamboli Y, Bhatia M, Haval KP, Al-Sehemi AG, Pannipara M. Computational Exploration of Anti-cancer Potential of Flavonoids against Cyclin-Dependent Kinase 8: An In Silico Molecular Docking and Dynamic Approach. ACS OMEGA 2023; 8:391-409. [PMID: 36643495 PMCID: PMC9835631 DOI: 10.1021/acsomega.2c04837] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Over the centuries, cancer has been considered one of the significant health threats. It holds the position in the list of deadliest diseases over the globe. In women, breast cancer is the most common among many cancers and is the second most common cancer all over the world, while lung cancer is the first. Cyclin-dependent kinase 8 (CDK8) has been identified as a critical oncogenic driver that is found in breast cancer and associated with tumor progression. Flavonoids were virtually screened against CDK8 using molecular docking, drug-likeness, ADMET prediction, and a molecular dynamics (MD) simulation approach to determine the potential flavonoid structure against CDK8. The results indicated that ZINC000005854718 showed the highest negative binding affinity of -10.7 kcal/mol with the targeted protein and passed all the drug-likeness parameters. Performed molecular dynamics simulation showed that docked complex systems have good conformational stability over 100 ns in different temperatures (298, 300, 305, 310, and 320 K). The comparison between calculated binding free energy via MM/PB(GB)SA methods and binding affinity calculated via molecular docking suggested tight binding of ZINC000005854718 with targeted protein. The results concluded that ZINC000005854718 has drug-like properties with tight and stable binding with the targeted protein.
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Affiliation(s)
- Sanket Rathod
- Department
of Pharmaceutical Chemistry, Bharati Vidyapeeth
College of Pharmacy, Kolhapur 416 013, Maharashtra, India
| | - Ketaki Shinde
- Department
of Quality Assurance Techniques, Poona College of Pharmacy, Bharati Vidyapeeth Deemed University, Pune 411 038, Maharashtra, India
| | - Jaykedar Porlekar
- Department
of Pharmaceutics, Bharati Vidyapeeth College
of Pharmacy, Kolhapur 416 013, Maharashtra, India
| | - Prafulla Choudhari
- Department
of Pharmaceutical Chemistry, Bharati Vidyapeeth
College of Pharmacy, Kolhapur 416 013, Maharashtra, India
| | - Rakesh Dhavale
- Department
of Pharmaceutics, Bharati Vidyapeeth College
of Pharmacy, Kolhapur 416 013, Maharashtra, India
| | - Deepak Mahuli
- Department
of Pharmacology, Bharati Vidyapeeth College
of Pharmacy, Kolhapur 416 013, Maharashtra, India
| | - Yasinalli Tamboli
- Wockhardt
Research Centre, D-4, MIDC, Chikalthana, Aurangabad 431 006, Maharashtra, India
| | - Manish Bhatia
- Department
of Pharmaceutical Chemistry, Bharati Vidyapeeth
College of Pharmacy, Kolhapur 416 013, Maharashtra, India
| | - Kishan P. Haval
- Department
of Chemistry, Dr. Babasaheb Ambedkar Marathwada
University Sub Campus, Osmanabad 413501, Maharashtra, India
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23
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Jha RK, Khan RJ, Parthiban A, Singh E, Jain M, Amera GM, Singh RP, Ramachandran P, Ramachandran R, Sachithanandam V, Muthukumaran J, Singh AK. Identifying the natural compound Catechin from tropical mangrove plants as a potential lead candidate against 3CL pro from SARS-CoV-2: An integrated in silico approach. J Biomol Struct Dyn 2022; 40:13392-13411. [PMID: 34644249 DOI: 10.1080/07391102.2021.1988710] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2, a member of beta coronaviruses, is a single-stranded, positive-sense RNA virus responsible for the COVID-19 pandemic. With global fatalities of the pandemic exceeding 4.57 million, it becomes crucial to identify effective therapeutics against the virus. A protease, 3CLpro, is responsible for the proteolysis of viral polypeptides into functional proteins, which is essential for viral pathogenesis. This indispensable activity of 3CLpro makes it an attractive target for inhibition studies. The current study aimed to identify potential lead molecules against 3CLpro of SARS-CoV-2 using a manually curated in-house library of antiviral compounds from mangrove plants. This study employed the structure-based virtual screening technique to evaluate an in-house library of antiviral compounds against 3CLpro of SARS-CoV-2. The library was comprised of thirty-three experimentally proven antiviral molecules extracted from different species of tropical mangrove plants. The molecules in the library were virtually screened using AutoDock Vina, and subsequently, the top five promising 3CLpro-ligand complexes along with 3CLpro-N3 (control molecule) complex were subjected to MD simulations to comprehend their dynamic behaviour and structural stabilities. Finally, the MM/PBSA approach was used to calculate the binding free energies of 3CLpro complexes. Among all the studied compounds, Catechin achieved the most significant binding free energy (-40.3 ± 3.1 kcal/mol), and was closest to the control molecule (-42.8 ± 5.1 kcal/mol), and its complex with 3CLpro exhibited the highest structural stability. Through extensive computational investigations, we propose Catechin as a potential therapeutic agent against SARS-CoV-2. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rajat Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P., India
| | - Rameez Jabeer Khan
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P., India
| | - A Parthiban
- National Centre for Sustainable Coastal Management, Ministry of Environment, Forest and Climate Change, Government of India, Anna University Campus, Chennai, Tamil Nadu, India.,Department of Chemistry, School of Arts and Sciences, Vinayaka Mission's Research Foundation, AVIT campus, Chennai, India
| | - Ekampreet Singh
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P., India
| | - Monika Jain
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P., India
| | - Gizachew Muluneh Amera
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P., India.,Department of Biotechnology, College of Natural and Computational Sciences, Wollo University, Dessie, Ethiopia
| | - Rashmi Prabha Singh
- Department of Biotechnology, IILM College of Engineering & Technology, Greater Noida, U.P, India
| | - Purvaja Ramachandran
- National Centre for Sustainable Coastal Management, Ministry of Environment, Forest and Climate Change, Government of India, Anna University Campus, Chennai, Tamil Nadu, India
| | - Ramesh Ramachandran
- National Centre for Sustainable Coastal Management, Ministry of Environment, Forest and Climate Change, Government of India, Anna University Campus, Chennai, Tamil Nadu, India
| | - V Sachithanandam
- National Centre for Sustainable Coastal Management, Ministry of Environment, Forest and Climate Change, Government of India, Anna University Campus, Chennai, Tamil Nadu, India
| | - Jayaraman Muthukumaran
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P., India
| | - Amit Kumar Singh
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P., India
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24
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Shaikh S, Ali S, Lim JH, Chun HJ, Ahmad K, Ahmad SS, Hwang YC, Han KS, Kim NR, Lee EJ, Choi I. Dipeptidyl peptidase-4 inhibitory potentials of Glycyrrhiza uralensis and its bioactive compounds licochalcone A and licochalcone B: An in silico and in vitro study. Front Mol Biosci 2022; 9:1024764. [PMID: 36250007 PMCID: PMC9564220 DOI: 10.3389/fmolb.2022.1024764] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a growing global public health issue, and dipeptidyl peptidase-4 (DPP-4) is a potential therapeutic target in T2DM. Several synthetic anti-DPP-4 medications can be used to treat T2DM. However, because of adverse effects, there is an unmet demand for the development of safe and effective medications. Natural medicines are receiving greater interest due to the inherent safety of natural compounds. Glycyrrhiza uralensis (licorice) is widely consumed and used as medicine. In this study, we investigated the abilities of a crude water extract (CWE) of G. uralensis and two of its constituents (licochalcone A (LicA) and licochalcone B (LicB)) to inhibit the enzymatic activity of DPP-4 in silico and in vitro. In silico studies showed that LicA and LicB bind tightly to the catalytic site of DPP-4 and have 11 amino acid residue interactions in common with the control inhibitor sitagliptin. Protein-protein interactions studies of LicA-DPP4 and LicB-DPP4 complexes with GLP1 and GIP reduced the DPP-4 to GLP1 and GIP interactions, indicated that these constituents might reduce the degradations of GLP1 and GIP. In addition, molecular dynamics simulations revealed that LicA and LicB stably bound to DPP-4 enzyme. Furthermore, DPP-4 enzyme assay showed the CWE of G. uralensis, LicA, and LicB concentration-dependently inhibited DPP-4; LicA and LicB had an estimated IC50 values of 347.93 and 797.84 μM, respectively. LicA and LicB inhibited DPP-4 at high concentrations, suggesting that these compounds could be used as functional food ingredients to manage T2DM.
