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Lee SB, Gupta H, Min BH, Ganesan R, Sharma SP, Won SM, Jeong JJ, Cha MG, Kwon GH, Jeong MK, Hyun JY, Eom JA, Park HJ, Yoon SJ, Lee SY, Choi MR, Kim DJ, Oh KK, Suk KT. A consortium of Hordeum vulgare and gut microbiota against non-alcoholic fatty liver disease via data-driven analysis. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2024; 52:250-260. [PMID: 38687561 DOI: 10.1080/21691401.2024.2347380] [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: 06/19/2023] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
Despite many recent studies on non-alcoholic fatty liver disease (NAFLD) therapeutics, the optimal treatment has yet to be determined. In this unfinished project, we combined secondary metabolites (SMs) from the gut microbiota (GM) and Hordeum vulgare (HV) to investigate their combinatorial effects via network pharmacology (NP). Additionally, we analyzed GM or barley - signalling pathways - targets - metabolites (GBSTMs) in combinatorial perspectives (HV, and GM). A total of 31 key targets were analysed via a protein-protein interaction (PPI) network, and JUN was identified as the uppermost target in NAFLD. On a bubble plot, we revealed that apelin signalling pathway, which had the lowest enrichment factor antagonize NAFLD. Holistically, we scrutinized GBSTM to identify key components (GM, signalling pathways, targets, and metabolites) associated with the Apelin signalling pathway. Consequently, we found that the primary GMs (Eubacterium limosum, Eggerthella sp. SDG-2, Alistipes indistinctus YIT 12060, Odoribacter laneus YIT 12061, Paraprevotella clara YIT 11840, Paraprevotella xylaniphila YIT 11841) to ameliorate NAFLD. The molecular docking test (MDT) suggested that tryptanthrin-JUN is an agonist, conversely, dihydroglycitein-HDAC5, 1,3-diphenylpropan-2-ol-NOS1, and (10[(Acetyloxy)methyl]-9-anthryl)methyl acetate-NOS2, which are antagonistic conformers in the apelin signalling pathway. Overall, these results suggest that combination therapy could be an effective strategy for treating NAFLD.
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Affiliation(s)
- Su-Been Lee
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Haripriya Gupta
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Byeong-Hyun Min
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Raja Ganesan
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Satya Priya Sharma
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Sung-Min Won
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Jin-Ju Jeong
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Min-Gi Cha
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Goo-Hyun Kwon
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Min-Kyo Jeong
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Ji-Ye Hyun
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Jung-A Eom
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Hee-Jin Park
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Sang-Jun Yoon
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Sang Youn Lee
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Mi-Ran Choi
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Dong Joon Kim
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Ki-Kwang Oh
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Ki-Tae Suk
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
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Fagnani E, Bonì F, Seneci P, Gornati D, Muzio L, Mastrangelo E, Milani M. Stabilization of the retromer complex: Analysis of novel binding sites of bis-1,3-phenyl guanylhydrazone 2a to the VPS29/VPS35 interface. Comput Struct Biotechnol J 2024; 23:1088-1093. [PMID: 38487369 PMCID: PMC10937258 DOI: 10.1016/j.csbj.2024.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
The stabilization of the retromer protein complex can be effective in the treatment of different neurological disorders. Following the identification of bis-1,3-phenyl guanylhydrazone 2a as an effective new compound for the treatment of amyotrophic lateral sclerosis, in this work we analyze the possible binding sites of this molecule to the VPS35/VPS29 dimer of the retromer complex. Our results show that the affinity for different sites of the protein assembly depends on compound charge and therefore slight changes in the cell microenvironment could promote different binding states. Finally, we describe a novel binding site located in a deep cleft between VPS29 and VPS35 that should be further explored to select novel molecular chaperones for the stabilization of the retromer complex.
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Affiliation(s)
- Elisa Fagnani
- Biophysics Institute, CNR-IBF, Via Corti 12, I-20133 Milano, Italy
- Department of Bioscience, University of Milan, Via Celoria 26, I-20133 Milano, Italy
| | - Francesco Bonì
- Biophysics Institute, CNR-IBF, Via Corti 12, I-20133 Milano, Italy
- Department of Bioscience, University of Milan, Via Celoria 26, I-20133 Milano, Italy
| | - Pierfausto Seneci
- Department of Chemistry, University of Milan, Via Celoria 26, I-20133 Milano, Italy
| | - Davide Gornati
- Department of Chemistry, University of Milan, Via Celoria 26, I-20133 Milano, Italy
| | - Luca Muzio
- INSPE—Institute of Experimental Neurology, San Raffaele Scientific Institute, Via Olgettina 60, I–20132 Milano, Italy
| | - Eloise Mastrangelo
- Biophysics Institute, CNR-IBF, Via Corti 12, I-20133 Milano, Italy
- Department of Bioscience, University of Milan, Via Celoria 26, I-20133 Milano, Italy
| | - Mario Milani
- Biophysics Institute, CNR-IBF, Via Corti 12, I-20133 Milano, Italy
- Department of Bioscience, University of Milan, Via Celoria 26, I-20133 Milano, Italy
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3
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Tao J, Luo J, Li K, Yang R, Lin Y, Ge J. Comprehensive genetic analysis uncovers the mutational spectrum of MFRP and its genotype-phenotype correlation in a large cohort of Chinese microphthalmia patients. Gene 2024; 926:148647. [PMID: 38848879 DOI: 10.1016/j.gene.2024.148647] [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: 03/11/2024] [Revised: 05/21/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
PURPOSE Microphthalmia is a severe congenital ocular disease featured by abnormal ocular development. The aim of this study was to detail the genetic and clinical characteristics of a large cohort of Chinese patients with microphthalmia related to MFRP variants, focusing on uncovering genotype-phenotype correlations. METHODS Fifty microphthalmia patients from 44 unrelated Chinese families were recruited. Whole-exome sequencing (WES) was conducted to analyze the coding regions and adjacent intronic regions of MFRP. Axial lengths (AL) were measured for all probands and available family members. Protein structures of mutations with high frequency in our cohort were predicted. The genotype-phenotype correlations were explored by statistical analysis. RESULTS Sixteen MFRP variants were detected in 17 families, accounting for 38.64 % of all microphthalmia families. There were 9 novel mutations (c.427+1G>C, c.428-2A>C, c.561_575del:p.A188_E192del, c.836G>A:p.C279Y, c.1010_1021del:p.H337_E340del:p.Y479*, c.1516_1517del:p.S506Pfs*66, c.1561T>G:p.C521G, c.1616G>A:p.R539H, and c.1735C>T:p.P579S) and six previously reported variants in MFRP, with p.E496K and p.H337_E340del being highly frequent, found in eight (47.06 %) and two families (11.76 %), respectively. Seven variants (43.75 %) were located in the C-terminal cysteine-rich frizzled-related domain (CRD) (7/16, 43.75 %). Protein prediction implicated p.E496K and p.H337_E340del mutations might lead to a destabilization of the MFRP protein. The average AL of all 42 eyes was 16.02 ± 1.05 mm, and 78.36 % of eyes with AL < 16 mm harbored p.E496K variant. Twenty-six eyes with variant variant had shorter AL than that of the other 16 eyes without this variant (p = 0.006), highlighting a novel genotype-phenotype correlation. CONCLUSIONS In this largest cohort of Chinese patients with microphthalmia, the 9 novel variants, high frequency of p.E496W, and mutation hotspots in CRD reveals unique insights into the MFRP mutation spectrum among Chinese patients, indicating ethnic variability. A new genotype-phenotype correlation that p.E496K variant associated with a shorter AL is unveiled. Our findings enhance the current knowledge of MFRP-associated microphthalmia and provide valuable information for prenatal diagnosis as well as future therapy.
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Affiliation(s)
- Jing Tao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100730, China
| | - Jingyi Luo
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Kaijing Li
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Runcai Yang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Yixiu Lin
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Jian Ge
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong 510000, China.
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Su J, Yang X, Xu H, Pei Y, Liu QS, Zhou Q, Jiang G. Screening (ant)agonistic activities of xenobiotics on the retinoic acid receptor alpha (RARα) using in vitro and in silico analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174717. [PMID: 38997027 DOI: 10.1016/j.scitotenv.2024.174717] [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: 05/13/2024] [Revised: 07/07/2024] [Accepted: 07/09/2024] [Indexed: 07/14/2024]
Abstract
Retinoic acid receptors (RARs) are known as crucial endocrine receptors that could mediate a broad diversity of biological processes. However, the data on endocrine disrupting effects of emerging chemicals by targeting RAR (ant)agonism are far from sufficient. Herein, we investigated the RARα agonistic or antagonistic activities for 75 emerging chemicals of concern, and explored their interactions with this receptor. A recombinant two-hybrid yeast assay was used to examine the RARα activities of the test chemicals, wherein 7 showed effects of RARα agonism and 54 exerted potentials of RARα antagonism. The representative chemicals with RARα agonistic activities, i.e. 4-hydroxylphenol (4-HP) and bisphenol AF (BPAF), significantly increased the mRNA levels of CRABP2 and CYP26A1, while 4 select chemicals with RARα antagonistic potentials, including bisphenol A (BPA), tetrabromobisphenol A (TBBPA), 4-tert-octylphenol (4-t-OP), and 4-n-nonylphenol (4-n-NP), conversely decreased the transcriptional levels of the test genes. The in silico molecular docking analysis using 3 different approaches further confirmed the substantial binding between the chemicals with RARα activities and this nuclear receptor protein. This work highlights the promising strategy for screening endocrine-disrupting effects of emerging chemicals of concern by targeting RARα (ant)agonism.
