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Ren L, Wang R, Wang Y, Tie F, Dong Q, Wang H, Hu N. Exploring the effect and mechanism of Hippophae rhamnoides L. triterpenoid acids on improving NAFLD based on network pharmacology and experimental validation in vivo and in vitro. JOURNAL OF ETHNOPHARMACOLOGY 2024; 335:118657. [PMID: 39127115 DOI: 10.1016/j.jep.2024.118657] [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: 05/15/2024] [Revised: 07/23/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Sea buckthorn (Hippophae rhamnoides L.) is a traditional Chinese medicinal and possesses a rich medical history in terms of treating gastric disorders, sputum and cough and liver injuries in oriental medicinal system. By reason of the complicated chemical constituents, the material basis and potential pharmacological mechanism of sea buckthorn acting on Non-alcoholic fatty liver disease (NAFLD) has not been clearly elucidated. AIM OF THE STUDY To explore the pharmacological efficacy and underlying mechanism of sea buckthorn triterpenoid acid enrichment (STE) in the treatment of NAFLD. MATERIALS AND METHODS The approaches of Network pharmacology and experiment validation in vitro and in vivo were applied in this study. Firstly, targets of triterpenoid acid compounds and NAFLD were collected from databases. The crucial targets were screened by the construction of protein-protein interaction (PPI) network. Furthermore, the potential signaling pathways and targets affected by STE was predicted by GO together with KEGG enrichment analysis. Finally, the experiment validation was carried out through high-fat feeding NAFLD mice and lipid accumulation HepG2 cell model. Lipids and liver related biochemical indicators were determined, Oil Red O and H&E staining were employed to observe fat accumulation. In addition, the expression levels of proteins of key target and signal pathway anticipated in network pharmacology were detected to elaborated its action mechanism. RESULTS A total of 180 intersecting potential targets for enhancing NAFLD with STE were eventually identified. 6 key targets including AKT1, TNF, IL6, INS, JUN, STAT3 and TP53 were further identified and the AMPK-SREBP1 pathway was enriched. Animal experiment result showed that STE treatment could significantly reduce the levels of TG, TC, LDL-C, ALT and AST, increase the levels of HDL-C in serum, and improve lipid accumulation of epididymal fat and liver. The results of the lipid accumulation cell model indicated that STE and key compound oleanolic acid could diminish intracellular lipid levels of TG, TC, LDL-C and number of lipid droplets. Western blot results showed that the above beneficial effects could be achieved by regulating the expression of p-AMPK/AMPK, SREBP1, FAS, ACC, SCD protein. CONCLUSION This study confirmed the effect of STE on improving NAFLD and the potential action mechanism was involved in the regulation of the AMPK-SREBP1 pathway.
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Affiliation(s)
- Lichengcheng Ren
- School of Medicine, Qinghai University, Xining, Qinghai, 810001, China; Qinghai Provincial Key Laboratory of Tibetan Medicine Research and CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, 810008, Xining, China
| | - Ruinan Wang
- Qinghai Provincial Key Laboratory of Tibetan Medicine Research and CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, 810008, Xining, China
| | - Yue Wang
- School of Medicine, Qinghai University, Xining, Qinghai, 810001, China; Qinghai Provincial Key Laboratory of Tibetan Medicine Research and CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, 810008, Xining, China
| | - Fangfang Tie
- Qinghai Provincial Key Laboratory of Tibetan Medicine Research and CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, 810008, Xining, China
| | - Qi Dong
- Qinghai Provincial Key Laboratory of Tibetan Medicine Research and CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, 810008, Xining, China
| | - Honglun Wang
- Qinghai Provincial Key Laboratory of Tibetan Medicine Research and CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, 810008, Xining, China
| | - Na Hu
- Qinghai Provincial Key Laboratory of Tibetan Medicine Research and CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, 810008, Xining, China.
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Setua S, Shabir S, Shaji P, Bulnes AM, Dhasmana A, Holla S, Mittal NK, Sahoo N, Saini T, Giorgianni F, Sikander M, Massey AE, Hafeez BB, Tripathi MK, Diego VP, Jaggi M, Yue J, Zafar N, Yallapu MM, Behrman SW, Khan S, Chauhan SC. Exosomes derived from tumor adjacent fibroblasts efficiently target pancreatic tumors. Acta Pharm Sin B 2024; 14:3009-3026. [PMID: 39027237 PMCID: PMC11252470 DOI: 10.1016/j.apsb.2024.04.003] [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: 09/26/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 07/20/2024] Open
Abstract
The application of extracellular vesicles, particularly exosomes (EXs), is rapidly expanding in the field of medicine, owing to their remarkable properties as natural carriers of biological cargo. This study investigates utilization of exosomes derived from stromal cells of tumor adjacent normal tissues (NAF-EXs) for personalized medicine, which can be derived at the time of diagnosis by endoscopic ultrasound. Herein, we show that exosomes (EXs) derived from NAFs demonstrate differential bio-physical characteristics, efficient cellular internalization, drug loading efficiency, pancreatic tumor targeting and delivery of payloads. NAF-derived EXs (NAF-EXs) were used for loading ormeloxifene (ORM), a potent anti-cancer and desmoplasia inhibitor as a model drug. We found that ORM maintains normal fibroblast cell phenotype and renders them incompatible to be triggered for a CAF-like phenotype, which may be due to regulation of Ca2+ influx in fibroblast cells. NAF-EXs-ORM effectively blocked oncogenic signaling pathways involved in desmoplasia and epithelial mesenchymal transition (EMT) and repressed tumor growth in xenograft mouse model. In conclusion, our data suggests preferential tropism of NAF-EXs for PDAC tumors, thus imply feasibility of developing a novel personalized medicine for PDAC patients using autologous NAF-EXs for improved therapeutic outcome of anti-cancer drugs. Additionally, it provides the opportunity of utilizing this biological scaffold for effective therapeutics in combination with standard therapeutic regimen.