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Affiliation(s)
- Sibhghatulla Shaikh
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea
| | - Shahid Ali
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea
| | - Jeong Ho Lim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea
| | - Hee Jin Chun
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Khurshid Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea
| | - Syed Sayeed Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea
| | - Ye Chan Hwang
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Ki Soo Han
- Neo Cremar Co., Ltd., Seoul, South Korea
| | - Na Ri Kim
- Neo Cremar Co., Ltd., Seoul, South Korea
| | - Eun Ju Lee
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea
- *Correspondence: Eun Ju Lee, ; Inho Choi,
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea
- *Correspondence: Eun Ju Lee, ; Inho Choi,
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He S, Nahhas AF, Habib AH, Alshehri MA, Alshamrani S, Asiri SA, Alnamshan MM, Helmi N, Al-Dhuayan I, Almulhim J, Alharbi AM, Su D, Kumari A, Rahaman A. Identification of compelling inhibitors of human norovirus 3CL protease to combat gastroenteritis: A structure-based virtual screening and molecular dynamics study. Front Chem 2022; 10:1034911. [PMID: 36247661 PMCID: PMC9561104 DOI: 10.3389/fchem.2022.1034911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Human noroviruses (NV) are the most prevalent cause of sporadic and pandemic acute gastroenteritis. NV infections cause substantial morbidity and death globally, especially amongst the aged, immunocompromised individuals, and children. There are presently no authorized NV vaccines, small-molecule therapies, or prophylactics for humans. NV 3 C L protease (3CLP) has been identified as a promising therapeutic target for anti-NV drug development. Herein, we employed a structure-based virtual screening method to screen a library of 700 antiviral compounds against the active site residues of 3CLP. We report three compounds, Sorafenib, YM201636, and LDC4297, that were revealed to have a higher binding energy (BE) value with 3CLP than the control (Dipeptidyl inhibitor 7) following a sequential screening, in-depth molecular docking and visualization, physicochemical and pharmacological property analysis, and molecular dynamics (MD) study. Sorafenib, YM201636, and LDC4297 had BEs of -11.67, -10.34, and -9.78 kcal/mol with 3CLP, respectively, while control had a BE of -6.38 kcal/mol. Furthermore, MD simulations of the two best compounds and control were used to further optimize the interactions, and a 100 ns MD simulation revealed that they form stable complexes with 3CLP. The estimated physicochemical, drug-like, and ADMET properties of these hits suggest that they might be employed as 3CLP inhibitors in the management of gastroenteritis. However, wet lab tests are a prerequisite to optimize them as NV 3CLP inhibitors.
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Affiliation(s)
- Shan He
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, China
- Institute for Nano Scale and Technology, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
- Suzhou Ultra-Water-Cleaning Tech, Pty, Ltd., Suzhou, Jiangsu, China
| | - Alaa F. Nahhas
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Alaa Hamed Habib
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed Ali Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Saleh Alshamrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Saeed A. Asiri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Mashael M. Alnamshan
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Nawal Helmi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, University of Jeddah, Jeddah, Saudi Arabia
| | - Ibtesam Al-Dhuayan
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Jawaher Almulhim
- Department of Biological Sciences, King Faisal University, Alahsa, Saudi Arabia
| | - Ahmed M. Alharbi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Dongxiao Su
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, China
- *Correspondence: Dongxiao Su, ; Ankita Kumari, ; Abdul Rahaman,
| | - Ankita Kumari
- School of Food Science and Engineering, South china University of Technology, Guangzhou, China
- *Correspondence: Dongxiao Su, ; Ankita Kumari, ; Abdul Rahaman,
| | - Abdul Rahaman
- School of Food Science and Engineering, South china University of Technology, Guangzhou, China
- *Correspondence: Dongxiao Su, ; Ankita Kumari, ; Abdul Rahaman,
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26
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Liu K, Chen X, Ren Y, Liu C, Yuan A, Zheng L, Li B, Zhang Y. Identification of a novel farnesoid X receptor agonist, kaempferol-7-O-rhamnoside, a compound ameliorating drug-induced liver injury based on virtual screening and in vitro validation. Toxicol Appl Pharmacol 2022; 454:116251. [PMID: 36150480 DOI: 10.1016/j.taap.2022.116251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/11/2022] [Accepted: 09/16/2022] [Indexed: 11/19/2022]
Abstract
Farnesoid X receptor (FXR), a bile acid receptor, plays an essential role in maintaining bile acid and liver homeostasis and has been recognized as an essential target for drug-induced liver injury (DILI). This study aimed to identify potential FXR agonists by virtual screening, molecular dynamics (MD) simulation, and biological assays. First, an in-house Traditional Chinese medicine compound database was screened using a virtual approach based on molecular docking to reveal potential FXR agonists. Secondly, MD was applied to analyze the process of agonist binding. Finally, the acetaminophen (APAP)-induced L02 cells model evaluated the pharmacodynamic activity of agonists treating DILI. Virtual screening results showed that kaempferol-7-O-rhamnoside was confirmed as the FXR agonist. MD results showed that kaempferol-7-O-rhamnoside could stably bind the FXR. In addition, in vitro cell-based assay showed that kaempferol-7-O-rhamnoside could promote the expression of the FXR gene and inhibit the Cyp7a1 gene expression in APAP-induced cells, significantly reducing the activities of AST, AKP and ROS, and enhancing the expression of GSH. The current study confirmed that kaempferol-7-O-rhamnoside might improve liver function by promoting proliferation, ameliorating oxidative stress, and regulating FXR target genes as observed in vitro. Therefore, in this study, discovering the FXR agonist, kaempferol-7-O-rhamnoside, provides valuable guidance for developing novel drugs against DILI.
