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Rughetti A, Bharti S, Savai R, Barmpoutsi S, Weigert A, Atre R, Siddiqi F, Sharma R, Khabiya R, Hirani N, Baig MS. Imperative role of adaptor proteins in macrophage toll-like receptor signaling pathways. Future Sci OA 2024; 10:2387961. [PMID: 39248050 PMCID: PMC11385170 DOI: 10.1080/20565623.2024.2387961] [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: 12/07/2023] [Accepted: 07/30/2024] [Indexed: 09/10/2024] Open
Abstract
Macrophages are integral part of the body's defense against pathogens and serve as vital regulators of inflammation. Adaptor molecules, featuring diverse domains, intricately orchestrate the recruitment and transmission of inflammatory responses through signaling cascades. Key domains involved in macrophage polarization include Toll-like receptors (TLRs), Src Homology2 (SH2) and other small domains, alongside receptor tyrosine kinases, crucial for pathway activation. This review aims to elucidate the enigmatic role of macrophage adaptor molecules in modulating macrophage activation, emphasizing their diverse roles and potential therapeutic and investigative avenues for further exploration.
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Affiliation(s)
- Aurelia Rughetti
- Laboratory of Tumor Immunology & Cell Therapy, Department of Experimental Medicine, Policlinico Umberto I, University of Rome "Sapienza", Rome, Italy
| | - Shreya Bharti
- Department of Biosciences & Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Rajkumar Savai
- Lung Microenvironmental Niche in Cancerogenesis, Institute for Lung Health (ILH), Justus Liebig University, Giessen, D-35390, Germany
- Max Planck Institute for Heart & Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), Bad Nauheim, D-61231, Germany
- Institute of Biochemistry, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, D-60590, Germany
| | - Spyridoula Barmpoutsi
- Lung Microenvironmental Niche in Cancerogenesis, Institute for Lung Health (ILH), Justus Liebig University, Giessen, D-35390, Germany
- Max Planck Institute for Heart & Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), Bad Nauheim, D-61231, Germany
| | - Andreas Weigert
- Institute of Biochemistry, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, D-60590, Germany
- Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, Frankfurt, D-60323, Germany
| | - Rajat Atre
- Department of Biosciences & Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Faaiza Siddiqi
- Department of Biosciences & Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Rahul Sharma
- Department of Biosciences & Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Rakhi Khabiya
- Department of Biosciences & Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Nik Hirani
- MRC Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH164TJ, UK
| | - Mirza S Baig
- Department of Biosciences & Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
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Kim D, Nita-Lazar A. Progress in mass spectrometry approaches to profiling protein-protein interactions in the studies of the innate immune system. JOURNAL OF PROTEINS AND PROTEOMICS 2024; 15:545-559. [PMID: 39380887 PMCID: PMC11460538 DOI: 10.1007/s42485-024-00156-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/04/2024] [Accepted: 06/24/2024] [Indexed: 10/10/2024]
Abstract
Understanding protein-protein interactions (PPIs) is pivotal for deciphering the intricacies of biological processes. Dysregulation of PPIs underlies a spectrum of diseases, including cancer, neurodegenerative disorders, and autoimmune conditions, highlighting the imperative of investigating these interactions for therapeutic advancements. This review delves into the realm of mass spectrometry-based techniques for elucidating PPIs and their profound implications in biological research. Mass spectrometry in the PPI research field not only facilitates the evaluation of protein-protein interaction modulators but also discovers unclear molecular mechanisms and sheds light on both on- and off-target effects, thus aiding in drug development. Our discussion navigates through six pivotal techniques: affinity purification mass spectrometry (AP-MS), proximity labeling mass spectrometry (PL-MS), cross-linking mass spectrometry (XL-MS), size exclusion chromatography coupled with mass spectrometry (SEC-MS), limited proteolysis-coupled mass spectrometry (LiP-MS), and thermal proteome profiling (TPP).