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Affiliation(s)
- Saini Setua
- Department of Pharmaceutical Sciences, College of Pharmacy, and College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, TN 36163, USA
| | - Shabia Shabir
- Department of Computer Science, Islamic University of Science and Technology, Awantipora, J&K 192122, India
| | - Poornima Shaji
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, the University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Ana Martinez Bulnes
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, the University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Anupam Dhasmana
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, the University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- Himalayan School of Biosciences and Cancer Research Institute, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Dehradun 248016, India
| | - Swathi Holla
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Nivesh K. Mittal
- Plough Center for Sterile Drug Delivery Solutions, UTHSC, Memphis, TN 38104, USA
| | - Nirakar Sahoo
- Department of Biology, College of Sciences, UTRGV, McAllen, TX 78539, USA
| | - Tripti Saini
- Department of Biology, College of Sciences, UTRGV, McAllen, TX 78539, USA
| | - Francesco Giorgianni
- Department of Pharmaceutical Sciences, College of Pharmacy, and College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, TN 36163, USA
| | - Mohammad Sikander
- Department of Pharmaceutical Sciences, College of Pharmacy, and College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, TN 36163, USA
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, the University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Andrew E. Massey
- Department of Pharmaceutical Sciences, College of Pharmacy, and College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, TN 36163, USA
- National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health, Bethesda, MD 20892, USA
| | - Bilal B. Hafeez
- Department of Pharmaceutical Sciences, College of Pharmacy, and College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, TN 36163, USA
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, the University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Manish K. Tripathi
- Department of Pharmaceutical Sciences, College of Pharmacy, and College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, TN 36163, USA
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, the University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Vincent P. Diego
- South Texas Diabetes and Obesity Institute, UTRGV, McAllen, TX 78504, USA
| | - Meena Jaggi
- Department of Pharmaceutical Sciences, College of Pharmacy, and College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, TN 36163, USA
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, the University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Junming Yue
- Department of Pharmaceutical Sciences, College of Pharmacy, and College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, TN 36163, USA
| | - Nadeem Zafar
- Dept. of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98195, USA
| | - Murali M. Yallapu
- Department of Pharmaceutical Sciences, College of Pharmacy, and College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, TN 36163, USA
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, the University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Stephen W. Behrman
- Department of Pharmaceutical Sciences, College of Pharmacy, and College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, TN 36163, USA
- Department of Surgery, Baptist Memorial Medical Education, Baptist Memorial Hospital, Memphis, TN 38120, USA
- Baptist Health Sciences University, Memphis, TN 38104, USA
| | - Sheema Khan
- Department of Pharmaceutical Sciences, College of Pharmacy, and College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, TN 36163, USA
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, the University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Subhash C. Chauhan
- Department of Pharmaceutical Sciences, College of Pharmacy, and College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, TN 36163, USA
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, the University of Texas Rio Grande Valley, McAllen, TX 78504, USA
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Tayal S, Bhatnagar S. Role of molecular mimicry in the SARS-CoV-2-human interactome for pathogenesis of cardiovascular diseases: An update to ImitateDB. Comput Biol Chem 2023; 106:107919. [PMID: 37463554 DOI: 10.1016/j.compbiolchem.2023.107919] [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: 01/15/2023] [Revised: 06/13/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
Mimicry of host proteins is a strategy employed by pathogens to hijack host functions. Domain and motif mimicry was explored in the experimental and predicted SARS-CoV-2-human interactome. The host first interactor proteins were also added to capture the continuum of the interactions. The domains and motifs of the proteins were annotated using NCBI CD Search and ScanProsite, respectively. Host and pathogen proteins with a common host interactor and similar domain/motif constitute a mimicry pair indicating global structural similarity (domain mimicry pair; DMP) or local sequence similarity (motif mimicry pair; MMP). 593 DMPs and 7,02,472 MMPs were determined. AAA, DEXDc and Macro domains were frequent among DMPs whereas glycosylation, myristoylation and RGD motifs were abundant among MMP. The proteins involved in mimicry were visualised as a SARS-CoV-2 mimicry interaction network. The host proteins were enriched in multiple CVD pathways indicating the role of mimicry in COVID-19 associated CVDs. Bridging nodes were identified as potential drug targets. Approved antihypertensive and anti-inflammatory drugs are proposed for repurposing against COVID-19 associated CVDs. The SARS-CoV-2 mimicry data has been updated in ImitateDB (http://imitatedb.sblab-nsit.net/SARSCoV2Mimicry). Determination of key mechanisms, proteins, pathways, drug targets and repurposing candidates is critical for developing therapeutics for SARS CoV-2 associated CVDs.