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Affiliation(s)
- Kaiyang Liu
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Xi Chen
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yue Ren
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Chaoqun Liu
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Anlei Yuan
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Lulu Zheng
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Beiyan Li
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yanling Zhang
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China.
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Targeting Glutaminase by Natural Compounds: Structure-Based Virtual Screening and Molecular Dynamics Simulation Approach to Suppress Cancer Progression. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27155042. [PMID: 35956989 PMCID: PMC9370672 DOI: 10.3390/molecules27155042] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/12/2022] [Accepted: 07/18/2022] [Indexed: 01/09/2023]
Abstract
Cancer cells change their glucose and glutamine (GLU) metabolism to obtain the energy required to continue growing. Glutaminase (GLS) plays a crucial role in promoting cell metabolism for cancer cell growth; targeting GLU metabolism by inhibiting GLS has attracted interest as a potential cancer management strategy. Herein, we employed a sequential screening of traditional Chinese medicine (TCM) database followed by drug-likeness and molecular dynamics simulations against the active site of GLS. We report 12 potent compounds after screening the TCM database against GLS, followed by a drug-likeness filter with Lipinski and Veber rule criteria. Among them, ZINC03978829 and ZINC32296657 were found to have higher binding energy (BE) values than the control compound 6-Diazo-5-Oxo-L-Norleucine, with BEs of -9.3 and -9.7 kcal/mol, respectively, compared to the BE of 6-Diazo-5-Oxo-L-Norleucine (-4.7 kcal/mol) with GLS. Molecular dynamics simulations were used to evaluate the results further, and a 100 ns MD simulation revealed that the hits form stable complexes with GLS and formed 2-5 hydrogen bond interactions. This study indicates that these hits might be employed as GLS inhibitors in the battle against cancer. However, more laboratory tests are a prerequisite to optimize them as GLS inhibitors.
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Abstract
Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.
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Affiliation(s)
- Serge Perez
- Centre de Recherche sur les Macromolecules Vegetales, University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041, France
| | - Olga Makshakova
- FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
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Ali S, Ahmad K, Shaikh S, Lim JH, Chun HJ, Ahmad SS, Lee EJ, Choi I. Identification and Evaluation of Traditional Chinese Medicine Natural Compounds as Potential Myostatin Inhibitors: An In Silico Approach. Molecules 2022; 27:molecules27134303. [PMID: 35807547 PMCID: PMC9268423 DOI: 10.3390/molecules27134303] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 12/04/2022] Open
Abstract
Myostatin (MSTN), a negative regulator of muscle mass, is reported to be increased in conditions linked with muscle atrophy, sarcopenia, and other muscle-related diseases. Most pharmacologic approaches that treat muscle disorders are ineffective, emphasizing the emergence of MSTN inhibition. In this study, we used computational screening to uncover natural small bioactive inhibitors from the Traditional Chinese Medicine database (~38,000 compounds) for the MSTN protein. Potential ligands were screened, based on binding affinity (150), physicochemical (53) and ADMET properties (17). We found two hits (ZINC85592908 and ZINC85511481) with high binding affinity and specificity, and their binding patterns with MSTN protein. In addition, molecular dynamic simulations were run on each complex to better understand the interaction mechanism of MSTN with the control (curcumin) and the hit compounds (ZINC85592908 and ZINC85511481). We determined that the hits bind to the active pocket site (Helix region) and trigger conformational changes in the MSTN protein. Since the stability of the ZINC85592908 compound was greater than the MSTN control, we believe that ZINC85592908 has therapeutic potential against the MSTN protein and may hinder downstream singling by inhibiting the MSTN protein and increasing myogenesis in the skeletal muscle tissues.
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Affiliation(s)
- Shahid Ali
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (S.A.); (K.A.); (S.S.); (J.H.L.); (H.J.C.); (S.S.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
| | - Khurshid Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (S.A.); (K.A.); (S.S.); (J.H.L.); (H.J.C.); (S.S.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
| | - Sibhghatulla Shaikh
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (S.A.); (K.A.); (S.S.); (J.H.L.); (H.J.C.); (S.S.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
| | - Jeong Ho Lim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (S.A.); (K.A.); (S.S.); (J.H.L.); (H.J.C.); (S.S.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
| | - Hee Jin Chun
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (S.A.); (K.A.); (S.S.); (J.H.L.); (H.J.C.); (S.S.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
| | - Syed Sayeed Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (S.A.); (K.A.); (S.S.); (J.H.L.); (H.J.C.); (S.S.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
| | - Eun Ju Lee
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (S.A.); (K.A.); (S.S.); (J.H.L.); (H.J.C.); (S.S.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (S.A.); (K.A.); (S.S.); (J.H.L.); (H.J.C.); (S.S.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
- Correspondence:
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30
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Khurshid B, Rehman AU, Luo R, Khan A, Wadood A, Anwar J. Heparin-Assisted Amyloidogenesis Uncovered through Molecular Dynamics Simulations. ACS OMEGA 2022; 7:15132-15144. [PMID: 35572757 PMCID: PMC9089684 DOI: 10.1021/acsomega.2c01034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/11/2022] [Indexed: 05/14/2023]
Abstract
Glycosaminoglycans (GAGs), in particular, heparan sulfate and heparin, are found colocalized with Aβ amyloid. They have been shown to enhance fibril formation, suggesting a possible pathological connection. We have investigated heparin's assembly of the KLVFFA peptide fragment using molecular dynamics simulation, to gain a molecular-level mechanistic understanding of how GAGs enhance fibril formation. The simulations reveal an exquisite process wherein heparin accelerates peptide assembly by first "gathering" the peptide molecules and then assembling them. Heparin does not act as a mere template but is tightly coupled to the peptides, yielding a composite protofilament structure. The strong intermolecular interactions suggest composite formation to be a general feature of heparin's interaction with peptides. Heparin's chain flexibility is found to be essential to its fibril promotion activity, and the need for optimal heparin chain length and concentration has been rationalized. These insights yield design rules (flexibility; chain-length) and protocol guidance (heparin:peptide molar ratio) for developing effective heparin mimetics and other functional GAGs.