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Affiliation(s)
- Doeun Kim
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA
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Shen X, Gu M, Zhan F, Cai H, Zhang K, Wang K, Li C. Porcine beta defensin 2 attenuates inflammatory responses in IPEC-J2 cells against Escherichia coli via TLRs-NF-κB/MAPK signaling pathway. BMC Vet Res 2024; 20:357. [PMID: 39127630 PMCID: PMC11316325 DOI: 10.1186/s12917-024-04220-7] [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: 04/19/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND Porcine beta defensin 2 (pBD2) is one of the porcine beta defensins that has antibacterial activity, and plays an important role in the immunomodulatory activity that protects cells from pathogens. It has been reported that pBD2 plays their immunomodulatory functions related to the TLR4-NF-κB signal pathways. However, it is not completely clear how pBD2 reduces the inflammatory response caused by pathogens. RESULTS In this study, the effect of pBD2 on the expression of genes in the TLRs signaling pathway was investigated after IPEC-J2 cells were challenged with E. coli. The results showed that pBD2 decreased the expression of IL-8 induced by E. coli (P < 0.05), and pBD2 significantly decreased the expression of TLR4, TLR5 and TLR7 (P < 0.05), as well as the key downstream genes p38 and JNK which activated by E. coli (P < 0.05). In addition, pBD2 inhibited the p-p65, p-p38 and p-JNK which were up-regulated by E. coli. CONCLUSIONS pBD2 could reduce the inflammatory response induced by E. coli perhaps by inhibiting the TLRs-TAK1-NF-κB/MAPK signaling pathway which was activated by E. coli in IPEC-J2 cells. Our study further reveals the immunomodulatory activity of recombinant pBD2 against E. coli, and provides insights into the molecular mechanisms that protect cells from E. coli infection.
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Affiliation(s)
- Xiaoyang Shen
- College of Animal Science and Technology, Henan Agricultural University, No. 218, PingAn Road, Zheng Dong New District, Zhengzhou, 460045, Henan, The People's Republic of China
| | - Mingke Gu
- College of Animal Science and Technology, Henan Agricultural University, No. 218, PingAn Road, Zheng Dong New District, Zhengzhou, 460045, Henan, The People's Republic of China
| | - Fengting Zhan
- College of Animal Science and Technology, Henan Agricultural University, No. 218, PingAn Road, Zheng Dong New District, Zhengzhou, 460045, Henan, The People's Republic of China
| | - Hanfang Cai
- College of Animal Science and Technology, Henan Agricultural University, No. 218, PingAn Road, Zheng Dong New District, Zhengzhou, 460045, Henan, The People's Republic of China
| | - Kun Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, The People's Republic of China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, No. 218, PingAn Road, Zheng Dong New District, Zhengzhou, 460045, Henan, The People's Republic of China.
| | - Chunli Li
- College of Animal Science and Technology, Henan Agricultural University, No. 218, PingAn Road, Zheng Dong New District, Zhengzhou, 460045, Henan, The People's Republic of China.
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Chen F, Wu P, Zhang H, Sun G. Signaling Pathways Triggering Therapeutic Hydrogels in Promoting Chronic Wound Healing. Macromol Biosci 2024; 24:e2300217. [PMID: 37831962 DOI: 10.1002/mabi.202300217] [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: 05/16/2023] [Revised: 10/08/2023] [Indexed: 10/15/2023]
Abstract
In recent years, there has been a significant increase in the prevalence of chronic wounds, such as pressure ulcers, diabetic foot ulcers, and venous ulcers of the lower extremities. The main contributors to chronic wound formation are bacterial infection, prolonged inflammation, and peripheral vascular disease. However, effectively treating these chronic wounds remains a global challenge. Hydrogels have extensively explored as wound healing dressing because of their excellent biocompatibility and structural similarity to extracellular matrix (ECM). Nonetheless, much is still unknown how the hydrogels promote wound repair and regeneration. Signaling pathways play critical roles in wound healing process by controlling and coordinating cells and biomolecules. Hydrogels, along with their therapeutic ingredients that impact signaling pathways, have the potential to significantly enhance the wound healing process and its ultimate outcomes. Understanding this interaction will undoubtedly provide new insights into developing advanced hydrogels for wound repair and regeneration. This paper reviews the latest studies on classical signaling pathways and potential targets influenced by hydrogel scaffolds in chronic wound healing. This work hopes that it will offer a different perspective in developing more efficient hydrogels for treating chronic wounds.