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Affiliation(s)
- Sonali Tayal
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi 110078, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi 110078, India.
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Dhasmana A, Dhasmana S, Agarwal S, Khan S, Haque S, Jaggi M, Yallapu MM, Chauhan SC. Integrative big transcriptomics data analysis implicates crucial role of MUC13 in pancreatic cancer. Comput Struct Biotechnol J 2023; 21:2845-2857. [PMID: 37216018 PMCID: PMC10192752 DOI: 10.1016/j.csbj.2023.04.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/24/2023] Open
Abstract
Big data analysis holds a considerable influence on several aspects of biomedical health science. It permits healthcare providers to gain insights from large and complex datasets, leading to improvements in the understanding, diagnosis, medication, and restraint of pathological conditions including cancer. The incidences of pancreatic cancer (PanCa) are sharply rising, and it will become the second leading cause of cancer related deaths by 2030. Various traditional biomarkers are currently in use but are not optimal in sensitivity and specificity. Herein, we determine the role of a new transmembrane glycoprotein, MUC13, as a potential biomarker of pancreatic ductal adenocarcinoma (PDAC) by using integrative big data mining and transcriptomic approaches. This study is helpful to identify and appropriately segment the data related to MUC13, which are scattered in various data sets. The assembling of the meaningful data, representation strategy was used to investigate the MUC13 associated information for the better understanding regarding its structural, expression profiling, genomic variants, phosphorylation motifs, and functional enrichment pathways. For further in-depth investigation, we have adopted several popular transcriptomic methods like DEGseq2, coding and non-coding transcript, single cell seq analysis, and functional enrichment analysis. All these analyzes suggest the presence of three nonsense MUC13 genomic transcripts, two protein transcripts, short MUC13 (s-MUC13, non-tumorigenic or ntMUC13), and long MUC13 (L-MUC13, tumorigenic or tMUC13), several important phosphorylation sites in tMUC13. Altogether, this data confirms that importance of tMUC13 as a potential biomarker, therapeutic target of PanCa, and its significance in pancreatic pathobiology.
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Affiliation(s)
- Anupam Dhasmana
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, USA
- Himalayan School of Biosciences and Cancer Research Institute, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Dehradun, India
| | - Swati Dhasmana
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, USA
| | | | - Sheema Khan
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, USA
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Meena Jaggi
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, USA
| | - Murali M. Yallapu
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, USA
| | - Subhash C. Chauhan
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, USA
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Laskar P, Dhasmana A, Kotnala S, Jaggi M, Yallapu MM, Chauhan SC. Glutathione-Responsive Tannic Acid-Assisted FRET Nanomedicine for Cancer Therapy. Pharmaceutics 2023; 15:1326. [PMID: 37242568 PMCID: PMC10222396 DOI: 10.3390/pharmaceutics15051326] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 05/28/2023] Open
Abstract
In cancer combination therapy, a multimodal delivery vector is used to improve the bioavailability of multiple anti-cancer hydrophobic drugs. Further, targeted delivery of therapeutics along with simultaneous monitoring of the drug release at the tumor site without normal organ toxicity is an emerging and effective strategy for cancer treatment. However, the lack of a smart nano-delivery system limits the application of this therapeutic strategy. To overcome this issue, a PEGylated dual drug, conjugated amphiphilic polymer (CPT-S-S-PEG-CUR), has been successfully synthesized by conjugating two hydrophobic fluorescent anti-cancer drugs, curcumin (CUR) and camptothecin (CPT), through an ester and a redox-sensitive disulfide (-S-S-) linkage, respectively, with a PEG chain via in situ two-step reactions. CPT-S-S-PEG-CUR is spontaneously self-assembled in the presence of tannic acid (TA, a physical crosslinker) into anionic, comparatively smaller-sized (~100 nm), stable nano-assemblies in water in comparison to only polymer due to stronger H-bond formation between polymer and TA. Further, due to the spectral overlap between CPT and CUR and a stable, smaller nano-assembly formation by the pro-drug polymer in water in presence of TA, a successful Fluorescence Resonance Energy Transfer (FRET) signal was generated between the conjugated CPT (FRET donor) and conjugated CUR (FRET acceptor). Interestingly, these stable nano-assemblies showed a preferential breakdown and release of CPT in a tumor-relevant redox environment (in the presence of 50 mM glutathione), leading to the disappearance of the FRET signal. These nano-assemblies exhibited a successful cellular uptake by the cancer cells and an enhanced antiproliferative effect in comparison to the individual drugs in cancer cells (AsPC1 and SW480). Such promising in vitro results with a novel redox-responsive, dual-drug conjugated, FRET pair-based nanosized multimodal delivery vector can be highly useful as an advanced theranostic system towards effective cancer treatment.