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Affiliation(s)
- Beenish Khurshid
- Department
of Biochemistry, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
| | - Ashfaq Ur Rehman
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697, United States
| | - Ray Luo
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697, United States
| | - Alamzeb Khan
- Department
of Pediatrics, Yale School of Medicine, Yale University, New Haven, Connecticut 06511, United States
| | - Abdul Wadood
- Department
of Biochemistry, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
| | - Jamshed Anwar
- Department
of Chemistry, University of Lancaster, Lancaster LA1 4YB, United Kingdom
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31
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Múnera M, Martínez D, Wortmann J, Zakzuk J, Keller W, Caraballo L, Puerta L. Structural and allergenic properties of the fatty acid binding protein from shrimp Litopenaeus vannamei. Allergy 2022; 77:1534-1544. [PMID: 34695231 DOI: 10.1111/all.15154] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 04/12/2021] [Accepted: 10/04/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND The shrimp Litopenaeus vannamei is an important source of food allergens but its allergenic repertoire is poorly characterized. Cross-reactivity between crustacean and mites has been reported, with tropomyosin, the most relevant allergen involved. The aim of this study was to investigate the structural and immunological properties of a recombinant Fatty Acid Binding Protein (FABP) family from L. vannamei (LvFABP). METHODS ELISA, skin prick test (SPT) and basophil activation assays were performed to determine IgE reactivity and allergenic activity of LvFABP. LC-MS/MS and Circular Dichroism experiments were done for structural analysis. B-cell epitope mapping with overlapping peptides, and cross-inhibition studies using human sera were done to identify antigenic regions and cross-reactivity. RESULTS The recombinant LvFABP bound serum IgE from 27% of 36 shrimp allergic patients and showed allergenic activity when tested for basophil activation and SPT in a selected number of them. CD-spectroscopy of LvFABP revealed that the protein is folded with a secondary structure composed of mainly β-strands and a smaller fraction of α helices. This is consistent with molecular modelling results, which exhibit a typical β barrel fold with two α-helices and ten β-strands. Epitope mapping identified two IgE-binding antigenic regions and inhibition assays found high cross-reactivity between LvFABP and Blo t 13, mediated by the antigenic region involving amino acids 54 to 72. CONCLUSIONS Our results show that LvFABP is a shrimp allergen that cross reacts with the house dust mite allergen Blo t 13 and has allergenic activity, which suggest that it could be clinically relevant in case of shellfish allergy. This new allergen, named Lit v 13, will also help to understand basic mechanisms of sensitization to shrimp.
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Affiliation(s)
- Marlon Múnera
- Institute for Immunological Research University of Cartagena Cartagena Colombia
| | - Dalgys Martínez
- Institute for Immunological Research University of Cartagena Cartagena Colombia
| | - Judith Wortmann
- Institute of Molecular Biosciences, BioTechMed Graz University of Graz Graz Austria
| | - Josefina Zakzuk
- Institute for Immunological Research University of Cartagena Cartagena Colombia
| | - Walter Keller
- Institute of Molecular Biosciences, BioTechMed Graz University of Graz Graz Austria
| | - Luis Caraballo
- Institute for Immunological Research University of Cartagena Cartagena Colombia
| | - Leonardo Puerta
- Institute for Immunological Research University of Cartagena Cartagena Colombia
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32
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Kumari A, kumar R, Sulabh G, Singh P, Kumar J, Singh VK, Ojha KK. In silico ADMET, molecular docking and molecular simulation-based study of glabridin’s natural and semisynthetic derivatives as potential tyrosinase inhibitors. ADVANCES IN TRADITIONAL MEDICINE 2022. [PMCID: PMC9000003 DOI: 10.1007/s13596-022-00640-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hyper-pigmentation conditions may develop due to erroneous melanogenesis cascade which leads to excess melanin production. Recently, inhibition of tyrosinase is the main focus of investigation as it majorly contributes to melanin production. This inhibition property can be exploited in medicine, agriculture, and in cosmetics. Present study aims to find a natural and safe alternative molecule as tyrosinase inhibitor. In this study, human tyrosinase enzyme was modelled due to unavailability of its crystal structure to look into the degree of efficacy of glabridin and its 15 derivatives as tyrosinase inhibitor. Docking was performed by Autodock Vina at the catalytic core enzyme. Glabridin effects on melanoma cell lines was also elucidated by analysing cytotoxicity and effect on melanin production. Computational ADME analysis was done by SwissADME. Molecular dynamic simulation was also performed to further evaluate the interaction profile of these molecules and kojic acid (positive inhibitor) with respect to apo protein. Notably, four derivatives 5′-formylglabridin, glabridin dimer, 5′-prenyl glabridin and R-glabridin exhibited better binding affinity than glabridin. Glabridin effectively inhibited melanin production in a dose dependent manner. Among these, 5′-formylglabridin displayed highest binding affinity with docking score − 9.2 kcal/mol. Molecular properties and bioactivity analysis by Molinspiration web server and by SwissADME also presented these molecules as potential drug candidates. The study explores the understanding for the development of suitable tyrosinase inhibitor/s for the prevention of hyperpigmentation. However, a detailed in vivo study is required for glabridin derivatives to suggest these molecules as anti-melanogenic compound.
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33
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Maran M, Gangadharan S, Emerson IA. Molecular dynamics study of quercetin families and its derivative compounds from Carica papaya leaf as breast cancer inhibitors. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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34
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Hu LC, Ding CH, Li HY, Li ZZ, Chen Y, Li LP, Li WZ, Liu WS. Identification of potential target endoribonuclease NSP15 inhibitors of SARS-COV-2 from natural products through high-throughput virtual screening and molecular dynamics simulation. J Food Biochem 2022; 46:e14085. [PMID: 35128681 PMCID: PMC9114918 DOI: 10.1111/jfbc.14085] [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: 11/13/2021] [Revised: 12/28/2021] [Accepted: 01/04/2022] [Indexed: 12/14/2022]
Abstract
SARS‐CoV‐2 wreaks havoc around the world, triggering the COVID‐19 pandemic. It has been confirmed that the endoribonuclease NSP15 is crucial to the viral replication, and thus identified as a potential drug target against COVID‐19. The NSP15 protein was used as the target to conduct high‐throughput virtual screening on 30,926 natural products from the NPASS database to identify potential NSP15 inhibitors. And 100 ns molecular dynamics simulations were performed on the NSP15 and NSP15‐NPC198199 system. In all, 10 natural products with high docking scores with NSP15 protein were obtained, among which compound NPC198199 scored the highest. The analysis of the binding mode between NPC198199 and NSP15 found that NPC198199 would form H‐bond interactions with multiple key residues at the catalytic site. Subsequently, a series of post‐dynamics simulation analyses (including RMSD, RMSF, PCA, DCCM, RIN, binding free energy, and H‐bond occupancy) were performed to further explore inhibitory mechanism of compound NPC198199 on NSP15 protein at the molecular level. The research strongly indicates that the 10 natural compounds screened can be used as potential inhibitors of NSP15, and provides valuable information for the subsequent drug discovery of anti‐SARS‐CoV‐2.