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Affiliation(s)
- Jiahui Su
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxi Yang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Hanqing Xu
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Wenzhou University, Wenzhou 325035, China
| | - Yao Pei
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian S Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Qunfang Zhou
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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Kummur KN, Panda SM, Patil MB, Tripathy U, Sidarai AH. Revealing the interaction mechanism between bovine serum albumin (BSA) and a fluorescent coumarin derivative: A multispectroscopic and in silico approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 318:124466. [PMID: 38761474 DOI: 10.1016/j.saa.2024.124466] [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: 01/18/2024] [Revised: 05/05/2024] [Accepted: 05/12/2024] [Indexed: 05/20/2024]
Abstract
The interaction of biomacromolecules with each other or with the ligands is essential for biological activity. In this context, the molecular recognition of bovine serum albumin (BSA) with 4-(Benzo[1,3]dioxol-5-yloxymethyl)-7-hydroxy-chromen-2-one (4BHC) is explored using multispectroscopic and computational techniques. UV-Vis spectroscopy helped in predicting the conformational variations in BSA. Using fluorescence spectroscopy, the quenching behaviour of the fluorophore upon interaction with the ligand is examined, which is found to be a static type of quenching; fluorescence lifetime studies further verify this. The binding constant is discovered to be in the range of 104 M-1, which indicates the moderate type of association that results in reversible binding, where the transport and release of ligands in the target tissue takes place. Fourier-transform infrared spectroscopy (FT-IR) measurements validate the secondary structure conformational changes of BSA after complexing with 4BHC. The thermodynamic factors obtained through temperature-dependent fluorescence studies suggest that the dominant kind of interaction force is hydrophobic in nature, and the interaction process is spontaneous. The alterations in the surrounding microenvironment of the binding site and conformational shifts in the structure of the protein are studied through 3D fluorescence and synchronous fluorescence studies. Molecular docking and molecular dynamics (MD) simulations agree with experimental results and explain the structural stability throughout the discussion. The outcomes might have possible applications in the field of pharmacodynamics and pharmacokinetics.
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Affiliation(s)
- Kavyashree Nagappa Kummur
- Department of Studies in Physics, Karnatak University, Pavatenagar, Dharwad, 580003, Karnataka, India
| | - Smita Manjari Panda
- Department of Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad, 826004, Jharkhand, India
| | | | - Umakanta Tripathy
- Department of Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad, 826004, Jharkhand, India.
| | - Ashok H Sidarai
- Department of Studies in Physics, Karnatak University, Pavatenagar, Dharwad, 580003, Karnataka, India.
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Lee N, Kim S, Lee NY, Jo H, Jeong P, Pagire HS, Pagire SH, Ahn JH, Jin MS, Park CS. Activation mechanism and novel binding sites of the BK Ca channel activator CTIBD. Life Sci Alliance 2024; 7:e202402621. [PMID: 39089879 PMCID: PMC11294680 DOI: 10.26508/lsa.202402621] [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: 01/26/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 08/04/2024] Open
Abstract
The large-conductance calcium-activated potassium (BKCa) channel, which is crucial for urinary bladder smooth muscle relaxation, is a potential target for overactive bladder treatment. Our prior work unveiled CTIBD as a promising BKCa channel activator, altering V 1/2 and G max This study investigates CTIBD's activation mechanism, revealing its independence from the Ca2+ and membrane voltage sensing of the BKCa channel. Cryo-electron microscopy disclosed that two CTIBD molecules bind to hydrophobic regions on the extracellular side of the lipid bilayer. Key residues (W22, W203, and F266) are important for CTIBD binding, and their replacement with alanine reduces CTIBD-mediated channel activation. The triple-mutant (W22A/W203A/F266A) channel showed the smallest V 1/2 shift with a minimal impact on activation and deactivation kinetics by CTIBD. At the single-channel level, CTIBD treatment was much less effective at increasing P o in the triple mutant, mainly because of a drastically increased dissociation rate compared with the WT. These findings highlight CTIBD's mechanism, offering crucial insights for developing small-molecule treatments for BKCa-related pathophysiological conditions.
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Affiliation(s)
- Narasaem Lee
- https://ror.org/024kbgz78 School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Subin Kim
- https://ror.org/024kbgz78 School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Na Young Lee
- https://ror.org/024kbgz78 School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Heeji Jo
- https://ror.org/024kbgz78 School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | | | - Haushabhau S Pagire
- https://ror.org/024kbgz78 Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Suvarna H Pagire
- https://ror.org/024kbgz78 Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Jin Hee Ahn
- https://ror.org/024kbgz78 Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Mi Sun Jin
- https://ror.org/024kbgz78 School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Chul-Seung Park
- https://ror.org/024kbgz78 School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
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7
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Pei H, Xie G, Yao X, Wang S, Yan J, Dai L, Wang Y. Exploring the binding affinity and characteristics of DcitOBP9 in citrus psyllids. Gene 2024; 923:148551. [PMID: 38759737 DOI: 10.1016/j.gene.2024.148551] [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: 01/31/2024] [Revised: 04/17/2024] [Accepted: 05/08/2024] [Indexed: 05/19/2024]
Abstract
Odorant-binding proteins (OBPs) are crucial in insect olfaction. The most abundant expressed OBP of citrus psyllids, DcitOBP9 encodes 148 amino acids. DcitOBP9 lacks a transmembrane structure and possesses a 17-amino acid signal peptide at the N-terminus. Characterized by the six conserved cysteine sites, DcitOBP9 is classified as the Classical-OBP family. RT-qPCR experiments revealed ubiquitous expression of DcitOBP9 across all developmental stages of the citrus psyllid, with predominant expression in adults antennae. Fluorescence competitive binding assays demonstrated DcitOBP9's strong affinity for ocimene, linalool, dodecanoic acid, and citral, and moderate affinity for dimethyl trisulfide. Additionally, it binds to myrcia, (-)-trans-caryophyllene, (±)-Citronellal, nonanal, and (+)-α-pinene. Among them, ocimene, linalool, and dodecanoic acid were dynamically bound to DcitOBP9, while citral was statically bound to DcitOBP9. Molecular docking simulations with the top five ligands indicated that amino acid residues V92, S72, P128, L91, L75, and A76 are pivotal in the interaction between DcitOBP9 and these odorants. These findings suggest DcitOBP9's involvement in the citrus psyllid's host plant recognition and selection behaviors, thereby laying a foundation for elucidating the potential physiological and biological functions of DcitOBP9 and developing attractants.
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Affiliation(s)
- Haoran Pei
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Gang Xie
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Xiang Yao
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Shenghui Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Jin Yan
- College of Food Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Liangying Dai
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China.
| | - Yunsheng Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China.
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Yang P, Wang W, Hu Y, Wang Y, Xu Z, Liao X. Exploring high hydrostatic pressure effects on anthocyanin binding to serum albumin and food-derived transferrins. Food Chem 2024; 452:139544. [PMID: 38723571 DOI: 10.1016/j.foodchem.2024.139544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/20/2024] [Accepted: 05/01/2024] [Indexed: 06/01/2024]
Abstract
This study investigated the effects of high hydrostatic pressure (HHP) on the binding interactions of cyanindin-3-O-glucoside (C3G) to bovine serum albumin, human serum albumin (HSA), bovine lactoferrin, and ovotransferrin. Fluorescence quenching revealed that HHP reduced C3G-binding affinity to HSA, while having a largely unaffected role for the other proteins. Notably, pretreating HSA at 500 MPa significantly increased its dissociation constant with C3G from 24.7 to 34.3 μM. Spectroscopic techniques suggested that HSA underwent relatively pronounced tertiary structural alterations after HHP treatments. The C3G-HSA binding mechanisms under pressure were further analyzed through molecular dynamics simulation. The localized structural changes in HSA under pressure might weaken its interaction with C3G, particularly polar interactions such as hydrogen bonds and electrostatic forces, consequently leading to a decreased binding affinity. Overall, the importance of pressure-induced structural alterations in proteins influencing their binding with anthocyanins was highlighted, contributing to optimizing HHP processing for anthocyanin-based products.
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Affiliation(s)
- Peiqing Yang
- Beijing Key Laboratory for Food Non-thermal processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Fruit & Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Wenxin Wang
- Beijing Key Laboratory for Food Non-thermal processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Fruit & Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Yichen Hu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China.
| | - Yongtao Wang
- Beijing Key Laboratory for Food Non-thermal processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Fruit & Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Zhenzhen Xu
- Beijing Key Laboratory for Food Non-thermal processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Fruit & Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-food Safety and Quality, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xiaojun Liao
- Beijing Key Laboratory for Food Non-thermal processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Fruit & Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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9
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Bach K, Dohnálek J, Škerlová J, Kuzmík J, Poláchová E, Stanchev S, Majer P, Fanfrlík J, Pecina A, Řezáč J, Lepšík M, Borshchevskiy V, Polovinkin V, Strisovsky K. Extensive targeting of chemical space at the prime side of ketoamide inhibitors of rhomboid proteases by branched substituents empowers their selectivity and potency. Eur J Med Chem 2024; 275:116606. [PMID: 38901105 DOI: 10.1016/j.ejmech.2024.116606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 06/22/2024]
Abstract
Rhomboid intramembrane serine proteases have been implicated in several pathologies, and emerge as attractive pharmacological target candidates. The most potent and selective rhomboid inhibitors available to date are peptidyl α-ketoamides, but their selectivity for diverse rhomboid proteases and strategies to modulate it in relevant contexts are poorly understood. This gap, together with the lack of suitable in vitro models, hinders ketoamide development for relevant eukaryotic rhomboid enzymes. Here we explore the structure-activity relationship principles of rhomboid inhibiting ketoamides by medicinal chemistry and enzymatic in vitro and in-cell assays with recombinant rhomboid proteases GlpG, human mitochondrial rhomboid PARL and human RHBDL2. We use X-ray crystallography in lipidic cubic phase to understand the binding mode of one of the best ketoamide inhibitors synthesized here containing a branched terminal substituent bound to GlpG. In addition, to extend the interpretation of the co-crystal structure, we use quantum mechanical calculations and quantify the relative importance of interactions along the inhibitor molecule. These combined experimental analyses implicates that more extensive exploration of chemical space at the prime side is unexpectedly powerful for the selectivity of rhomboid inhibiting ketoamides. Together with variations in the peptide sequence at the non-prime side, or its non-peptidic alternatives, this strategy enables targeted tailoring of potent and selective ketoamides towards diverse rhomboid proteases including disease-relevant ones such as PARL and RHBDL2.