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Affiliation(s)
- Partha Laskar
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- The Ångström Laboratory, Macromolecular Chemistry, Department of Chemistry, Uppsala University, 751 21 Uppsala, Sweden
| | - Anupam Dhasmana
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- Cancer Research Institute, Himalayan School of Biosciences, Swami Rama Himalayan University, Dehradun 248016, India
| | - Sudhir Kotnala
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Meena Jaggi
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Murali M. Yallapu
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Subhash C. Chauhan
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
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Anusha M, Tejaswini V, Udhaya Kumar S, Prashantha CN, Vasudevan K, George Priya Doss C. Gene network interaction analysis to elucidate the antimicrobial resistance mechanisms in the Clostridiumdifficile. Microb Pathog 2023; 178:106083. [PMID: 36958645 DOI: 10.1016/j.micpath.2023.106083] [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: 12/07/2022] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 03/25/2023]
Abstract
Antimicrobial resistance has caused chaos worldwide due to the depiction of multidrug-resistant (MDR) infective microorganisms. A thorough examination of antimicrobial resistance (AMR) genes and associated resistant mechanisms is vital to solving this problem. Clostridium difficile (C. difficile) is an opportunistic nosocomial bacterial strain that has acquired exogenous AMR genes that confer resistance to antimicrobials such as erythromycin, azithromycin, clarithromycin, rifampicin, moxifloxacin, fluoroquinolones, vancomycin, and others. A network of interactions, including 20 AMR genes, was created and analyzed. In functional enrichment analysis, Cellular components (CC), Molecular Functions (MF), and Biological Processes (BP) were discovered to have substantial involvement. Mutations in the rpl genes, which encode ribosomal proteins, confer resistance in Gram-positive bacteria. Full erythromycin and azithromycin cross-resistance can be conferred if more than one of the abovementioned genes is present. In the enriched BP, rps genes related to transcriptional regulation and biosynthesis were found. The genes belong to the rpoB gene family, which has previously been related to rifampicin resistance. The genes rpoB, gyrA, gyrB, rpoS, rpl genes, rps genes, and Van genes are thought to be the hub genes implicated in resistance in C. difficile. As a result, new medications could be developed using these genes. Overall, our observations provide a thorough understanding of C. difficile AMR mechanisms.
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Affiliation(s)
- M Anusha
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, 560064, India
| | - V Tejaswini
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, 560064, India
| | - S Udhaya Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, India
| | - C N Prashantha
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, 560064, India
| | - Karthick Vasudevan
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, 560064, India.
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, India.
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Bhardwaj T, Ahmad I, Somvanshi P. Systematic analysis to identify novel disease indications and plausible potential chemical leads of glutamate ionotropic receptor NMDA type subunit 1, GRIN1. J Mol Recognit 2023; 36:e2997. [PMID: 36259267 DOI: 10.1002/jmr.2997] [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: 07/19/2022] [Revised: 09/19/2022] [Accepted: 10/07/2022] [Indexed: 12/15/2022]
Abstract
Schizophrenia is a mental illness affecting the normal lifestyle of adults and early adolescents incurring major symptoms as jumbled speech, involvement in everyday activities eventually got reduced, patients always struggle with attention and memory, reason being both the genetic and environmental factors responsible for altered brain chemistry and structure, resulting in schizophrenia and associated orphan diseases. The network biology describes the interactions among genes/proteins encoding molecular mechanisms of biological processes, development, and diseases. Besides, all the molecular networks, protein-protein Interaction Networks have been significant in distinguishing the pathogenesis of diseases and thereby drug discovery. The present meta-analysis prioritizes novel disease indications viz. rare and orphan diseases associated with target Glutamate Ionotropic Receptor NMDA Type Subunit 1, GRIN1 using text mining knowledge-based tools. Furthermore, ZINC database was virtually screened, and binding conformation of selected compounds was performed and resulted in the identification of Narciclasine (ZINC04097652) and Alvespimycin (ZINC73138787) as potential inhibitors. Furthermore, docked complexes were subjected to MD simulation studies which suggests that the identified leads could be a better potential drug to recuperate schizophrenia.