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Affiliation(s)
- Liang-Chang Hu
- Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Chuan-Hua Ding
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Hong-Ying Li
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Zhen-Zhen Li
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Ying Chen
- School of Pharmacy, Weifang Medical University, Weifang, China
| | - Li-Peng Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wan-Zhong Li
- School of Pharmacy, Weifang Medical University, Weifang, China
| | - Wen-Shan Liu
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang, China
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35
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Targeting Cytotoxin-Associated Antigen A, a Virulent Factor of Helicobacter pylori-Associated Gastric Cancer: Structure-Based In Silico Screening of Natural Compounds. Molecules 2022; 27:molecules27030732. [PMID: 35164000 PMCID: PMC8838247 DOI: 10.3390/molecules27030732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/10/2022] Open
Abstract
Gastric cancer is the fifth most frequent cancer and the third major cause of mortality worldwide. Helicobacter pylori, a bacterial infection linked with GC, injects the cytotoxin-associated antigen A (CagA; an oncoprotein) into host cells. When the phosphorylated CagA protein enters the cell, it attaches to other cellular components, interfering with normal cellular signaling pathways. CagA plays an important role in the progression of GC by interacting with phosphatidylserine of the host cell membrane. Therefore, disrupting the CagA-phosphatidylserine connection using small molecules appears to be a promising therapeutic approach. In this report, we screened the natural compounds from ZINC database against the CagA protein using the bioinformatics tools. Hits were initially chosen based on their physicochemical, absorption, distribution, metabolism, excretion, and toxicity (ADMET) characteristics, as well as other drug-like characteristics. To locate safe and effective hits, the PAINS filter, binding affinities estimation, and interaction analysis were used. Three compounds with high binding affinity and specificity for the CagA binding pocket were discovered. The final hits, ZINC153731, ZINC69482055, and ZINC164387, were found to bind strongly with CagA protein, with binding energies of -11.53, -10.67, and -9.21 kcal/mol, respectively, which were higher than that of the control compound (-7.25 kcal/mol). Further, based on binding affinity and interaction pattern, two leads (ZINC153731, ZINC69482055) were chosen for molecular dynamics (MD) simulation analysis. MD results showed that they displayed stability in their vicinity at 100 ns. This study suggested that these compounds could be used as possible inhibitors of CagA protein in the fight against GC. However, additional benchwork tests are required to validate them as CagA protein inhibitors.
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Li F, Zhao J, Wei Y, Jiao X, Li Q. Holistic review of polysaccharides isolated from pumpkin: Preparation methods, structures and bioactivities. Int J Biol Macromol 2021; 193:541-552. [PMID: 34656536 DOI: 10.1016/j.ijbiomac.2021.10.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/06/2021] [Accepted: 10/06/2021] [Indexed: 10/20/2022]
Abstract
Pumpkin polysaccharides have arrested researchers' attention in fields of food supplements for healthy product and traditional Chinese medicine due to their multiple bioactivities with non-toxic and highly biocompatible. This review emphatically summarized recent progresses in the primary and spatial structural features, various bioactivities, structure-to-function associations, different preparation techniques, and absorption characteristics across intestinal epithelial and in vivo bio-distribution of pumpkin polysaccharides. Additionally, current challenges and future trends in development of pumpkin polysaccharides were pointed out. We found that pumpkin polysaccharides were primary structure (e.g. glucan, galactoglucan, galactomannan, galactan, homogalacturonan (HG), and rhamnogalacturonan-Ι (RG-Ι)) and special structure diverse (e.g. hollow helix, linear, and sphere-like) and significant functional foods or therapeutic agents (e.g. oral hypoglycemic agents). Moreover, we found that the molecular weight (Mw), uronic acid, linkage types, and modifications all could affect their bioactivities (e.g. anti-oxidant, anti-coagulant, and anti-diabetic activities), and pumpkin polysaccharides may across intestinal epithelial into the blood reaching to target organs. Collectively, the structures diversity and pharmacological values of pumpkin polysaccharides support their therapeutic potentials and sanitarian functions.
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Affiliation(s)
- Fei Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; National Engineering Research Center for Fruits and Vegetables Processing, Beijing 100083, China
| | - Jing Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; National Engineering Research Center for Fruits and Vegetables Processing, Beijing 100083, China
| | - Yunlu Wei
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; National Engineering Research Center for Fruits and Vegetables Processing, Beijing 100083, China
| | - Xu Jiao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; National Engineering Research Center for Fruits and Vegetables Processing, Beijing 100083, China
| | - Quanhong Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; National Engineering Research Center for Fruits and Vegetables Processing, Beijing 100083, China.
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Identification of Potent Natural Resource Small Molecule Inhibitor to Control Vibrio cholera by Targeting Its Outer Membrane Protein U: An In Silico Approach. Molecules 2021; 26:molecules26216517. [PMID: 34770925 PMCID: PMC8588037 DOI: 10.3390/molecules26216517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 11/16/2022] Open
Abstract
Vibrio cholerae causes the diarrheal disease cholera which affects millions of people globally. The outer membrane protein U (OmpU) is the outer membrane protein that is most prevalent in V. cholerae and has already been recognized as a critical component of pathogenicity involved in host cell contact and as being necessary for the survival of pathogenic V. cholerae in the host body. Computational approaches were used in this study to screen a total of 37,709 natural compounds from the traditional Chinese medicine (TCM) database against the active site of OmpU. Following a sequential screening of the TCM database, we report three lead compounds-ZINC06494587, ZINC85510056, and ZINC95910434-that bind strongly to OmpU, with binding affinity values of -8.92, -8.12, and -8.78 kcal/mol, which were higher than the control ligand (-7.0 kcal/mol). To optimize the interaction, several 100 ns molecular dynamics simulations were performed, and the resulting complexes were shown to be stable in their vicinity. Additionally, these compounds were predicted to have good drug-like properties based on physicochemical properties and ADMET assessments. This study suggests that further research be conducted on these compounds to determine their potential use as cholera disease treatment.