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Affiliation(s)
- Kathrin Bach
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic; Department of Molecular Genetics, Faculty of Science, Charles University, Viničná 5, Prague, 128 44, Czech Republic
| | - Jan Dohnálek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic; University of Chemistry and Technology, Technická 5, Prague, 166 28, Czech Republic
| | - Jana Škerlová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Ján Kuzmík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Edita Poláchová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic; First Faculty of Medicine, Charles University, Kateřinská 32, Prague, 121 08, Czech Republic
| | - Stancho Stanchev
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Adam Pecina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Valentin Borshchevskiy
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry) Forschungszentrum Jülich 52428 Jülich, Germany
| | - Vitaly Polovinkin
- ELI Beamlines Centre, ELI ERIC, Za Radnicí 835, 252 41, Dolní Břežany, Czech Republic
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic.
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10
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Kushwah AS, Dixit H, Upadhyay V, Verma SK, Prasad R. The study of iron- and copper-binding proteome of Fusarium oxysporum and its effector candidates. Proteins 2024; 92:1097-1112. [PMID: 38666709 DOI: 10.1002/prot.26696] [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: 07/05/2023] [Revised: 03/26/2024] [Accepted: 04/08/2024] [Indexed: 08/07/2024]
Abstract
Fusarium oxysporum f.sp. lycopersici is a phytopathogen which causes vascular wilt disease in tomato plants. The survival tactics of both pathogens and hosts depend on intricate interactions between host plants and pathogenic microbes. Iron-binding proteins (IBPs) and copper-binding proteins (CBPs) play a crucial role in these interactions by participating in enzyme reactions, virulence, metabolism, and transport processes. We employed high-throughput computational tools at the sequence and structural levels to investigate the IBPs and CBPs of F. oxysporum. A total of 124 IBPs and 37 CBPs were identified in the proteome of Fusarium. The ranking of amino acids based on their affinity for binding with iron is Glu > His> Asp > Asn > Cys, and for copper is His > Asp > Cys respectively. The functional annotation, determination of subcellular localization, and Gene Ontology analysis of these putative IBPs and CBPs have unveiled their potential involvement in a diverse array of cellular and biological processes. Three iron-binding glycosyl hydrolase family proteins, along with four CBPs with carbohydrate-binding domains, have been identified as potential effector candidates. These proteins are distinct from the host Solanum lycopersicum proteome. Moreover, they are known to be located extracellularly and function as enzymes that degrade the host cell wall during pathogen-host interactions. The insights gained from this report on the role of metal ions in plant-pathogen interactions can help develop a better understanding of their fundamental biology and control vascular wilt disease in tomato plants.
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Affiliation(s)
- Ankita Singh Kushwah
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Himisha Dixit
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Vipin Upadhyay
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Shailender Kumar Verma
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
- Department of Environmental Studies, University of Delhi, North Campus, Delhi, India
| | - Ramasare Prasad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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11
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Golda M, Hoffka G, Cherry S, Tropea JE, Lountos GT, Waugh DS, Wlodawer A, Tőzsér J, Mótyán JA. P1' specificity of the S219V/R203G mutant tobacco etch virus protease. Proteins 2024; 92:1085-1096. [PMID: 38666764 PMCID: PMC11303109 DOI: 10.1002/prot.26693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/26/2024] [Accepted: 04/08/2024] [Indexed: 08/07/2024]
Abstract
Proteases that recognize linear amino acid sequences with high specificity became indispensable tools of recombinant protein technology for the removal of various fusion tags. Due to its stringent sequence specificity, the catalytic domain of the nuclear inclusion cysteine protease of tobacco etch virus (TEV PR) is also a widely applied reagent for enzymatic removal of fusion tags. For this reason, efforts have been made to improve its stability and modify its specificity. For example, P1' autoproteolytic cleavage-resistant mutant (S219V) TEV PR was found not only to be nearly impervious to self-inactivation, but also exhibited greater stability and catalytic efficiency than the wild-type enzyme. An R203G substitution has been reported to further relax the P1' specificity of the enzyme, however, these results were obtained from crude intracellular assays. Until now, there has been no rigorous comparison of the P1' specificity of the S219V and S219V/R203G mutants in vitro, under carefully controlled conditions. Here, we compare the P1' amino acid preferences of these single and double TEV PR mutants. The in vitro analysis was performed by using recombinant protein substrates representing 20 P1' variants of the consensus TENLYFQ*SGT cleavage site, and synthetic oligopeptide substrates were also applied to study a limited set of the most preferred variants. In addition, the enzyme-substrate interactions were analyzed in silico. The results indicate highly similar P1' preferences for both enzymes, many side-chains can be accommodated by the S1' binding sites, but the kinetic assays revealed lower catalytic efficiency for the S219V/R203G than for the S219V mutant.
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Affiliation(s)
- Mária Golda
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Gyula Hoffka
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - Scott Cherry
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Joseph E. Tropea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - George T. Lountos
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - David S. Waugh
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Alexander Wlodawer
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - János András Mótyán
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
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12
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Navratna V, Kumar A, Rana JK, Mosalaganti S. Structure of the human systemic RNAi defective transmembrane protein 1 (hSIDT1) reveals the conformational flexibility of its lipid binding domain. Life Sci Alliance 2024; 7:e202402624. [PMID: 38925866 PMCID: PMC11208740 DOI: 10.26508/lsa.202402624] [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: 01/26/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
In Caenorhabditis elegans, inter-cellular transport of the small non-coding RNA causing systemic RNAi is mediated by the transmembrane protein SID1, encoded by the sid1 gene in the systemic RNAi defective (sid) loci. SID1 shares structural and sequence similarity with cholesterol uptake protein 1 (CHUP1) and is classified as a member of the ChUP family. Although systemic RNAi is not an evolutionarily conserved process, the sid gene products are found across the animal kingdom, suggesting the existence of other novel gene regulatory mechanisms mediated by small non-coding RNAs. Human homologs of sid gene products-hSIDT1 and hSIDT2-mediate contact-dependent lipophilic small non-coding dsRNA transport. Here, we report the structure of recombinant human SIDT1. We find that the extra-cytosolic domain of hSIDT1 adopts a double jelly roll fold, and the transmembrane domain exists as two modules-a flexible lipid binding domain and a rigid transmembrane domain core. Our structural analyses provide insights into the inherent conformational dynamics within the lipid binding domain in ChUP family members.
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Affiliation(s)
- Vikas Navratna
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Jaimin K Rana
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Shyamal Mosalaganti
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Biophysics, College of Literature, Science and the Arts, University of Michigan, Ann Arbor, MI, USA
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13
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Fu W, Shentu C, Chen D, Qiu J, Zong C, Yu H, Zhang Y, Chen Y, Liu X, Xu T. Network pharmacology combined with affinity ultrafiltration to elucidate the potential compounds of Shaoyao Gancao Fuzi Decoction for the treatment of rheumatoid arthritis. JOURNAL OF ETHNOPHARMACOLOGY 2024; 330:118268. [PMID: 38677569 DOI: 10.1016/j.jep.2024.118268] [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: 03/04/2024] [Revised: 04/13/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Shaoyao Gancao Fuzi Decoction (SGFD), has been employed for thousands of years in the treatment of rheumatoid arthritis (RA) with remarkable clinical efficacy. However, the material basis underlying the effectiveness of SGFD still remains unclear. AIM OF THE REVIEW This study aims to elucidate the material basis of SGFD through the application of network pharmacology and biological affinity ultrafiltration. RESULTS UPLC-Q-TOF-MS/MS was employed to characterize the components in SGFD, the identified 145 chemical components were mainly categorized into alkaloids, flavonoids, triterpenoids, and monoterpenoids according to the structures. Network pharmacology method was utilized to identify potential targets and signaling pathways of SGFD in the RA treatment, and the anti-inflammatory and anti-RA effects of SGFD were validated through in vivo and in vitro experiments. Moreover, as the significant node in the pharmacology network, TNF-α, a classical therapeutic target in RA, was subsequent employed to screen the interacting compounds in SGFD via affinity ultrafiltration screening method, 6 active molecules (i.e.,glycyrrhizic acid, paeoniflorin, formononetin, isoliquiritigenin, benzoyl mesaconitine, and glycyrrhetinic acid) were exhibited significant interactions. Finally, the significant anti-inflammatory and anti-TNF-α effects of these compounds were validated at the cellular level. CONCLUSIONS In conclusion, this study comprehensively elucidates the pharmacodynamic material basis of SGFD, offering a practical reference model for the systematic investigation of traditional Chinese medicine formulas.
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Affiliation(s)
- Weiliang Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Chengyu Shentu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Dan Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Junjie Qiu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, No. 366, Xingke Road, Lingxi Town, Cangnan County, Wenzhou, Zhejiang Province, 325899, China
| | - Chuhong Zong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Hengyuan Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Yiwei Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Yong Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, No. 366, Xingke Road, Lingxi Town, Cangnan County, Wenzhou, Zhejiang Province, 325899, China
| | - Xuesong Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, No. 366, Xingke Road, Lingxi Town, Cangnan County, Wenzhou, Zhejiang Province, 325899, China.
| | - Tengfei Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, No. 366, Xingke Road, Lingxi Town, Cangnan County, Wenzhou, Zhejiang Province, 325899, China.