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Affiliation(s)
- Fang Chen
- Hebei Provincial Key Laboratory of Skeletal Metabolic Physiology of Chronic Kidney Disease, Affiliated Hospital of Hebei University, Baoding, 071000, China
- First Department of Bone Injury, Luzhou Municipal Hospital of Traditional Chinese Medicine, Luzhou, Sichuan, 646000, China
| | - Pingli Wu
- College of Chemistry and Materials Science, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Hebei University, Baoding, 071002, China
| | - Haisong Zhang
- Hebei Provincial Key Laboratory of Skeletal Metabolic Physiology of Chronic Kidney Disease, Affiliated Hospital of Hebei University, Baoding, 071000, China
| | - Guoming Sun
- Sunogel Biotechnologies Inc., Lutherville Timonium, 9 W Ridgely Road Ste 270, Maryland, 21093, USA
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Prateeksha P, Howlader MSI, Hansda S, Naidu P, Das M, Abo-Aziza F, Das H. Secretome of Dental Pulp-Derived Stem Cells Reduces Inflammation and Proliferation of Glioblastoma Cells by Deactivating Mapk-Akt Pathway. DISEASES & RESEARCH 2023; 3:74-86. [PMID: 38213319 PMCID: PMC10783424 DOI: 10.54457/dr.202302006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Background Dental pulp-derived stem cells (DPSC) is a promising therapy as they modulate the immune response, so we evaluated the inhibitory effect of DPSC secretome (DPSC℗) on the proliferation and inflammation in human glioblastoma (GBM) cells (U-87 MG) and elucidated the concomitant mechanisms involved. Methods The U87-MG cells were cultured with DPSC℗ for 24 h and assessed the expression of inflammatory molecules using quantitative reverse transcription-polymerase chain reaction (qRT-PCR), generation of reactive oxygen species (ROS), and mitochondrial functionality using a seahorse flux analyzer. MTT (3-(4, 5-dimethylthiazolyl-2)-2, 5-diphenyltetrazolium bromide) assay and cell cycle analysis were performed to evaluate the proliferation and cell cycle. Finally, the protein levels were determined by western blot. Results DPSC℗ reduced the inflammation and proliferation of U-87 MG cells by down-regulating the pro-inflammatory markers and up-regulating anti-inflammatory markers expressions through ROS-mediated signaling. Moreover, DPSC℗ significantly reduced the mitochondrial membrane potential (MMP) in the cells. The cellular bioenergetics revealed that all the parameters of oxygen consumption rate (OCAR) and the extracellular acidification rate (ECAR) were significantly decreased in the GBM cells after the addition of DPSC℗. Additionally, DPSC℗ decreased the GBM cell proliferation by arresting the cell cycle at the G1 phase through activation (phosphorylation) of checkpoint molecule CHK1. Furthermore, mechanistically, we found that the DPSC℗ impedes the phosphorylation of the mitogen-activated protein kinases (P38 MAPK) and protein kinase B (AKT) pathway. Conclusion Our findings lend the first evidence of the inhibitory effects of DPSC℗ on proliferation and inflammation in GBM cells by altering the P38 MAPK-AKT pathway.
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Affiliation(s)
- Prateeksha Prateeksha
- Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, USA
| | - Md Sariful Islam Howlader
- Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, USA
| | - Surajit Hansda
- Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, USA
| | - Prathyusha Naidu
- Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, USA
| | - Manjusri Das
- Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, USA
| | - Faten Abo-Aziza
- Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, USA
| | - Hiranmoy Das
- Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, USA
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Baig MS, Thurston TLM, Sharma R, Atre R, Saqib U, Khabiya R, Bharti S, Poh CL. Editorial: Targeting signalling pathways in inflammatory diseases. Front Immunol 2023; 14:1241440. [PMID: 37593741 PMCID: PMC10431928 DOI: 10.3389/fimmu.2023.1241440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023] Open
Affiliation(s)
- Mirza S. Baig
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Teresa L. M. Thurston
- Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
| | - Rahul Sharma
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Rajat Atre
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Uzma Saqib
- School of Life Sciences, Devi Ahilya Vishwavidyalaya (DAVV), Indore, India
| | - Rakhi Khabiya
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Shreya Bharti
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Chit L. Poh
- Centre for Virus and Vaccine Research, Sunway University, Bandar Sunway, Malaysia
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Yuan W, Weaver YM, Earnest S, Taylor CA, Cobb MH, Weaver BP. Modulating p38 MAPK signaling by proteostasis mechanisms supports tissue integrity during growth and aging. Nat Commun 2023; 14:4543. [PMID: 37507441 PMCID: PMC10382525 DOI: 10.1038/s41467-023-40317-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
The conserved p38 MAPK family is activated by phosphorylation during stress responses and inactivated by phosphatases. C. elegans PMK-1 p38 MAPK initiates innate immune responses and blocks development when hyperactivated. Here we show that PMK-1 signaling is enhanced during early aging by modulating the stoichiometry of non-phospho-PMK-1 to promote tissue integrity and longevity. Loss of pmk-1 function accelerates progressive declines in neuronal integrity and lysosome function compromising longevity which has both cell autonomous and cell non-autonomous contributions. CED-3 caspase cleavage limits phosphorylated PMK-1. Enhancing p38 signaling with caspase cleavage-resistant PMK-1 protects lysosomal and neuronal integrity extending a youthful phase. PMK-1 works through a complex transcriptional program to regulate lysosome formation. During early aging, the absolute phospho-p38 amount is maintained but the reservoir of non-phospho-p38 diminishes to enhance signaling without hyperactivation. Our findings show that modulating the stoichiometry of non-phospho-p38 dynamically supports tissue-homeostasis during aging without hyper-activation of stress response.