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In silico study of some selective phytochemicals against a hypothetical SARS-CoV-2 spike RBD using molecular docking tools. Comput Biol Med 2021. [DOI: 10.1016/j.compbiomed.2021.104818
expr 849028860 + 881472580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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Nag A, Paul S, Banerjee R, Kundu R. In silico study of some selective phytochemicals against a hypothetical SARS-CoV-2 spike RBD using molecular docking tools. Comput Biol Med 2021; 137:104818. [PMID: 34481181 PMCID: PMC8401086 DOI: 10.1016/j.compbiomed.2021.104818] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 02/07/2023]
Abstract
Background This world is currently witnessing a pandemic outbreak of ‘COVID-19′ caused by a positive-strand RNA virus ‘SARS-CoV-2’. Millions have succumbed globally to the disease, and the numbers are increasing day by day. The viral genome enters into the human host through interaction between the spike protein (S) and host angiotensin-converting enzyme-2 (ACE2) proteins. S is the common target for most recently rolled-out vaccines across regions. A recent surge in single/multiple mutations in S region is of great concern as it may escape vaccine induced immunity. So far, the treatment regime with repurposed drugs has not been too successful. Hypothesis Natural compounds are capable of targeting mutated spike protein by binding to its active site and destabilizing the spike-host ACE2 interaction. Materials and methods A hypothetical mutated spike protein was constructed by incorporating twelve different mutations from twelve geographical locations simultaneously into the receptor-binding domain (RBD) and docked with ACE2 and seven phytochemicals namely allicin, capsaicin, cinnamaldehyde, curcumin, gingerol, piperine and zingeberene. Molecular Dynamic (MD) simulation and Principal Component Analysis (PCA) were finally used for validation of the docking results. Result The docking results showed that curcumin and piperine were most potent to bind ACE2, mutated spike, and mutated spike-ACE2 complex, thereby restricting viral entry. ADME analysis also proved their drug candidature. The docking complexes were found to be stable by MD simulation. Conclusion This result provides a significant insight about the phytochemicals' role, namely curcumin and piperine, as the potential therapeutic entities against mutated spike protein of SARS-CoV-2.
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Affiliation(s)
- Anish Nag
- Department of Life Sciences, CHRIST (Deemed to Be University), Bangalore 560029, India
| | - Subhabrata Paul
- School of Biotechnology, Presidency University, Canal Bank Rd, DG Block, Action Area 1D, New Town, West Bengal 700156, India
| | - Ritesh Banerjee
- School of Biological and Environmental Sciences, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Rita Kundu
- Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, India.
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Zhang Y, Zhao Z, Chen H, Fu Y, Wang W, Li Q, Li X, Wang X, Fan G, Zhang Y. The Underlying Molecular Mechanisms Involved in Traditional Chinese Medicine Smilax china L. for the Treatment of Pelvic Inflammatory Disease. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2021; 2021:5552532. [PMID: 33927774 PMCID: PMC8052137 DOI: 10.1155/2021/5552532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/04/2021] [Accepted: 03/21/2021] [Indexed: 02/07/2023]
Abstract
Smilax china L. (SCL) is extensively used in the treatment of pelvic inflammatory disease (PID). This study aimed to clarify the potential active ingredients of SCL and mechanisms on PID. SCL was widely distributed in Japan, South Korea, and China, which was traditionally considered heat-clearing, detoxicating, and dampness-eliminating medicine. Systems pharmacology revealed that 32 compounds in SCL may interact with 19 targets for immunoenhancement, antiapoptosis, anti-inflammation, and antioxidant activity of the PID model. Molecular docking revealed that isorhamnetin, moracin M, rutin, and oxyresveratrol may have higher binding potential with prostaglandin-endoperoxide synthase 2 (PTGS2), mitogen-activated protein kinase 1 (MAPK1), siderocalin (LCN2), tumor necrosis factor (TNF), and matrix metalloprotein-9 (MMP9), respectively. Molecular dynamics simulation showed that the binding modes of moracin M-MAPK1, rutin-TNF, and oxyresveratrol-MMP9 complexes were more stable, evidenced by relatively smaller fluctuations in root mean square deviation values. Conclusively, SCL may treat PID by inhibiting inflammatory factors, antitissue fibrosis, and microbial growth.
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Affiliation(s)
- Yunsen Zhang
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zikuang Zhao
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Huimin Chen
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yutong Fu
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Wenxiang Wang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qi Li
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xuanhao Li
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaobo Wang
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Ethnic Medicine Academic Heritage Innovation Research Center, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Gang Fan
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yi Zhang
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Ethnic Medicine Academic Heritage Innovation Research Center, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- NMPA Key Laboratory for Quality Evaluation of Traditional Chinese Medicine (Traditional Chinese Patent Medicine), Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Liu WS, Li HG, Ding CH, Zhang HX, Wang RR, Li JQ. Screening potential FDA-approved inhibitors of the SARS-CoV-2 major protease 3CL pro through high-throughput virtual screening and molecular dynamics simulation. Aging (Albany NY) 2021; 13:6258-6272. [PMID: 33678621 PMCID: PMC7993695 DOI: 10.18632/aging.202703] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/03/2021] [Indexed: 04/16/2023]
Abstract
It has been confirmed that the new coronavirus SARS-CoV-2 caused the global pandemic of coronavirus disease 2019 (COVID-19). Studies have found that 3-chymotrypsin-like protease (3CLpro) is an essential enzyme for virus replication, and could be used as a potential target to inhibit SARS-CoV-2. In this work, 3CLpro was used as the target to complete the high-throughput virtual screening of the FDA-approved drugs, and Indinavir and other 10 drugs with high docking scores for 3CLpro were obtained. Studies on the binding pattern of 3CLpro and Indinavir found that Indinavir could form the stable hydrogen bond (H-bond) interactions with the catalytic dyad residues His41-Cys145. Binding free energy study found that Indinavir had high binding affinity with 3CLpro. Subsequently, molecular dynamics simulations were performed on the 3CLpro and 3CLpro-Indinavir systems, respectively. The post-dynamic analyses showed that the conformational state of the 3CLpro-Indinavir system transformed significantly and the system tended to be more stable. Moreover, analyses of the residue interaction network (RIN) and H-bond occupancy revealed that the residue-residue interaction at the catalytic site of 3CLpro was significantly enhanced after binding with Indinavir, which in turn inactivated the protein. In short, through this research, we hope to provide more valuable clues against COVID-19.
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Affiliation(s)
- Wen-Shan Liu
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China
| | - Han-Gao Li
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China
| | - Chuan-Hua Ding
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China
| | - Hai-Xia Zhang
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China
| | - Rui-Rui Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Jia-Qiu Li
- Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China
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Scherbinina SI, Toukach PV. Three-Dimensional Structures of Carbohydrates and Where to Find Them. Int J Mol Sci 2020; 21:E7702. [PMID: 33081008 PMCID: PMC7593929 DOI: 10.3390/ijms21207702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.