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14
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Fernandez-Ciruelos B, Albanese M, Adhav A, Solomin V, Ritchie-Martinez A, Taverne F, Velikova N, Jirgensons A, Marina A, Finn PW, Wells JM. Repurposing Hsp90 inhibitors as antimicrobials targeting two-component systems identifies compounds leading to loss of bacterial membrane integrity. Microbiol Spectr 2024; 12:e0014624. [PMID: 38917423 PMCID: PMC11302729 DOI: 10.1128/spectrum.00146-24] [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: 01/16/2024] [Accepted: 05/14/2024] [Indexed: 06/27/2024] Open
Abstract
The discovery of antimicrobials with novel mechanisms of action is crucial to tackle the foreseen global health crisis due to antimicrobial resistance. Bacterial two-component signaling systems (TCSs) are attractive targets for the discovery of novel antibacterial agents. TCS-encoding genes are found in all bacterial genomes and typically consist of a sensor histidine kinase (HK) and a response regulator. Due to the conserved Bergerat fold in the ATP-binding domain of the TCS HK and the human chaperone Hsp90, there has been much interest in repurposing inhibitors of Hsp90 as antibacterial compounds. In this study, we explore the chemical space of the known Hsp90 inhibitor scaffold 3,4-diphenylpyrazole (DPP), building on previous literature to further understand their potential for HK inhibition. Six DPP analogs inhibited HK autophosphorylation in vitro and had good antimicrobial activity against Gram-positive bacteria. However, mechanistic studies showed that their antimicrobial activity was related to damage of bacterial membranes. In addition, DPP analogs were cytotoxic to human embryonic kidney cell lines and induced the cell arrest phenotype shown for other Hsp90 inhibitors. We conclude that these DPP structures can be further optimized as specific disruptors of bacterial membranes providing binding to Hsp90 and cytotoxicity are lowered. Moreover, the X-ray crystal structure of resorcinol, a substructure of the DPP derivatives, bound to the HK CheA represents a promising starting point for the fragment-based design of novel HK inhibitors. IMPORTANCE The discovery of novel antimicrobials is of paramount importance in tackling the imminent global health crisis of antimicrobial resistance. The discovery of novel antimicrobials with novel mechanisms of actions, e.g., targeting bacterial two-component signaling systems, is crucial to bypass existing resistance mechanisms and stimulate pharmaceutical innovations. Here, we explore the possible repurposing of compounds developed in cancer research as inhibitors of two-component systems and investigate their off-target effects such as bacterial membrane disruption and toxicity. These results highlight compounds that are promising for further development of novel bacterial membrane disruptors and two-component system inhibitors.
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Affiliation(s)
- Blanca Fernandez-Ciruelos
- Host-Microbe Interactomics Group, Dept. Animal Sciences, Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Marco Albanese
- Oxford Drug Design (ODD), Oxford Centre for Innovation, Oxford, United Kingdom
- School of Computer Science, University of Buckingham, Buckingham, United Kingdom
| | - Anmol Adhav
- Macromolecular Crystallography Group, Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Cientificas (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Vitalii Solomin
- Organic Synthesis Methodology Group, Latvian Institute of Organic Synthesis (LIOS), Riga, Latvia
| | - Arabela Ritchie-Martinez
- Host-Microbe Interactomics Group, Dept. Animal Sciences, Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Femke Taverne
- Host-Microbe Interactomics Group, Dept. Animal Sciences, Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Nadya Velikova
- Host-Microbe Interactomics Group, Dept. Animal Sciences, Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Aigars Jirgensons
- Organic Synthesis Methodology Group, Latvian Institute of Organic Synthesis (LIOS), Riga, Latvia
| | - Alberto Marina
- Macromolecular Crystallography Group, Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Cientificas (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Paul W. Finn
- Oxford Drug Design (ODD), Oxford Centre for Innovation, Oxford, United Kingdom
- School of Computer Science, University of Buckingham, Buckingham, United Kingdom
| | - Jerry M. Wells
- Host-Microbe Interactomics Group, Dept. Animal Sciences, Wageningen University & Research (WUR), Wageningen, the Netherlands
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15
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Riaz A, Kaleem A, Abdullah R, Iqtedar M, Hoessli DC, Aftab M. In silico approaches to study the human asparagine synthetase: An insight of the interaction between the enzyme active sites and its substrates. PLoS One 2024; 19:e0307448. [PMID: 39093903 PMCID: PMC11296641 DOI: 10.1371/journal.pone.0307448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 06/28/2024] [Indexed: 08/04/2024] Open
Abstract
Cancer is a leading concern and important cause of death worldwide. Cancer is a non-communicable illness defined as uncontrolled division of cells. It can develop into metastatic cancer when tumor cells migrate to other organs. In recent years evidence has emerged that the bioavailability of Asn play a crucial role in cancer metastasis. Asn is a non-essential amino acid formed from an ATP dependent catalyzed reaction by the enzyme asparagine synthetase (ASNS), where Asp and Gln are converted to Asn and Glu, respectively. The human ASNS enzyme consist of 561 amino acids, with a molecular weight of 64 KDa. ASNS governs the activation of transcriptional factors that regulate the process of metastasis. In this work the 3D model of ASNS in E. coli (AS-B) and the human ASNS docked with its different ligands have been used to study the 3D mechanism of the conversion of Asp and Gln to Asn and Glu, in human ASNS. The stability evaluation of the docked complexes was checked by molecular dynamic simulation through the bioinformatic tool Desmond. The binding residues and their interactions can be exploited for the development of inhibitors, as well as for finding new drug molecules against ASNS and prevention of metastatic cancer.
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Affiliation(s)
- Anam Riaz
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
| | - Afshan Kaleem
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
| | - Roheena Abdullah
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
| | - Mehwish Iqtedar
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
| | - Daniel C. Hoessli
- Panjwani Center for Molecular Medicine and Drug Research, University of Karachi, Karachi, Pakistan
| | - Mahwish Aftab
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
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16
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Takeda K, Sarata A, Terasaki M, Kubota A, Shimizu K, Kamata R. Assessment of the Aryl Hydrocarbon Receptor-Mediated Effects of Aromatic Sensitizers in Paper Recycling Effluent Employing Zebrafish Embryos and in Silico Docking. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024. [PMID: 39092783 DOI: 10.1002/etc.5969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024]
Abstract
Aromatic sensitizers and related substances (SRCs), which are crucial in the paper industry for facilitating color-forming and color-developing chemical reactions, inadvertently contaminate effluents during paper recycling. Owing to their structural resemblance to endocrine-disrupting aromatic organic compounds, concerns have arisen about potential adverse effects on aquatic organisms. We focused on SRC effects via the aryl hydrocarbon receptor (AHR), employing molecular docking simulations and zebrafish (Danio rerio) embryo exposure assessments. Molecular docking revealed heightened binding affinities between certain SRCs in the paper recycling effluents and zebrafish Ahr2 and human AHR, which are pivotal components in the SRC toxicity mechanism. Fertilized zebrafish eggs were exposed to SRCs for up to 96 h post fertilization; among these substances, benzyl 2-naphthyl ether (BNE) caused morphological abnormalities, such as pericardial edema and shortened body length, at relatively low concentrations (1 μM) during embryogenesis. Gene expression of cytochrome P450 1A (cyp1a) and ahr2 was also significantly increased by BNE. Co-exposure to the AHR antagonist CH-223191 only partially mitigated BNE's phenotypic effects, despite the effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin being relatively well restored by CH-223191, indicating BNE's AHR-independent toxic mechanisms. Furthermore, some SRCs, including BNE, exhibited in silico binding affinity to the estrogen receptor and upregulation of cyp19a1b gene expression. Therefore, additional insights into the toxicity of SRCs and their mechanisms are essential. The present results provide important information on SRCs and other papermaking chemicals that could help minimize the environmental impact of the paper industry. Environ Toxicol Chem 2024;00:1-13. © 2024 SETAC.
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Affiliation(s)
- Kazuki Takeda
- Laboratory of Toxicology, School of Veterinary Medicine, Kitasato University, Towada-shi, Aomori, Japan
- Department of Computer Science, Tokyo Institute of Technology, Yokohama-shi, Kanagawa, Japan
| | - Aoi Sarata
- Laboratory of Toxicology, School of Veterinary Medicine, Kitasato University, Towada-shi, Aomori, Japan
| | - Masanori Terasaki
- Environmental Chemistry Laboratory, Graduate School of Arts and Sciences, Iwate University, Morioka City, Iwate, Japan
| | - Akira Kubota
- Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
| | - Keita Shimizu
- Laboratory of Toxicology, School of Veterinary Medicine, Kitasato University, Towada-shi, Aomori, Japan
| | - Ryo Kamata
- Laboratory of Toxicology, School of Veterinary Medicine, Kitasato University, Towada-shi, Aomori, Japan
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17
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Rodriguez DCP, Weber KC, Sundberg B, Glasgow A. MAGPIE: An interactive tool for visualizing and analyzing protein-ligand interactions. Protein Sci 2024; 33:e5027. [PMID: 38989559 PMCID: PMC11237554 DOI: 10.1002/pro.5027] [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: 03/03/2024] [Revised: 04/22/2024] [Accepted: 05/05/2024] [Indexed: 07/12/2024]
Abstract
Quantitative tools to compile and analyze biomolecular interactions among chemically diverse binding partners would improve therapeutic design and aid in studying molecular evolution. Here we present Mapping Areas of Genetic Parsimony In Epitopes (MAGPIE), a publicly available software package for simultaneously visualizing and analyzing thousands of interactions between a single protein or small molecule ligand (the "target") and all of its protein binding partners ("binders"). MAGPIE generates an interactive three-dimensional visualization from a set of protein complex structures that share the target ligand, as well as sequence logo-style amino acid frequency graphs that show all the amino acids from the set of protein binders that interact with user-defined target ligand positions or chemical groups. MAGPIE highlights all the salt bridge and hydrogen bond interactions made by the target in the visualization and as separate amino acid frequency graphs. Finally, MAGPIE collates the most common target-binder interactions as a list of "hotspots," which can be used to analyze trends or guide the de novo design of protein binders. As an example of the utility of the program, we used MAGPIE to probe how different antibody fragments bind a viral antigen; how a common metabolite binds diverse protein partners; and how two ligands bind orthologs of a well-conserved glycolytic enzyme for a detailed understanding of evolutionarily conserved interactions involved in its activation and inhibition. MAGPIE is implemented in Python 3 and freely available at https://github.com/glasgowlab/MAGPIE, along with sample datasets, usage examples, and helper scripts to prepare input structures.