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Affiliation(s)
- Tulika Bhardwaj
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Irshad Ahmad
- Department of Medical Rehabilitation Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Pallavi Somvanshi
- School of Computational & Integrative Sciences (SC&IS), Jawaharlal Nehru University, New Delhi, India.,Special Centre of Systems Medicine (SCSM), Jawaharlal Nehru University, New Delhi, India
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Mathew B, Bathla S, Williams KR, Nairn AC. Deciphering Spatial Protein-Protein Interactions in Brain Using Proximity Labeling. Mol Cell Proteomics 2022; 21:100422. [PMID: 36198386 PMCID: PMC9650050 DOI: 10.1016/j.mcpro.2022.100422] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 01/18/2023] Open
Abstract
Cellular biomolecular complexes including protein-protein, protein-RNA, and protein-DNA interactions regulate and execute most biological functions. In particular in brain, protein-protein interactions (PPIs) mediate or regulate virtually all nerve cell functions, such as neurotransmission, cell-cell communication, neurogenesis, synaptogenesis, and synaptic plasticity. Perturbations of PPIs in specific subsets of neurons and glia are thought to underly a majority of neurobiological disorders. Therefore, understanding biological functions at a cellular level requires a reasonably complete catalog of all physical interactions between proteins. An enzyme-catalyzed method to biotinylate proximal interacting proteins within 10 to 300 nm of each other is being increasingly used to characterize the spatiotemporal features of complex PPIs in brain. Thus, proximity labeling has emerged recently as a powerful tool to identify proteomes in distinct cell types in brain as well as proteomes and PPIs in structures difficult to isolate, such as the synaptic cleft, axonal projections, or astrocyte-neuron junctions. In this review, we summarize recent advances in proximity labeling methods and their application to neurobiology.
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Affiliation(s)
- Boby Mathew
- Yale/NIDA Neuroproteomics Center, New Haven, Connecticut, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA.
| | - Shveta Bathla
- Yale/NIDA Neuroproteomics Center, New Haven, Connecticut, USA; Department of Psychiatry, Yale University, New Haven, Connecticut, USA
| | - Kenneth R Williams
- Yale/NIDA Neuroproteomics Center, New Haven, Connecticut, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center, New Haven, Connecticut, USA; Department of Psychiatry, Yale University, New Haven, Connecticut, USA.
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Wei Y, Yu N, Wang Z, Hao Y, Wang Z, Yang Z, Liu J, Wang J. Analysis of the multi-physiological and functional mechanism of wheat alkylresorcinols based on reverse molecular docking and network pharmacology. Food Funct 2022; 13:9091-9107. [PMID: 35943408 DOI: 10.1039/d2fo01438f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Alkylresorcinols (ARs) are phenolic lipids present in the bran part of whole grain wheat and rye, which possess antioxidant, anti-inflammatory, anti-cancer and anti-tumor properties. The physiological activities of ARs have been proven to be diverse; however, the specific molecular mechanisms are still unclear. In this study, reverse virtual screening and network pharmacology were used to explore the potential molecular mechanisms of the physiological function of ARs and their endogenous metabolites. The Metascape database was used for GO enrichment and KEGG pathway analysis. Furthermore, molecular docking was used to investigate the interactions between active compounds and potential targets. The results showed that the bioavailability of most ARs and their endogenous metabolites was 0.55 and 0.56, while the bioavailability of certain endogenous metabolites was only 0.11. Multiplex analysis was used to screen 73 important targets and 4 core targets (namely, HSP90AA1, EP300, HSP90AB1 and ERBB2) out of the 163 initial targets. The important targets involved in the key KEGG pathway were pathways in cancer (hsa05200), lipid and atherosclerosis (hsa05417), Th17 cell differentiation (hsa04659), chemical carcinogenesis-receptor activation (hsa05207), and prostate cancer (hsa05215). The compounds involved in the core targets were AR-C21, AR-C19, AR-C17, 3,5-DHPHTA-S, 3,5-DHPHTA-G, 3,5-DHPPTA, 3,5-DHPPTA-S, 3,5-DHPPTA-G, 3,5-DHPPTA-Gly and 3,5-DHPPA-G. The interaction force between them was mainly related to hydrogen bonds and van der Waals. Overall, the physiological activities of ARs are not only related to their multiple targets, but may also be related to the synergistic effect of their endogenous metabolites.
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Affiliation(s)
- Yulong Wei
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University (BTBU), Beijing 100048, China.
| | - Ning Yu
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Ziyuan Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University (BTBU), Beijing 100048, China.
| | - Yiming Hao
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University (BTBU), Beijing 100048, China.
| | - Zongwei Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University (BTBU), Beijing 100048, China.
| | - Zihui Yang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University (BTBU), Beijing 100048, China.
| | - Jie Liu
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University (BTBU), Beijing 100048, China.
| | - Jing Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University (BTBU), Beijing 100048, China.