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Affiliation(s)
- Wang Yuan
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yi M Weaver
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Svetlana Earnest
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Clinton A Taylor
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Melanie H Cobb
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Benjamin P Weaver
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA.
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Rajpoot S, Kumar A, Gaponenko V, Thurston TL, Mehta D, Faisal SM, Zhang KY, Jha HC, Darwhekar GN, Baig MS. Dorzolamide suppresses PKCδ -TIRAP-p38 MAPK signaling axis to dampen the inflammatory response. Future Med Chem 2023. [PMID: 37129027 DOI: 10.4155/fmc-2022-0260] [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] [Indexed: 05/03/2023] Open
Abstract
Background: Sepsis is a syndrome due to microbial infection causing impaired multiorgan function. Its underlying cause is immune dysfunction and macrophages play an essential role. Methods: TIRAP interaction with PKCδ in macrophage was studied, revealing downstream signaling by Western blot and quantitative reverse transcriptase PCR. Dorzolamide (DZD) disrupting TIRAP-PKCδ interaction was identified by virtual screening and validated in vitro and in septic mice. Results: The study highlights the indispensable role of TIRAP-PKCδ in p38 MAPK-activation, NF-κB- and AP-1-mediated proinflammatory cytokines expression, whereas DZD significantly attenuated the signaling. Conclusion: Targeting TIRAP-PKCδ interaction by DZD is a novel therapeutic approach for treating sepsis.
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Affiliation(s)
- Sajjan Rajpoot
- Department of Biosciences & Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Ashutosh Kumar
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Vadim Gaponenko
- Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Teresa Lm Thurston
- MRC Centre for Molecular Bacteriology & Infection, Imperial College London, London, SW7 2AZ, UK
| | - Dolly Mehta
- Department of Pharmacology & Center for Lung & Vascular Biology, College of Medicine, The University of Illinois, Chicago, IL 60612, USA
| | - Syed M Faisal
- National Institute of Animal Biotechnology, Hyderabad, 500032, India
| | - Kam Yj Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Hem C Jha
- Department of Biosciences & Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Gajanan N Darwhekar
- Acropolis Institute of Pharmaceutical Education & Research, Indore, 453771, India
| | - Mirza S Baig
- Department of Biosciences & Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
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TIRAP, TRAM, and Toll-Like Receptors: The Untold Story. Mediators Inflamm 2023; 2023:2899271. [PMID: 36926280 PMCID: PMC10014160 DOI: 10.1155/2023/2899271] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 03/09/2023] Open
Abstract
Toll-like receptors (TLRs) are the most studied receptors among the pattern recognition receptors (PRRs). They act as microbial sensors, playing major roles in the regulation of the innate immune system. TLRs mediate their cellular functions through the activation of MyD88-dependent or MyD88-independent signaling pathways. Myd88, or myeloid differentiation primary response 88, is a cytosolic adaptor protein essential for the induction of proinflammatory cytokines by all TLRs except TLR3. While the crucial role of Myd88 is well described, the contribution of other adaptors in mediating TLR signaling and function has been underestimated. In this review, we highlight important results demonstrating that TIRAP and TRAM adaptors are also required for full signaling activity and responses induced by most TLRs.