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Affiliation(s)
- Sofya I. Scherbinina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
- Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia
| | - Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
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Jha RK, Khan RJ, Amera GM, Singh E, Pathak A, Jain M, Muthukumaran J, Singh AK. Identification of promising molecules against MurD ligase from Acinetobacter baumannii: insights from comparative protein modelling, virtual screening, molecular dynamics simulations and MM/PBSA analysis. J Mol Model 2020; 26:304. [DOI: 10.1007/s00894-020-04557-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
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Khan RJ, Jha RK, Singh E, Jain M, Amera GM, Singh RP, Muthukumaran J, Singh AK. Identification of promising antiviral drug candidates against non-structural protein 15 (NSP15) from SARS-CoV-2: an in silico assisted drug-repurposing study. J Biomol Struct Dyn 2020; 40:438-448. [DOI: 10.1080/07391102.2020.1814870] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Rameez Jabeer Khan
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P., India
| | - Rajat Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P., India
| | - Ekampreet Singh
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P., India
| | - Monika Jain
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P., India
| | - Gizachew Muluneh Amera
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P., India
| | - Rashmi Prabha Singh
- Department of Biotechnology, IILM College of Engineering & Technology, Greater Noida, U.P., India
| | - Jayaraman Muthukumaran
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P., India
| | - Amit Kumar Singh
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, U.P., India
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Arantes PR, Pedebos C, Polêto MD, Pol-Fachin L, Verli H. The Lazy Life of Lipid-Linked Oligosaccharides in All Life Domains. J Chem Inf Model 2020; 60:631-643. [PMID: 31769974 DOI: 10.1021/acs.jcim.9b00904] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lipid-linked oligosaccharides (LLOs) play an important role in the N-glycosylation pathway as the donor substrate of oligosaccharyltransferases (OSTs), which are responsible for the en bloc transfer of glycan chains onto a nascent polypeptide. The lipid component of LLO in both eukarya and archaea consists of a dolichol, and an undecaprenol in prokarya, whereas the number of isoprene units may change between species. Given the potential relevance of LLOs and their related enzymes to diverse biotechnological applications, obtaining reliable LLO models from distinct domains of life could support further studies on complex formation and their processing by OSTs, as well as protein engineering on such systems. In this work, molecular modeling techniques, such as quantum mechanics calculations, molecular dynamics simulations, and metadynamics were employed to study eukaryotic (Glc3-Man9-GlcNAc2-PP-Dolichol), bacterial (Glc1-GalNAc5-Bac1-PP-Undecaprenol), and archaeal (Glc1-Man1-Gal1-Man1-Glc1-Gal1-Glc1-P-Dolichol) LLOs in membrane bilayers. Microsecond molecular dynamics simulations and metadynamics calculations of LLOs revealed that glycan chains are more prone to interact with the membrane lipid head groups, while the PP linkages are positioned at the lipid phosphate head groups level. The dynamics of isoprenoid chains embedded within the bilayer are described, and membrane dynamics and related properties are also investigated. Overall, there are similarities regarding the structure and dynamics of the eukaryotic, the bacterial, and the archaeal LLOs in bilayers, which can support the comprehension of their association with OSTs. These data may support future studies on the transferring mechanism of the oligosaccharide chain to an acceptor protein.
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Affiliation(s)
- Pablo R Arantes
- Centro de Biotecnologia , Universidade Federal do Rio Grande do Sul , Porto Alegre , RS 91509-900 , Brazil.,Laboratory of Genetic Toxicology , Federal University of Health Sciences of Porto Alegre - UFCSPA, Sarmento Leite, 245, Lab.714 , Porto Alegre , RS 90050-170 , Brazil
| | - Conrado Pedebos
- Centro de Biotecnologia , Universidade Federal do Rio Grande do Sul , Porto Alegre , RS 91509-900 , Brazil.,School of Chemistry , University of Southampton , Southampton , SO17 1BJ , U.K
| | - Marcelo D Polêto
- Centro de Biotecnologia , Universidade Federal do Rio Grande do Sul , Porto Alegre , RS 91509-900 , Brazil.,Departamento de Biologia Geral , Universidade Federal de Viçosa , Viçosa , MG 36570-000 , Brazil
| | | | - Hugo Verli
- Centro de Biotecnologia , Universidade Federal do Rio Grande do Sul , Porto Alegre , RS 91509-900 , Brazil
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de Meirelles JL, Nepomuceno FC, Peña-García J, Schmidt RR, Pérez-Sánchez H, Verli H. Current Status of Carbohydrates Information in the Protein Data Bank. J Chem Inf Model 2020; 60:684-699. [PMID: 31961683 DOI: 10.1021/acs.jcim.9b00874] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Carbohydrates are well known for their physicochemical, biological, functional, and therapeutic characteristics. Unfortunately, their chemical nature imposes severe challenges for the structural elucidation of these phenomena, impairing not only the depth of our understanding of carbohydrates but also the development of new biotechnological and therapeutic applications based on these molecules. In the recent past, the amount of structural information, obtained mainly from X-ray crystallography, has increased progressively, as well as its quality. In this context, the current work presents a global analysis of the carbohydrate information available in the Protein Data Bank (PDB). From high quality structures, it is clear that most of the data are highly concentrated on a few sets of residue types, on their monosaccharidic forms, and connected by a small diversity of glycosidic linkages. The geometries of these linkages can be mostly associated with the types of linkages instead of residues, while the level of puckering distortion was characterized, quantified, and located in a pseudorotational equilibrium landscape, not only to local minima but also to transitional states. These qualitative and quantitative analyses offer a global picture of the carbohydrate structural content in the PDB, potentially supporting the building of new models for carbohydrate-related biological phenomena at the atomistic level, including new developments on force field parameters.