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Affiliation(s)
- Daniel C. Pineda Rodriguez
- Department of Biochemistry and Molecular BiophysicsColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Kyle C. Weber
- Department of Biochemistry and Molecular BiophysicsColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Belen Sundberg
- Department of Biochemistry and Molecular BiophysicsColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Anum Glasgow
- Department of Biochemistry and Molecular BiophysicsColumbia University Irving Medical CenterNew YorkNew YorkUSA
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18
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Xiang J, Chen J, Liu Y, Ye H, Han Y, Li P, Gao M, Huang Y. Tannic acid as a biphasic modulator of tau protein liquid-liquid phase separation. Int J Biol Macromol 2024; 275:133578. [PMID: 38960272 DOI: 10.1016/j.ijbiomac.2024.133578] [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: 05/03/2024] [Revised: 06/20/2024] [Accepted: 06/29/2024] [Indexed: 07/05/2024]
Abstract
Tannic acid (TA) is a natural polyphenol that shows great potential in the field of biomedicine due to its anti-inflammatory, anti-oxidant, anti-bacterial, anti-tumor, anti-virus, and neuroprotective activities. Recent studies have revealed that liquid-liquid phase separation (LLPS) is closely associated with protein aggregation. Therefore, modulating LLPS offers new insights into the treatment of neurodegenerative diseases. In this study, we investigated the influence of TA on the LLPS of the Alzheimer's-related protein tau and the underlying mechanism. Our findings indicate that TA affects the LLPS of tau in a biphasic manner, with initial promotion and subsequent suppression as the TA to tau molar ratio increases. TA modulates tau phase separation through a combination of hydrophobic interactions and hydrogen bonds. The balance between TA-tau and tau-tau interactions is found to be relevant to the material properties of TA-induced tau condensates. We further illustrate that the modulatory activity of TA in phase separation is highly dependent on the target proteins. These findings enhance our understanding of the forces driving tau LLPS under different conditions, and may facilitate the identification and optimization of compounds that can rationally modulate protein phase transition in the future.
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Affiliation(s)
- Jiani Xiang
- Key Laboratory of Industrial Fermentation, Ministry of Education, Hubei University of Technology, Wuhan 430068, China; Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Jingxin Chen
- Key Laboratory of Industrial Fermentation, Ministry of Education, Hubei University of Technology, Wuhan 430068, China; Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Yanqing Liu
- Key Laboratory of Industrial Fermentation, Ministry of Education, Hubei University of Technology, Wuhan 430068, China; Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Haiqiong Ye
- Key Laboratory of Industrial Fermentation, Ministry of Education, Hubei University of Technology, Wuhan 430068, China; Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Yue Han
- Key Laboratory of Industrial Fermentation, Ministry of Education, Hubei University of Technology, Wuhan 430068, China; Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Ping Li
- Key Laboratory of Industrial Fermentation, Ministry of Education, Hubei University of Technology, Wuhan 430068, China; Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Meng Gao
- Key Laboratory of Industrial Fermentation, Ministry of Education, Hubei University of Technology, Wuhan 430068, China; Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China.
| | - Yongqi Huang
- Key Laboratory of Industrial Fermentation, Ministry of Education, Hubei University of Technology, Wuhan 430068, China; Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China.
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19
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Sundararajan S, Karunakaran K, Muniyan R. Structure based virtual screening and discovery of novel inhibitors against FabD protein of Mycobacterium tuberculosis. J Biomol Struct Dyn 2024; 42:6280-6291. [PMID: 37424186 DOI: 10.1080/07391102.2023.2233622] [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: 03/03/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
Abstract
The highly flexible nature of Mycobacterium tuberculosis (Mtb) can be owed to its tough cell wall and multiple gene interaction system which makes it resistant to frontline TB drugs. Mycolic acids are the key components of the unique cell wall that protects the organism from external threats. Proteins of the fatty acid synthesis pathway are evolutionarily conserved that enables cellular survival in harsh conditions and hence have become attractive targets. Malonyl Co-A Acyl carrier protein transacylase (FabD; MCAT, EC2.3.1.39) is an enzyme in the branching point of the unique and vast fatty acid synthase (FAS-I and FAS-II) systems of Mtb. In the present investigation, in-silico structure based drug discovery with the compounds from an open source library (NPASS) is used for target fishing and employed to understand the interaction with the target protein FabD. The potential hit compounds were filtered using exhaustive docking, considering the binding energy, key residue interaction and drug likeness property. Three compounds from the library namely NPC475074 (Hit 1), NPC260631 (Hit 2) and NPC313985 (Hit 3) with binding energies -14.45, -13.29 and -12.37 respectively were taken for molecular dynamic simulation. The results suggested that Hit 3 (NPC313985) has stable interaction with FabD protein. This article further elaborates the interaction of the identified novel compounds Hit 1 and Hit 3 along with the other known compound (Hit 2) against Mtb FabD protein. The hit compounds identified from this study could be further evaluated against mutated FabD protein and considered for in-vitro evaluation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sadhana Sundararajan
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Keerthana Karunakaran
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Rajiniraja Muniyan
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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20
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Brascher TC, de Bortoli L, Toledo-Silva G, Zacchi FL, Razzera G. In silico structural features of the CgNR5A: CgDAX complex and its role in regulating gene expression of CYP target genes in Crassostrea gigas. CHEMOSPHERE 2024; 361:142443. [PMID: 38815811 DOI: 10.1016/j.chemosphere.2024.142443] [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: 02/27/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 06/01/2024]
Abstract
Contamination of aquatic environments has been steadily increasing due to human activities. The Pacific oyster Crassostrea gigas has been used as a key species in studies assessing the impacts of contaminants on human health and the aquatic biome. In this context, cytochrome P450 (CYPs) play a crucial role in xenobiotic metabolism. In vertebrates many of these CYPs are regulated by nuclear receptors (NRs) and little is known about the NRs role in C. gigas. Particularly, the CgNR5A represents a homologue of SF1 and LRH-1 found in vertebrates. Members of this group can regulate genes of CYPs involved in lipid/steroid metabolism, with their activity regulated by other NR, called as DAX-1, generating a NR complex on DNA response elements (REs). As C. gigas does not exhibit steroid biosynthesis pathways, CgNR5A may play other physiological roles. To clarify this issue, we conducted an in silico investigation of the interaction between CgNR5A and DNA to identify potential C. gigas CYP target genes. Using molecular docking and dynamics simulations of the CgNR5A on DNA molecules, we identified a monomeric interaction with extended REs. This RE was found in the promoter region of 30 CYP genes and also the NR CgDAX. When the upstream regulatory region was analyzed, CYP2C39, CYP3A11, CYP4C21, CYP7A1, CYP17A1, and CYP27C1 were mapped as the main genes regulated by CgNR5A. These identified CYPs belong to families known for their involvement in xenobiotic and lipid/steroid metabolism. Furthermore, we reconstructed a trimeric complex, previously proposed for vertebrates, with CgNR5A:CgDAX and subjected it to molecular dynamics simulations analysis. Heterotrimeric complex remained stable during the simulations, suggesting that CgDAX may modulate CgNR5A transcriptional activity. This study provides insights into the potential physiological processes involving these NRs in the regulation of CYPs associated with xenobiotic and steroid/lipid metabolism.
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Affiliation(s)
- Theo Cardozo Brascher
- Programa de Pós-Graduação em Bioquímica, Departamento de Bioquímica, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil; Laboratório de Biomarcadores de Contaminação Aquática e Imunoquímica, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Leonardo de Bortoli
- Programa de Pós-Graduação em Bioquímica, Departamento de Bioquímica, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil; Laboratório de Biomarcadores de Contaminação Aquática e Imunoquímica, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil; Laboratório de Genômica, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Guilherme Toledo-Silva
- Laboratório de Genômica, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Flávia Lucena Zacchi
- Laboratório de Moluscos Marinhos, Universidade Federal de Santa Catarina, Florianópolis, SC, 88061-600, Brazil
| | - Guilherme Razzera
- Programa de Pós-Graduação em Bioquímica, Departamento de Bioquímica, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil; Laboratório de Biomarcadores de Contaminação Aquática e Imunoquímica, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil.
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21
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Verma J, Vashisth H. Molecular basis for differential recognition of an allosteric inhibitor by receptor tyrosine kinases. Proteins 2024; 92:905-922. [PMID: 38506327 PMCID: PMC11222054 DOI: 10.1002/prot.26685] [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: 11/13/2023] [Revised: 02/08/2024] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
Understanding kinase-inhibitor selectivity continues to be a major objective in kinase drug discovery. We probe the molecular basis of selectivity of an allosteric inhibitor (MSC1609119A-1) of the insulin-like growth factor-I receptor kinase (IGF1RK), which has been shown to be ineffective for the homologous insulin receptor kinase (IRK). Specifically, we investigated the structural and energetic basis of the allosteric binding of this inhibitor to each kinase by combining molecular modeling, molecular dynamics (MD) simulations, and thermodynamic calculations. We predict the inhibitor conformation in the binding pocket of IRK and highlight that the charged residues in the histidine-arginine-aspartic acid (HRD) and aspartic acid-phenylalanine-glycine (DFG) motifs and the nonpolar residues in the binding pocket govern inhibitor interactions in the allosteric pocket of each kinase. We suggest that the conformational changes in the IGF1RK residues M1054 and M1079, movement of the ⍺C-helix, and the conformational stabilization of the DFG motif favor the selectivity of the inhibitor toward IGF1RK. Our thermodynamic calculations reveal that the observed selectivity can be rationalized through differences observed in the electrostatic interaction energy of the inhibitor in each inhibitor/kinase complex and the hydrogen bonding interactions of the inhibitor with the residue V1063 in IGF1RK that are not attained with the corresponding residue V1060 in IRK. Overall, our study provides a rationale for the molecular basis of recognition of this allosteric inhibitor by IGF1RK and IRK, which is potentially useful in developing novel inhibitors with improved affinity and selectivity.
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Affiliation(s)
- Jyoti Verma
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824
| | - Harish Vashisth
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824
- Department of Chemistry, University of New Hampshire, Durham, NH 03824
- Integrated Applied Mathematics Program, University of New Hampshire, Durham, NH 03824
- Molecular and Cellular Biotechnology Program, University of New Hampshire, Durham, NH 03824
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22
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Medvedev KE, Schaeffer RD, Grishin NV. DrugDomain: The evolutionary context of drugs and small molecules bound to domains. Protein Sci 2024; 33:e5116. [PMID: 38979784 PMCID: PMC11231930 DOI: 10.1002/pro.5116] [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: 03/22/2024] [Revised: 06/27/2024] [Accepted: 06/29/2024] [Indexed: 07/10/2024]
Abstract
Interactions between proteins and small organic compounds play a crucial role in regulating protein functions. These interactions can modulate various aspects of protein behavior, including enzymatic activity, signaling cascades, and structural stability. By binding to specific sites on proteins, small organic compounds can induce conformational changes, alter protein-protein interactions, or directly affect catalytic activity. Therefore, many drugs available on the market today are small molecules (72% of all approved drugs in the last 5 years). Proteins are composed of one or more domains: evolutionary units that convey function or fitness either singly or in concert with others. Understanding which domain(s) of the target protein binds to a drug can lead to additional opportunities for discovering novel targets. The evolutionary classification of protein domains (ECOD) classifies domains into an evolutionary hierarchy that focuses on distant homology. Previously, no structure-based protein domain classification existed that included information about both the interaction between small molecules or drugs and the structural domains of a target protein. This data is especially important for multidomain proteins and large complexes. Here, we present the DrugDomain database that reports the interaction between ECOD of human target proteins and DrugBank molecules and drugs. The pilot version of DrugDomain describes the interaction of 5160 DrugBank molecules associated with 2573 human proteins. It describes domains for all experimentally determined structures of these proteins and incorporates AlphaFold models when such structures are unavailable. The DrugDomain database is available online: http://prodata.swmed.edu/DrugDomain/.