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Rosignoli S, Paiardini A. Boosting the Full Potential of PyMOL with Structural Biology Plugins. Biomolecules 2022; 12:biom12121764. [PMID: 36551192 PMCID: PMC9775141 DOI: 10.3390/biom12121764] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Over the past few decades, the number of available structural bioinformatics pipelines, libraries, plugins, web resources and software has increased exponentially and become accessible to the broad realm of life scientists. This expansion has shaped the field as a tangled network of methods, algorithms and user interfaces. In recent years PyMOL, widely used software for biomolecules visualization and analysis, has started to play a key role in providing an open platform for the successful implementation of expert knowledge into an easy-to-use molecular graphics tool. This review outlines the plugins and features that make PyMOL an eligible environment for supporting structural bioinformatics analyses.
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Onyango H, Odhiambo P, Angwenyi D, Okoth P. In Silico Identification of New Anti-SARS-CoV-2 Main Protease (M pro) Molecules with Pharmacokinetic Properties from Natural Sources Using Molecular Dynamics (MD) Simulations and Hierarchical Virtual Screening. J Trop Med 2022; 2022:3697498. [PMID: 36263438 PMCID: PMC9576439 DOI: 10.1155/2022/3697498] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/27/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022] Open
Abstract
Infectious agents such as SARS-CoV, MERS-CoV, and SARS-CoV-2 have emerged in recent years causing epidemics with high mortality rates. The quick development of novel therapeutic compounds is required in the fight against such pathogenic agents. Unfortunately, the traditional drug development methods are time-consuming and expensive. In this study, computational algorithms were utilized for virtual screening of a library of natural compounds in the ZINC database for their affinity towards SARS-CoV-2 Mpro. Compounds such as cinanserin, nelfinavir, baicalin, baicalein, candesartan cilexetil, chloroquine, dipyridamole, and hydroxychloroquine have the ability to prevent SARS-CoV-2 Mpro from facilitating COVID 19 infection; thus, they treat COVID 19. However, these drugs majorly act to reduce the symptoms of the disease. No anti-viral drug against COVID 19 virus infection has been discovered and approved. Therefore, this study sought to explore natural inhibitors of SARS-CoV-2 Mpro to develop a pharmacophore model for virtual screening of natural compounds in the ZINC database as potential candidates for SARS-CoV-2 Mpro inhibitors and as therapeutic molecules against COVID 19. This study undertook in silico methods to identify the best anti-viral candidates targeting SAR-CoV-2 Mpro from natural sources in the ZINC database. Initially, reported anti-SARS-CoV-2 Mpro molecules were integrated into designing a pharmacophore model utilizing PharmaGist. Later, the pharmacophore model was loaded into ZINCPHARMER and screened against the ZINC database to identify new probable drug candidates. The root means square deviation (RMSD) values of the potential drug candidates informed the selection of some of them, which were docked with SARS-CoV-2 Mpro to comprehend their interactions. From the molecular docking results, the top four candidates (ZINC000254823011, ZINC000072307130, ZINC000013627512, and ZINC000009418994) against SARS-CoV-2 Mpro, with binding energies ranging from -8.2 kcal/mol to -8.6 kcal/mol, were examined for their oral bioavailability and other pharmacokinetic properties. Consequently, ZINC000072307130 emerged as the only orally bioavailable drug candidate with desirable pharmacokinetic properties. This candidate drug was used to perform MD simulations, and the outcomes revealed that ZINC000072307130 formed a stable complex with the viral main protease. Consequently, ZINC000072307130 emerges as a potential anti-SARS-CoV-2 Mpro inhibitor for the production of new COVID 19 drugs.
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Affiliation(s)
- Harrison Onyango
- Department of Biological Sciences (Molecular Biology, Computational Biology and Bioinformatics Section), School of Natural and Applied Sciences, Masinde Muliro University of Science and Technology, P. O BOX 190, Kakamega 50100, Kenya
| | - Patrick Odhiambo
- Department of Biological Sciences (Molecular Biology, Computational Biology and Bioinformatics Section), School of Natural and Applied Sciences, Masinde Muliro University of Science and Technology, P. O BOX 190, Kakamega 50100, Kenya
| | - David Angwenyi
- Department of Mathematics, School of Natural and Applied Sciences, Masinde Muliro University of Science and Technology, P. O BOX 190, Kakamega 50100, Kenya
| | - Patrick Okoth
- Department of Biological Sciences (Molecular Biology, Computational Biology and Bioinformatics Section), School of Natural and Applied Sciences, Masinde Muliro University of Science and Technology, P. O BOX 190, Kakamega 50100, Kenya
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