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Affiliation(s)
- João L de Meirelles
- Programa de Pos-Graduacao em Biologia Celular e Molecular (PPGBCM), Centro de Biotecnologia , Universidade Federal do Rio Grande do Sul (UFRGS) , Av. Bento Goncalves, 9500 , Porto Alegre , Brazil 91509-900
| | - Felipe C Nepomuceno
- Programa de Pos-Graduacao em Biologia Celular e Molecular (PPGBCM), Centro de Biotecnologia , Universidade Federal do Rio Grande do Sul (UFRGS) , Av. Bento Goncalves, 9500 , Porto Alegre , Brazil 91509-900
| | - Jorge Peña-García
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department , Universidad Católica de Murcia (UCAM) , Murcia , Spain 30107
| | - Ricardo Rodríguez Schmidt
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department , Universidad Católica de Murcia (UCAM) , Murcia , Spain 30107
| | - Horacio Pérez-Sánchez
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department , Universidad Católica de Murcia (UCAM) , Murcia , Spain 30107
| | - Hugo Verli
- Programa de Pos-Graduacao em Biologia Celular e Molecular (PPGBCM), Centro de Biotecnologia , Universidade Federal do Rio Grande do Sul (UFRGS) , Av. Bento Goncalves, 9500 , Porto Alegre , Brazil 91509-900
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Chen X, Lu F, Luo G, Ren Y, Ma J, Zhang Y. Discovery of selective farnesoid X receptor agonists for the treatment of hyperlipidemia from traditional Chinese medicine based on virtual screening and in vitro validation. J Biomol Struct Dyn 2019; 38:4461-4470. [PMID: 31842697 DOI: 10.1080/07391102.2019.1695665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Farnesoid X receptor (FXR), a bile acid receptor, has important roles in maintaining bile acid and cholesterol homeostasis, which is an attractive target for hyperlipidemia. Present study aimed to discover potential selective FXR agonists over G-protein coupled bile acid receptor 1 (GPBAR1, TGR5) from traditional Chinese medicine (TCM) by using virtual screening, in vitro studies and molecular dynamics simulation (MD). Ligand-based pharmacophore model for FXR was firstly built to screen FXR agonists from the Traditional Chinese Medicine Database (TCMD). Then, 21 FXR crystal structures were clustered in two types and two representative structures (PDB ID: 3OMM and 3P89) were, respectively, used to carry out molecular docking to refine the screened result. Moreover, the pharmacophore model for GPBAR1 was built to screen selective FXR agonists with no activity on GPBAR1. A set of 24 candidate selective FXR agonists which fitvalue of FXR pharmacophore model and docking score of 3OMM and 3P89 were in the top 100 and cannot match the pharmacophore model for GPBAR1 were obtained. By the lipid-lowering activity test in HepG2 cell lines, Arctigenin was identified to be potential selective FXR agonist with the activity of 20 μmol·L-1. After down-regulating FXR, Arctigenin could increase the mRNA of FXR while exerted no effect on the mRNA of GPBAR1. MD was further used to interpret the mechanism of Arctigenin with the representative structures. This research provided a new screening procedure for finding selective candidate compounds and appropriate docking models of a target by considering the structure diversity of PDB structures, which was applied to discovery novel selective FXR agonists to treat hyperlipidemia.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xi Chen
- School of Chinese Material Medica, State Administration of Traditional Chinese Medicine, Research Center of TCM-Information Engineering, Beijing University of Chinese Medicine, Beijing, China
| | - Fang Lu
- School of Chinese Material Medica, State Administration of Traditional Chinese Medicine, Research Center of TCM-Information Engineering, Beijing University of Chinese Medicine, Beijing, China
| | - Ganggang Luo
- School of Chinese Material Medica, State Administration of Traditional Chinese Medicine, Research Center of TCM-Information Engineering, Beijing University of Chinese Medicine, Beijing, China
| | - Yue Ren
- School of Chinese Material Medica, State Administration of Traditional Chinese Medicine, Research Center of TCM-Information Engineering, Beijing University of Chinese Medicine, Beijing, China
| | - Jing Ma
- School of Chinese Material Medica, State Administration of Traditional Chinese Medicine, Research Center of TCM-Information Engineering, Beijing University of Chinese Medicine, Beijing, China
| | - Yanling Zhang
- School of Chinese Material Medica, State Administration of Traditional Chinese Medicine, Research Center of TCM-Information Engineering, Beijing University of Chinese Medicine, Beijing, China
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48
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Wu JW, Zhang H, Li WY, Tang X, Li HL, Lu XH, Zheng ZH, Ma Y, Wang RL. Design potential selective inhibitors for human leukocyte common antigen-related (PTP-LAR) with fragment replace approach. J Biomol Struct Dyn 2019; 38:5338-5348. [DOI: 10.1080/07391102.2019.1699862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jing-Wei Wu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Huan Zhang
- Department of Pharmacy, Tianjin Medical University General Hospital, Tianjin, China
| | - Wei-Ya Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xue Tang
- Tasly Research Institute, Tasly Holding Group Co., Ltd, Tianjin, China
| | - Hong-Lian Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xin-Hua Lu
- New Drug Research and Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering and Research Center, Hebei Industry Microbial Metabolic Engineering &Technology Research Center, Key Laboratory for New Drug Screening Technology of Shijiazhuang City, Shijiazhuang, Hebei, China
| | - Zhi-Hui Zheng
- New Drug Research and Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering and Research Center, Hebei Industry Microbial Metabolic Engineering &Technology Research Center, Key Laboratory for New Drug Screening Technology of Shijiazhuang City, Shijiazhuang, Hebei, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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Liu WS, Wang RR, Yue H, Zheng ZH, Lu XH, Wang SQ, Dong WL, Wang RL. Design, synthesis, biological evaluation and molecular dynamics studies of 4-thiazolinone derivatives as protein tyrosine phosphatase 1B (PTP1B) inhibitors. J Biomol Struct Dyn 2019; 38:3814-3824. [PMID: 31490104 DOI: 10.1080/07391102.2019.1664333] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a key negative regulator of insulin signaling pathway, and more and more studies have shown that it is a potential target for the treatment of type 2 diabetes mellitus (T2DM). In this study, 17 new 4-thiazolinone derivatives were designed and synthesized as novel PTP1B inhibitors, and ADMET prediction confirmed that these compounds were to be drug-like. In vitro enzyme activity experiments were performed on these compounds, and it was found that a plurality of compounds had good inhibitory activity and high selectivity against PTP1B protein. Among them, compound 7p exhibited the best inhibitory activity with an IC50 of 0.92 μM. The binding mode of compound 7p and PTP1B protein was explored, revealing the reason for its high efficiency. In addition, molecular dynamics simulations for the PTP1BWT and PTP1Bcomp#7p systems revealed the effects of compound 7p on PTP1B protein at the molecular level. In summary, the study reported for the first time that 4-thiazolinone derivatives as a novel PTP1B inhibitor had good inhibitory activity and selectivity for the treatment of T2DM, providing more options for the development of PTP1B inhibitors. AbbreviationsBBBblood-brain barrierCDC25Bcell division cycle 25 homolog BCYP2D6Cytochrome P450 2D6 bindingDCCMdynamic cross-correlation mapDSDiscovery StudioH bondhydrogen bondHIAhuman intestinal absorptionLARleukocyte antigen-related phosphataseMDmolecular dynamicsMEG-2maternal-effect germ-cell defective 2MM-PBSAmolecular mechanics Poisson Boltzmann surface area)PCAprincipal component analysisPDBProtein Data BankpNPPp-nitrophenyl phosphatePPBplasma protein bindingPTP1Bprotein tyrosine phosphotase 1BRMSDroot mean square deviationRMSFroot mean square fluctuationSHP-1src homologous phosphatase-1SHP-2src homologous phosphatase-2SPCsingle-point chargeTCPTPT cell protein tyrosine phosphataseT2DMType 2 diabetes mellitusVDWvan der WaalsCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wen-Shan Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Rui-Rui Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Hai Yue
- Inner Mongolia Institute for Drug Control, Huhhot, Inner Mongolia, China
| | - Zhi-Hui Zheng
- New Drug Research & Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering & Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Key Laboratory for New Drug Screening Technology of Shijiazhuang City, Shijiazhuang, Hebei, China
| | - Xin-Hua Lu
- New Drug Research & Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering & Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Key Laboratory for New Drug Screening Technology of Shijiazhuang City, Shijiazhuang, Hebei, China
| | - Shu-Qing Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Li Dong
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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50
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Advance in Cordyceps militaris (Linn) Link polysaccharides: Isolation, structure, and bioactivities: A review. Int J Biol Macromol 2019; 132:906-914. [DOI: 10.1016/j.ijbiomac.2019.04.020] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/26/2019] [Accepted: 04/03/2019] [Indexed: 01/01/2023]
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