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Affiliation(s)
- Kirill E. Medvedev
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - R. Dustin Schaeffer
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Nick V. Grishin
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasTexasUSA
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23
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Shelake G, Baviskar S, Panda AK, Solankure S, Pandey K, Chauthe S, Behera SK. Exploring the rare variants associated with Type 2 Diabetes Mellitus in Indian population and its disease-drug association studies: an in-silico approach. J Biomol Struct Dyn 2024; 42:6307-6322. [PMID: 37440426 DOI: 10.1080/07391102.2023.2233634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 07/01/2023] [Indexed: 07/15/2023]
Abstract
The diversified eating habits and religious culture of Indian population may be one of the reasons they largely contribute to the global diabetes burden. In the present investigation, an in-silico approach was carried out to explore hub genes in the Indian population with Type 2 Diabetes Mellitus (T2DM) that are scantily reported in the GWAS catalogue and probable potential anti-diabetic drugs from plants. This computational approach unwrapped LEP (leptin) as the hub gene among 170 genes analyzed with 14 non-synonymous single nucleotide polymorphisms (nsSNPs) with MAF < 0.01. The mutation of the LEP gene leads to a decrease in leptin concentration, which increases the risk of obesity and T2DM. According to the DUET webserver, 11 of 14 mutations examined were found to destabilize the LEP protein. Among 14, four barely reported LEP variants rs781301976 (I45N), rs776443424 (S52F), rs200915360 (D76Y), and rs1191666811 (D162N) were unzipped to be associated with T2DM, which may be the probable potential drug targets. The virtual screening revealed Vescalagin as having the highest binding energy among 336 natural compounds. Molecular docking of Vescalagin depicted higher binding energy (-9.0 kcal/mol) against mutated LEP [rs200915360 (D76Y)] compared to wild (-8.9 kcal/mol) and LEP-Metformin complexes. The trajectory analysis of MD simulations revealed that Vescalagin was more effective than Metformin in stabilizing the system. The present study suggests that the associations of the investigated nsSNPs in LEP [rs200915360 (D76Y)] and others can be key factors in the predominant role of T2DM morbidity in the Indian population that can be used as potential markers and drug targets for T2DM therapeutics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ganesh Shelake
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gandhinagar, Gujarat, India
| | - Shraddha Baviskar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gandhinagar, Gujarat, India
| | - Amrita Kumari Panda
- Department of Biotechnology, Sant Gahira Guru Vishwavidyalaya, Sarguja, Ambikapur, Chhattisgarh, India
| | - Sunetra Solankure
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gandhinagar, Gujarat, India
| | - Komal Pandey
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gandhinagar, Gujarat, India
| | - Siddheshwar Chauthe
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gandhinagar, Gujarat, India
| | - Santosh Kumar Behera
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gandhinagar, Gujarat, India
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24
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Simon JP, Dong S. In-silico screening of missense nsSNPs in Delta-opioid receptor protein and their restoring tendency on MCRT interaction; focusing on dynamic nature. Int J Biol Macromol 2024; 275:133710. [PMID: 38977046 DOI: 10.1016/j.ijbiomac.2024.133710] [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: 04/29/2024] [Revised: 06/30/2024] [Accepted: 07/05/2024] [Indexed: 07/10/2024]
Abstract
Delta-opioid receptor protein (OPRD1) is one of the potential targets for treating pain. The presently available opioid agonists are known to cause unnecessary side effects. To discover a novel opioid agonist, our research group has synthesized a chimeric peptide MCRT and proved its potential activity through in vivo analysis. Non-synonymous SNPs (nsSNPs) missense mutations affect the functionality and stability of proteins leading to diseases. The current research was focused on understanding the role of MCRT in restoring the binding tendency of OPRD1 nsSNPs missense mutations on dynamic nature in comparison with Deltorphin-II and morphiceptin. The deleterious effects of nsSNPs were analyzed using various bioinformatics tools for predicting structural, functional, and oncogenic influence. The shortlisted nine nsSNPs were predicted for allergic reactions, domain changes, post-translation modification, multiple sequence alignment, secondary structure, molecular dynamic simulation (MDS), and peptide docking influence. Further, the docked complex of three shortlisted deleterious nsSNPs was analyzed using an MDS study, and the highly deleterious shortlisted nsSNP A149T was further analyzed for higher trajectory analysis. MCRT restored the binding tendency influence caused by nsSNPs on the dynamics of stability, functionality, binding affinity, secondary structure, residues connection, motion, and folding of OPRD1 protein.
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Affiliation(s)
- Jerine Peter Simon
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China
| | - Shouliang Dong
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China,; Key Laboratory of Preclinical Study for New Drugs of Gansu Province, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China.
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25
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Ahmed MH, Khan K, Tauseef S, Jalal K, Haroon U, Uddin R, Abdellattif MH, Khan A, Al-Harrasi A. Identification of therapeutic drug target of Shigella Flexneri serotype X through subtractive genomic approach and in-silico screening based on drug repurposing. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 122:105611. [PMID: 38823431 DOI: 10.1016/j.meegid.2024.105611] [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: 04/28/2024] [Revised: 05/26/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
Shigellosis, induced by Shigella flexneri, constitutes a significant health burden in developing nations, particularly impacting socioeconomically disadvantaged communities. Designated as the second most prevalent cause of diarrheal illness by the World Health Organization (WHO), it precipitates an estimated 212,000 fatalities annually. Within the spectrum of S. flexneri strains, serotype X is notably pervasive and resilient, yet its comprehensive characterization remains deficient. The present investigation endeavors to discern potential pharmacological targets and repurpose existing drug compounds against S. flexneri serotype X. Employing the framework of subtractive genomics, the study interrogates the reference genome of S. flexneri Serotype X (strain 2,002,017; UP000001884) to delineate its proteome into categories of non-homologous, non-paralogous, essential, virulent, and resistant constituents, thereby facilitating the identification of therapeutic targets. Subsequently, a screening of approximately 9000 compounds from the FDA library against the identified drug target aims to delineate efficacious agents for combating S. flexneri serotype X infections. The application of subtractive genomics methodology yields prognostic insights, unveiling non-paralogous proteins (n = 4122), non-homologues (n = 1803), essential (n = 1246), drug-like (n = 389), resistant (n = 167), alongside 42 virulent proteins within the reference proteome. This iterative process culminates in the identification of Serine O-acetyltransferase as a viable drug target. Subsequent virtual screening endeavors to unearth FDA-approved medicinal compounds capable of inhibiting Serine O-acetyltransferase. Noteworthy candidates such as DB12983, DB15085, DB16098, DB16185, and DB16262 emerge, exhibiting potential for mitigating S. flexneri Serotype X. Despite the auspicious findings, diligent scrutiny is imperative to ascertain the efficacy and safety profile of the proposed drug candidates vis-à-vis S. flexneri.
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Affiliation(s)
- Muhammad Hassan Ahmed
- Shaheed Zulfiqar Ali Bhutto Institute of Science and Technology (SZABIST), Pakistan; Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan
| | - Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan
| | - Saba Tauseef
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan
| | - Khurshid Jalal
- HEJ Research Institute of Chemistry International Center for Chemical and Biological Sciences, University of Karachi, Pakistan
| | - Urooj Haroon
- Department of Chemistry, Federal Urdu University of Arts, Science and Technology, Karachi, Pakistan
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan.
| | - Magda H Abdellattif
- Chemistry Department, College of Sciences, University College of Taraba, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman.
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26
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Vijayakumar S, Kumar H, Basu S, Chandy S, Anbarasu A, Manoharan A, Ramaiah S. Changing Landscape of Antimicrobial Resistance in Neonatal Sepsis: An in silico Analyses of Multidrug Resistance in Klebsiella pneumoniae. Pediatr Infect Dis J 2024; 43:777-784. [PMID: 38621154 DOI: 10.1097/inf.0000000000004358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
BACKGROUND Neonatal sepsis poses a critical healthcare concern, as multidrug-resistant Klebsiella pneumoniae ( K. pneumoniae ) infections are on the rise. Understanding the antimicrobial susceptibility patterns and underlying resistance mechanism is crucial for effective treatment. OBJECTIVES This study aimed to comprehensively investigate the antimicrobial susceptibility patterns of K. pneumoniae strains responsible for neonatal sepsis using in silico tools. We sought to identify trends and explore reasons for varying resistance levels, particularly for β-lactams and fluoroquinolone. METHODS K. pneumoniae isolated from neonates at Kanchi Kamakoti CHILDS Trust Hospital (2017-2020) were analyzed for antimicrobial resistance. Elevated resistance to β-lactam and fluoroquinolone antibiotics was further investigated through molecular docking and interaction analysis. β-lactam affinity with penicillin-binding proteins and β-lactamases was examined. Mutations in ParC and GyrA responsible for quinolone resistance were introduced to investigate ciprofloxacin interactions. RESULTS Of 111 K. pneumoniae blood sepsis isolates in neonates, high resistance was detected to β-lactams such as cefixime (85.91%, n = 71), ceftriaxone (84.9%, n = 106), cefotaxime (84.9%, n = 82) and fluoroquinolone (ciprofloxacin- 79.44%, n = 107). Molecular docking revealed low β-lactam binding toward penicillin-binding proteins and higher affinities for β-lactamases, attributing to the reduced β-lactam efficiency. Additionally, ciprofloxacin showed decreased affinity toward mutant ParC and GyrA in comparison to their corresponding wild-type proteins. CONCLUSION Our study elucidates altered resistance profiles in neonatal sepsis caused by K. pneumoniae , highlighting mechanisms of β-lactam and fluoroquinolone resistance. It underscores the urgent need for the development of sustainable therapeutic alternatives to address the rising antimicrobial resistance in neonatal sepsis.