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10
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Hatami E, B Nagesh PK, Sikander M, Dhasmana A, Chauhan SC, Jaggi M, Yallapu MM. Tannic Acid Exhibits Antiangiogenesis Activity in Nonsmall-Cell Lung Cancer Cells. ACS OMEGA 2022; 7:23939-23949. [PMID: 35847334 PMCID: PMC9281317 DOI: 10.1021/acsomega.2c02727] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nonsmall-cell lung cancer (NSCLC) is the most common type of lung cancer, with a dismal prognosis. NSCLC is a highly vascularized tumor, and chemotherapy is often hampered by the development of angiogenesis. Therefore, suppression of angiogenesis is considered a potential treatment approach. Tannic acid (TA), a natural polyphenol, has been demonstrated to have anticancer properties in a variety of cancers; however, its angiogenic properties have yet to be studied. Hence, in the current study, we investigated the antiproliferative and antiangiogenic effects of TA on NSCLC cells. The (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) (MTS) assay revealed that TA induced a dose- and time-dependent decrease in the proliferation of A549 and H1299 cells. However, TA had no significant toxicity effects on human bronchial epithelial cells. Clonogenicity assay revealed that TA suppressed colony formation ability in NSCLC cells in a dose-dependent manner. The anti-invasiveness and antimigratory potential of TA were confirmed by Matrigel and Boyden chamber studies, respectively. Importantly, TA also decreased the ability of human umbilical vein endothelial cells (HUVEC) to form tube-like networks, demonstrating its antiangiogenic properties. Extracellular vascular endothelial growth factor (VEGF) release was reduced in TA-treated cells compared to that in control cells, as measured by the enzyme-linked immunosorbent assay (ELISA). Overall, these results demonstrate that TA can induce antiproliferative and antiangiogenic effects against NSCLC.
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Affiliation(s)
- Elham Hatami
- Department
of Pharmaceutical Sciences, University of
Tennessee Health Science Center, Memphis, Tennessee 38163, United States
- Department
of Bioengineering, University of California, Los Angeles, California 90095, United States
| | - Prashanth K. B Nagesh
- Department
of Pharmaceutical Sciences, University of
Tennessee Health Science Center, Memphis, Tennessee 38163, United States
- Laboratory
of Signal Transduction, Memorial Sloan Kettering
Cancer Center, New York, New York 10065, United States
- Department
of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, Texas 78504, United States
| | - Mohammed Sikander
- Department
of Pharmaceutical Sciences, University of
Tennessee Health Science Center, Memphis, Tennessee 38163, United States
- Department
of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, Texas 78504, United States
- South
Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, Texas 78504, United States
| | - Anupam Dhasmana
- Department
of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, Texas 78504, United States
- South
Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, Texas 78504, United States
| | - Subhash C. Chauhan
- Department
of Pharmaceutical Sciences, University of
Tennessee Health Science Center, Memphis, Tennessee 38163, United States
- Department
of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, Texas 78504, United States
- South
Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, Texas 78504, United States
| | - Meena Jaggi
- Department
of Pharmaceutical Sciences, University of
Tennessee Health Science Center, Memphis, Tennessee 38163, United States
- Department
of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, Texas 78504, United States
- South
Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, Texas 78504, United States
| | - Murali M. Yallapu
- Department
of Pharmaceutical Sciences, University of
Tennessee Health Science Center, Memphis, Tennessee 38163, United States
- Department
of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, Texas 78504, United States
- South
Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, Texas 78504, United States
- . Tel: 956-296-1734
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11
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Artificial intelligence and machine-learning approaches in structure and ligand-based discovery of drugs affecting central nervous system. Mol Divers 2022; 27:959-985. [PMID: 35819579 DOI: 10.1007/s11030-022-10489-3] [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: 04/27/2022] [Accepted: 06/21/2022] [Indexed: 12/11/2022]
Abstract
CNS disorders are indications with a very high unmet medical needs, relatively smaller number of available drugs, and a subpar satisfaction level among patients and caregiver. Discovery of CNS drugs is extremely expensive affair with its own unique challenges leading to extremely high attrition rates and low efficiency. With explosion of data in information age, there is hardly any aspect of life that has not been touched by data driven technologies such as artificial intelligence (AI) and machine learning (ML). Drug discovery is no exception, emergence of big data via genomic, proteomic, biological, and chemical technologies has driven pharmaceutical giants to collaborate with AI oriented companies to revolutionise drug discovery, with the goal of increasing the efficiency of the process. In recent years many examples of innovative applications of AI and ML techniques in CNS drug discovery has been reported. Research on therapeutics for diseases such as schizophrenia, Alzheimer's and Parkinsonism has been provided with a new direction and thrust from these developments. AI and ML has been applied to both ligand-based and structure-based drug discovery and design of CNS therapeutics. In this review, we have summarised the general aspects of AI and ML from the perspective of drug discovery followed by a comprehensive coverage of the recent developments in the applications of AI/ML techniques in CNS drug discovery.