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Affiliation(s)
- Santhiya Vijayakumar
- From the Department of Integrative Biology
- Medical and Biological Computing Laboratory
| | - Hithesh Kumar
- Medical and Biological Computing Laboratory
- Department of Bio-Sciences, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore
| | - Soumya Basu
- Department of Biotechnology, NIST University, Brahmapur
| | - Sara Chandy
- Department of Research, The CHILDS Trust Medical Research Foundation and Kanchi Kamakoti CHILDS Trust Hospital, Chennai
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory
- Department of Biotechnology, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, India
| | - Anand Manoharan
- Department of Research, The CHILDS Trust Medical Research Foundation and Kanchi Kamakoti CHILDS Trust Hospital, Chennai
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory
- Department of Bio-Sciences, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore
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27
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Zhou Y, Kang L, Xu R, Zhao D, Wang J, Wu J, Lin H, Ding Z, Zou Y. Mitochondrial outer membrane protein Samm50 protects against hypoxia-induced cardiac injury by interacting with Shmt2. Cell Signal 2024; 120:111219. [PMID: 38723737 DOI: 10.1016/j.cellsig.2024.111219] [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: 03/07/2024] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]
Abstract
Cardiac remodeling is a critical process following myocardial infarction (MI), potentially leading to heart failure if untreated. The significance of mitochondrial homeostasis in MI remains insufficiently understood. Samm50 is an essential component of mitochondria. Our study aimed to investigate its role in hypoxia-induced cardiac injury and the underlying mechanisms. First, we observed that Samm50 was dynamically downregulated in mice with MI compared to the control mice. In vitro, Samm50 was also downregulated in oxygen-glucose-deprived neonatal rat cardiomyocytes and fibroblasts. Overexpression and knockdown of Samm50 mitigated and exacerbated cardiac apoptosis and fibrosis, while also improving and worsening mitochondrial homeostasis, respectively. Protein interactions with Samm50 during the protective process were identified via immune-coprecipitation/mass spectroscopy. Mechanistically, serine hydroxymethyltransferase 2 (Shmt2) interacted with Samm50, acting as a crucial element in the protective process by hindering the transfer of Bax from the cytoplasm to the mitochondria and subsequent activation of caspase-3. Inhibition of Shmt2 diminished the protective effect of Samm50 overexpression against cardiac injury. Finally, Samm50 overexpression in vivo mitigated cardiac remodeling and enhanced cardiac function in both acute and chronic MI. In conclusion, Samm50 overexpression mitigated hypoxia-induced cardiac remodeling by inhibiting apoptosis and fibrosis, with Shmt2 acting as a key regulator in this protective process. The Samm50/Shmt2 axis represents a newly discovered mitochondria-related pathway for mitigating hypoxia-induced cardiac injury.
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Affiliation(s)
- Yufei Zhou
- Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Le Kang
- Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Ran Xu
- Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Di Zhao
- Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jienan Wang
- Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jiaying Wu
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Hong Lin
- Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zhiwen Ding
- Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
| | - Yunzeng Zou
- Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
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Campos-Fernández E, Alqualo NO, Vaz ER, Rodrigues CM, Alonso-Goulart V. Unveiling the characteristics of D4 and R4 aptamers for their future use in prostate cancer clinical practice. Biophys Chem 2024; 311:107259. [PMID: 38763045 DOI: 10.1016/j.bpc.2024.107259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 04/24/2024] [Accepted: 05/12/2024] [Indexed: 05/21/2024]
Abstract
The DNA and RNA aptamers D4 and R4, respectively, emerged from the modification of PC-3 cell-binding aptamer A4. Our objective was to characterize the aptamers in silico and in vitro and begin to identify their target molecules. We represented their structures using computational algorithms; evaluated their binding to several prostate cell lines and their effects on the viability and migration of these cells; and determined their dissociation constant by flow cytometry. We analyzed circulating prostate tumor cells from patients using D4, R4, anti-CD133 and anti-CD44. Finally, the target proteins of both aptamers were precipitated and identified by mass spectrometry to simulate their in silico docking. The aptamers presented similar structures and bound to prostate tumor cells without modifying the cellular parameters studied, but with different affinities. The ligand cells for both aptamers were CD44+, indicating that they could identify cells in the mesenchymal stage of the metastatic process. The possible target proteins NXPE1, ADAM30, and MUC6 need to be further studied to better understand their interaction with the aptamers. These results support the development of new assays to determine the clinical applications of D4 and R4 aptamers in prostate cancer.
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Affiliation(s)
- Esther Campos-Fernández
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Nathalia Oliveira Alqualo
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Emília Rezende Vaz
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Cláudia Mendonça Rodrigues
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Vivian Alonso-Goulart
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil.
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Yan H, He B, He L, Ye H. Screening study on significant Chinese herb for anti-idiopathic pulmonary fibrosis by combining clinical experience prescriptions and molecular dynamics simulation technologies. J Biomol Struct Dyn 2024; 42:6393-6409. [PMID: 37963492 DOI: 10.1080/07391102.2023.2263792] [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: 03/09/2023] [Accepted: 07/01/2023] [Indexed: 11/16/2023]
Abstract
Various techniques such as data mining, network pharmacology, molecular docking and molecular dynamics simulation were used in this study to screen and validate effective herbal medicines for the treatment of idiopathic pulmonary fibrosis (IPF) and to reveal their mechanisms of action at the molecular level. The use of this approach will provide new tools and ideas for future drug screening, especially for the application of herbal medicines in the treatment of complex diseases. Among them, the five identified core targets, including IL6, TP53, AKT1, VEGFA, and TNF, as well as a series of major active compounds, will be important references for future anti-IPF drug development. This information will accelerate the discovery and development of relevant drugs. Meanwhile, this study further confirmed the potential value of four Chinese herbal medicines, including Gancao, Danshen, Huangqin, and Sanqi, in the treatment of IPF. This will promote more clinical trials and practices to confirm and optimise the application of these herbs. Finally, this study is an important theoretical guide to enhance the advantages of Chinese herbal medicines in the prevention and treatment of major and difficult diseases, as well as to understand and utilise the potential efficacy of Chinese herbal medicines. This will further promote the scientific research and clinical application of herbal medicines and provide more possibilities for future disease treatmentCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Haiting Yan
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Beibei He
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Li He
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hua Ye
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Tom AA, Rajendran V, Thottasseri AA, Goswami K, Roy S, Gopan G, Mani M, Kannan T. Antiplasmodial action of 4-nitrobenzenesulfonamide chalcones: Design, synthesis, characterisation, in vitro and in silico evaluation against blood stages of Plasmodium falciparum 3D7. Drug Dev Res 2024; 85:e22233. [PMID: 39030842 DOI: 10.1002/ddr.22233] [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: 03/24/2024] [Revised: 06/13/2024] [Accepted: 06/29/2024] [Indexed: 07/22/2024]
Abstract
Malaria is an intracellular protozoan parasitic disease caused by Plasmodium species with significant morbidity and mortality in endemic regions. The complex lifecycle of the parasite and the emergence of drug-resistant Plasmodium falciparum have hampered the efficacy of current anti-malarial agents. To circumvent this situation, the present study attempts to demonstrate the blood-stage anti-plasmodial action of 26 hybrid compounds containing the three privileged bioactive scaffolds (sulfonamide, chalcone, and nitro group) with synergistic and multitarget action. These three parent scaffolds exhibit divergent activities, such as antibacterial, anti-malarial, anti-fungal, anti-inflammatory, and anticancer. All the synthesised compounds were characterised using various spectroscopic techniques. The in vitro blood-stage inhibitory activity of 26 hybrid compounds was evaluated against mixed-stage culture (asynchronize) of human malarial parasite P. falciparum, Pf 3D7 at different concentrations ranging from 25.0 µg/mL to 0.78 µg/mL using SYBR 1 green assay, with IC50 values determined after 48 h of treatment based on the drug-response curves. Two potent compounds (11 and 10), with 2-Br and 2,6-diCl substitutions, showed pronounced activity with IC50 values of 5.4 µg/mL and 5.6 µg/mL, whereas others displayed varied activity with IC50 values ranging from 7.0 µg/mL to 22.0 µg/mL. Both 11 and 10 showed greater susceptibility towards mature-stage trophozoites than ring-stage parasites. The hemolytic and in vitro cytotoxicity assays revealed that compounds 11 and 10 did not cause any toxic effects on host red blood cells (uninfected), human-derived Mo7e cells, and murine-derived BA/F3 cells. The in vitro observations are consistent with the in silico studies using P. falciparum-dihydrofolate reductase, where 11 and 10 showed a binding affinity of -10.4 Kcal/mol. This is the first report of the hybrid scaffold, 4-nitrobenzenesulfonamide chalcones, demonstrating its potential as an anti-plasmodial agent.