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12
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Panditrao G, Bhowmick R, Meena C, Sarkar RR. Emerging landscape of molecular interaction networks: Opportunities, challenges and prospects. J Biosci 2022. [PMID: 36210749 PMCID: PMC9018971 DOI: 10.1007/s12038-022-00253-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Network biology finds application in interpreting molecular interaction networks and providing insightful inferences using graph theoretical analysis of biological systems. The integration of computational bio-modelling approaches with different hybrid network-based techniques provides additional information about the behaviour of complex systems. With increasing advances in high-throughput technologies in biological research, attempts have been made to incorporate this information into network structures, which has led to a continuous update of network biology approaches over time. The newly minted centrality measures accommodate the details of omics data and regulatory network structure information. The unification of graph network properties with classical mathematical and computational modelling approaches and technologically advanced approaches like machine-learning- and artificial intelligence-based algorithms leverages the potential application of these techniques. These computational advances prove beneficial and serve various applications such as essential gene prediction, identification of drug–disease interaction and gene prioritization. Hence, in this review, we have provided a comprehensive overview of the emerging landscape of molecular interaction networks using graph theoretical approaches. With the aim to provide information on the wide range of applications of network biology approaches in understanding the interaction and regulation of genes, proteins, enzymes and metabolites at different molecular levels, we have reviewed the methods that utilize network topological properties, emerging hybrid network-based approaches and applications that integrate machine learning techniques to analyse molecular interaction networks. Further, we have discussed the applications of these approaches in biomedical research with a note on future prospects.
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Affiliation(s)
- Gauri Panditrao
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune, 411008 India
| | - Rupa Bhowmick
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune, 411008 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Chandrakala Meena
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune, 411008 India
| | - Ram Rup Sarkar
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune, 411008 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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13
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Noor H, Ikram A, Rathinavel T, Kumarasamy S, Nasir Iqbal M, Bashir Z. Immunomodulatory and anti-cytokine therapeutic potential of curcumin and its derivatives for treating COVID-19 - a computational modeling. J Biomol Struct Dyn 2021; 40:5769-5784. [PMID: 33491580 DOI: 10.1080/07391102.2021.1873190] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The unavailability of vaccine and medicines raised serious issues during COVID-19 pandemic and peoples from different parts of world relied on traditional medicine for their immediate recovery from COVID-19 and it found effective also. The current research aims to target COVID-19 immunological human host receptors i.e. angiotensin-converting enzyme (ACE)-2, interleukin (IL)-1β, IL-6, tumor necrosis factor-alpha (TNF-α) and protease-activated receptor (PAR)-1 using curcumin derivatives to prevent viral infection and control overproduction of early clinical responses of COVID-19. Targeting these host proteins will mitigate the infection and will filter out many complications caused by these proteins in COVID-19 patients. It is proven through computer-aided computational modeling approaches, total 30 compounds of curcumin and its derivatives were chosen. Drug-likeness parameters were calculated for curcumin and its derivatives and 20 curcumin analogs were selected for docking analysis. From docking analysis of 20 curcumin analogs against five chosen human host receptor targets reveals 11 curcumin analogs possess least binding affinity and best interaction at active sites subjected to absorption, distribution, metabolism, excretion (ADME) analysis. Density functional theory (DFT) analysis of five final shortlisted curcumin derivatives was done to show least binding affinity toward chosen host target protein. Molecular dynamics simulation (MDS) was performed to observe behavior and interaction of potential drug hydrazinocurcumin against target proteins ACE-2 and PAR-1. It was performed at 100 nanoseconds and showed satisfactory results. Finally, our investigation reveals that hydrazinocurcumin possesses immunomodulatory and anti-cytokine therapeutic potential against COVID-19 and it can act as COVID-19 warrior drug molecule and promising choice of drug for COVID-19 treatment, however, it needs further in vivo clinical evaluation to commercialize as COVID-19 drug.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hasnat Noor
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Ayesha Ikram
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | | | | | - Muhammad Nasir Iqbal
- Department of Biosciences, COMSATS University, Islamabad Campus, Islamabad, Pakistan
| | - Zohaib Bashir
- Department of Bioinformatics, Hazara University, Mansehra, Pakistan
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14
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Sikander M, Malik S, Rodriguez A, Yallapu MM, Narula AS, Satapathy SK, Dhevan V, Chauhan SC, Jaggi M. Role of Nutraceuticals in COVID-19 Mediated Liver Dysfunction. Molecules 2020; 25:E5905. [PMID: 33322162 PMCID: PMC7764432 DOI: 10.3390/molecules25245905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/05/2020] [Accepted: 12/09/2020] [Indexed: 01/08/2023] Open
Abstract
COVID-19 is known as one of the deadliest pandemics of the century. The rapid spread of this deadly virus at incredible speed has stunned the planet and poses a challenge to global scientific and medical communities. Patients with COVID-19 are at an increased risk of co-morbidities associated with liver dysfunction and injury. Moreover, hepatotoxicity induced by antiviral therapy is gaining importance and is an area of great concern. Currently, alternatives therapies are being sought to mitigate hepatic damage, and there has been growing interest in the research on bioactive phytochemical agents (nutraceuticals) due to their versatility in health benefits reported in various epidemiological studies. Therefore, this review provides information and summarizes the juncture of antiviral, immunomodulatory, and hepatoprotective nutraceuticals that can be useful during the management of COVID-19.
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Affiliation(s)
- Mohammed Sikander
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA; (M.S.); (S.M.); (A.R.); (M.M.Y.); (S.C.C.)
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Shabnam Malik
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA; (M.S.); (S.M.); (A.R.); (M.M.Y.); (S.C.C.)
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Anyssa Rodriguez
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA; (M.S.); (S.M.); (A.R.); (M.M.Y.); (S.C.C.)
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Murali M. Yallapu
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA; (M.S.); (S.M.); (A.R.); (M.M.Y.); (S.C.C.)
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Acharan S. Narula
- Narula Research, LLC, 107 Boulder Bluff, Chapel Hill, NC 27516, USA;
| | - Sanjaya K. Satapathy
- Division of Hepatology, Department of Internal Medicine, Sandra Atlas Bass Center for Liver Diseases and Transplantation, Barbara and Zucker School of Medicine, Northwell Health, Manhasset, NY 11030, USA;
| | - Vijian Dhevan
- Department of Surgery, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA;
| | - Subhash C. Chauhan
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA; (M.S.); (S.M.); (A.R.); (M.M.Y.); (S.C.C.)
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Meena Jaggi
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA; (M.S.); (S.M.); (A.R.); (M.M.Y.); (S.C.C.)
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
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15
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Chauhan N, Dhasmana A, Jaggi M, Chauhan SC, Yallapu MM. miR-205: A Potential Biomedicine for Cancer Therapy. Cells 2020; 9:cells9091957. [PMID: 32854238 PMCID: PMC7564275 DOI: 10.3390/cells9091957] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022] Open
Abstract
microRNAs (miRNAs) are a class of small non-coding RNAs that regulate the expression of their target mRNAs post transcriptionally. miRNAs are known to regulate not just a gene but the whole gene network (signaling pathways). Accumulating evidence(s) suggests that miRNAs can work either as oncogenes or tumor suppressors, but some miRNAs have a dual nature since they can act as both. miRNA 205 (miR-205) is one such highly conserved miRNA that can act as both, oncomiRNA and tumor suppressor. However, most reports confirm its emerging role as a tumor suppressor in many cancers. This review focuses on the downregulated expression of miR-205 and discusses its dysregulation in breast, prostate, skin, liver, gliomas, pancreatic, colorectal and renal cancers. This review also confers its role in tumor initiation, progression, cell proliferation, epithelial to mesenchymal transition, and tumor metastasis. Restoration of miR-205 makes cells more sensitive to drug treatments and mitigates drug resistance. Additionally, the importance of miR-205 in chemosensitization and its utilization as potential biomedicine and nanotherapy is described. Together, this review research article sheds a light on its application as a diagnostic and therapeutic marker, and as a biomedicine in cancer.
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Affiliation(s)
- Neeraj Chauhan
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA; (N.C.); (A.D.); (M.J.); (S.C.C.)
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Anupam Dhasmana
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA; (N.C.); (A.D.); (M.J.); (S.C.C.)
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Meena Jaggi
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA; (N.C.); (A.D.); (M.J.); (S.C.C.)
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Subhash C. Chauhan
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA; (N.C.); (A.D.); (M.J.); (S.C.C.)
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Murali M. Yallapu
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA; (N.C.); (A.D.); (M.J.); (S.C.C.)
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- Correspondence: ; Tel.: +1-(956)-296-1734
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16
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Singh N, Rai S, Bhatnagar R, Bhatnagar S. Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases. In Silico Biol 2020; 14:115-133. [PMID: 35001887 PMCID: PMC8842779 DOI: 10.3233/isb-210238] [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] [Indexed: 11/20/2022]
Abstract
Large-scale visualization and analysis of HPIs involved in microbial CVDs can provide crucial insights into the mechanisms of pathogenicity. The comparison of CVD associated HPIs with the entire set of HPIs can identify the pathways specific to CVDs. Therefore, topological properties of HPI networks in CVDs and all pathogens was studied using Cytoscape3.5.1. Ontology and pathway analysis were done using KOBAS 3.0. HPIs of Papilloma, Herpes, Influenza A virus as well as Yersinia pestis and Bacillus anthracis among bacteria were predominant in the whole (wHPI) and the CVD specific (cHPI) network. The central viral and secretory bacterial proteins were predicted virulent. The central viral proteins had higher number of interactions with host proteins in comparison with bacteria. Major fraction of central and essential host proteins interacts with central viral proteins. Alpha-synuclein, Ubiquitin ribosomal proteins, TATA-box-binding protein, and Polyubiquitin-C &B proteins were the top interacting proteins specific to CVDs. Signaling by NGF, Fc epsilon receptor, EGFR and ubiquitin mediated proteolysis were among the top enriched CVD specific pathways. DEXDc and HELICc were enriched host mimicry domains that may help in hijacking of cellular machinery by pathogens. This study provides a system level understanding of cardiac damage in microbe induced CVDs.
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Affiliation(s)
- Nirupma Singh
- Computational and Structural Biology Laboratory, Department of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India
| | - Sneha Rai
- Computational and Structural Biology Laboratory, Department of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India
| | | | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Department of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India.,Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
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