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Affiliation(s)
- Anju Agnes Tom
- Department of Chemistry, Pondicherry University, Puducherry, India
| | - Vinoth Rajendran
- Department of Microbiology, Pondicherry University, Puducherry, India
| | | | - Koustav Goswami
- Department of Chemistry, Pondicherry University, Puducherry, India
| | - Souvik Roy
- Department of Chemistry, Pondicherry University, Puducherry, India
| | - Gopika Gopan
- Department of Microbiology, Pondicherry University, Puducherry, India
| | - Maheswaran Mani
- Department of Microbiology, Pondicherry University, Puducherry, India
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Adame M, Vázquez H, Juárez-López D, Corzo G, Amezcua M, López D, González Z, Schcolnik-Cabrera A, Morales-Martínez A, Villegas E. Expression and characterization of scFv-6009FV in Pichia pastoris with improved ability to neutralize the neurotoxin Cn2 from Centruroides noxius. Int J Biol Macromol 2024; 275:133461. [PMID: 38945343 DOI: 10.1016/j.ijbiomac.2024.133461] [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: 05/07/2024] [Revised: 06/11/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024]
Abstract
Small single-chain variable fragments (scFv) are promising biomolecules to inhibit and neutralize toxins and to act as antivenoms. In this work, we aimed to produce a functional scFv-6009FV in the yeast Pichia pastoris, which inhibits the pure Cn2 neurotoxin and the whole venom of Centruroides noxius. We were able to achieve yields of up to 31.6 ± 2 mg/L in flasks. Furthermore, the protein showed a structure of 6.1 % α-helix, 49.1 % β-sheet, and 44.8 % of random coil by CD. Mass spectrometry confirmed the amino acid sequence and showed no glycosylation profile for this molecule. Purified scFv-6009FV allowed us to develop anti-scFvs in rabbits, which were then used in affinity columns to purify other scFvs. Determination of its half-maximal inhibitory concentration value (IC50) was 40 % better than the scFvs produced by E. coli as a control. Finally, we found that scFv-6009FV was able to inhibit ex vivo the pure Cn2 toxin and the whole venom from C. noxius in murine rescue experiments. These results demonstrated that under the conditions assayed here, P. pastoris is suited to produce scFv-6009FV that, compared to scFvs produced by E. coli, maintains the characteristics of an antibody and neutralizes the Cn2 toxin more effectively.
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Affiliation(s)
- Mariel Adame
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Hilda Vázquez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Daniel Juárez-López
- Instituto de Investigaciones Biomédicas, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Gerardo Corzo
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Mónica Amezcua
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Daniela López
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Zuriel González
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | | | - Adriana Morales-Martínez
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Elba Villegas
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México.
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Kim ED, Wu X, Lee S, Tibbs GR, Cunningham KP, Di Zanni E, Perez ME, Goldstein PA, Accardi A, Larsson HP, Nimigean CM. Propofol rescues voltage-dependent gating of HCN1 channel epilepsy mutants. Nature 2024:10.1038/s41586-024-07743-z. [PMID: 39085604 DOI: 10.1038/s41586-024-07743-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 06/20/2024] [Indexed: 08/02/2024]
Abstract
Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels1 are essential for pacemaking activity and neural signalling2,3. Drugs inhibiting HCN1 are promising candidates for management of neuropathic pain4 and epileptic seizures5. The general anaesthetic propofol (2,6-di-iso-propylphenol) is a known HCN1 allosteric inhibitor6 with unknown structural basis. Here, using single-particle cryo-electron microscopy and electrophysiology, we show that propofol inhibits HCN1 by binding to a mechanistic hotspot in a groove between the S5 and S6 transmembrane helices. We found that propofol restored voltage-dependent closing in two HCN1 epilepsy-associated polymorphisms that act by destabilizing the channel closed state: M305L, located in the propofol-binding site in S5, and D401H in S6 (refs. 7,8). To understand the mechanism of propofol inhibition and restoration of voltage-gating, we tracked voltage-sensor movement in spHCN channels and found that propofol inhibition is independent of voltage-sensor conformational changes. Mutations at the homologous methionine in spHCN and an adjacent conserved phenylalanine in S6 similarly destabilize closing without disrupting voltage-sensor movements, indicating that voltage-dependent closure requires this interface intact. We propose a model for voltage-dependent gating in which propofol stabilizes coupling between the voltage sensor and pore at this conserved methionine-phenylalanine interface in HCN channels. These findings unlock potential exploitation of this site to design specific drugs targeting HCN channelopathies.
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Affiliation(s)
- Elizabeth D Kim
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Xiaoan Wu
- Department of Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sangyun Lee
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Gareth R Tibbs
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Kevin P Cunningham
- Department of Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL, USA
- School of Life Sciences, University of Westminster, London, UK
| | - Eleonora Di Zanni
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Marta E Perez
- Department of Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Peter A Goldstein
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Alessio Accardi
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - H Peter Larsson
- Department of Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL, USA.
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA.
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Singh D, Mittal N, Mittal P, Tiwari N, Khan SUD, Ali MAM, Chaudhary AA, Siddiqui MH. In silico molecular screening of bioactive natural compounds of rosemary essential oil and extracts for pharmacological potentials against rhinoviruses. Sci Rep 2024; 14:17426. [PMID: 39075176 PMCID: PMC11286848 DOI: 10.1038/s41598-024-68450-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 07/23/2024] [Indexed: 07/31/2024] Open
Abstract
Rhinoviruses (RVs) cause upper respiratory tract infections and pneumonia in children and adults. These non-enveloped viruses contain viral coats of four capsid proteins: VP1, VP2, VP3, and VP4. The canyon on VP1 used cell surface receptor ICAM-1 as the site of attachment and for the internalization of viruses. To date, there has been no drug or vaccine available against RVs. In this study, bioactive natural compounds of rosemary (Salvia rosmarinus L.), which are known for their pharmacological potential, were considered to target the VP1 protein. A total of 30 bioactive natural compounds of rosemary were taken as ligands to target viral proteins. The PkCSM tool was used to detect their adherence to Lipinski's rule of five and the ADMET properties of the selected ligands. Further, the CB-Dock tool was used for molecular docking studies between the VP1 protein and ligands. Based on the molecular docking and ADMET profiling results, phenethyl amine (4 methoxy benzyl) was selected as the lead compound. A comparative study was performed between the lead compound and two antiviral drugs, Placonaril and Nitazoxanide, to investigate the higher potential of natural compounds over synthetic drugs. Placonaril also targets VP1 but failed in clinical trials while Nitazoxanide was examined in clinical trials against rhinoviruses. It was discovered from this study that the (4 methoxy benzyl) phenethyl amine exhibited less toxicity in comparison to other tested drugs against RVs. More research is needed to determine its potential and make it a good medication against RVs.
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Affiliation(s)
- Dhananjay Singh
- Department of Biosciences, Integral University, Kursi Road, Lucknow, 226026, India
| | - Nishu Mittal
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, 225003, India
| | - Pooja Mittal
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, 140401, India
| | - Neeraj Tiwari
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, 225003, India
| | - Salah Ud-Din Khan
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), 11623, Riyadh, Saudi Arabia
| | - Mohamed A M Ali
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), 11623, Riyadh, Saudi Arabia
- Department of Biochemistry, Faculty of Science, Ain Shams University, Abbassia, Cairo, 11566, Egypt
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), 11623, Riyadh, Saudi Arabia.
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Fan C, Basharat Z, Mah K, Wei CR. Computational approach for drug discovery against Gardnerella vaginalis in quest for safer and effective treatments for bacterial vaginosis. Sci Rep 2024; 14:17437. [PMID: 39075099 PMCID: PMC11286753 DOI: 10.1038/s41598-024-68443-2] [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: 05/20/2024] [Accepted: 07/23/2024] [Indexed: 07/31/2024] Open
Abstract
Bacterial vaginosis (BV), primarily attributed to Gardnerella vaginalis, poses significant challenges due to antibiotic resistance and suboptimal treatment outcomes. This study presents an integrated approach to identify potential drug targets and screen compounds against this bacterium by leveraging a computational methodology. Subtractive proteomics of the reference strain ASM286196v1/UMB0386 (assembly accession: GCA_002861965.1) facilitated the prioritization of proteins with essential bacterial functions and pathways as potential drug targets. We selected 3-deoxy-7-phosphoheptulonate synthase (aroG gene product; also known as DAHP synthase) for downstream analysis. Molecular docking was employed in PyRx (AutoDock Vina) to predict binding affinities between aroG inhibitors from the ZINC database and 3-deoxy-7-phosphoheptulonate synthase. Molecular dynamics simulations of 100 ns, using GROMACS, validated the stability of drug-target interactions. Additionally, ADMET profiling aided in the selection of compounds with favorable pharmacokinetic properties and safety profile for human hosts. PBPK profiling showed that ZINC98088375 had the highest bioavailability and efficient systemic circulation. Conversely, ZINC5113880 demonstrated the lowest absorption rate (39.661%). Moreover, cirrhosis, steatosis, and renal impairment appeared to influence blood concentration of the drug, impacting bioavailability. The integrative -omics approach utilized in this study underscores the potential of computer-aided drug design and offers a rational strategy for targeted inhibitor discovery against G. vaginalis. The strategy is an attempt to address the limitations of current BV treatments, including antibiotic resistance, and pave way for the development of safer and more effective therapeutics.
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Affiliation(s)
- Chenyue Fan
- Department of Research and Development, Shing Huei Group, Taipei, 10617, Taiwan
- College of Pharmacy, University of Arizona, Tuscon, AZ, 85721, USA
| | | | - Karmen Mah
- Department of Research and Development, Shing Huei Group, Taipei, 10617, Taiwan
| | - Calvin R Wei
- Department of Research and Development, Shing Huei Group, Taipei, 10617, Taiwan.
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Abdolmaleki S, Ganjalikhani hakemi M, Ganjalikhany MR. An in silico investigation on the binding site preference of PD-1 and PD-L1 for designing antibodies for targeted cancer therapy. PLoS One 2024; 19:e0304270. [PMID: 39052609 PMCID: PMC11271968 DOI: 10.1371/journal.pone.0304270] [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: 01/31/2024] [Accepted: 05/08/2024] [Indexed: 07/27/2024] Open
Abstract
Cancer control and treatment remain a significant challenge in cancer therapy and recently immune checkpoints has considered as a novel treatment strategy to develop anti-cancer drugs. Many cancer types use the immune checkpoints and its ligand, PD-1/PD-L1 pathway, to evade detection and destruction by the immune system, which is associated with altered effector function of PD-1 and PD-L1 overexpression on cancer cells to deactivate T cells. In recent years, mAbs have been employed to block immune checkpoints, therefore normalization of the anti-tumor response has enabled the scientists to develop novel biopharmaceuticals. In vivo affinity maturation of antibodies in targeted therapy has sometimes failed, and current experimental methods cannot accommodate the accurate structural details of protein-protein interactions. Therefore, determining favorable binding sites on the protein surface for modulator design of these interactions is a major challenge. In this study, we used the in silico methods to identify favorable binding sites on the PD-1 and PD-L1 and to optimize mAb variants on a large scale. At first, all the binding areas on PD-1 and PD-L1 have been identified. Then, using the RosettaDesign protocol, thousands of antibodies have been generated for 11 different regions on PD-1 and PD-L1 and then the designs with higher stability, affinity, and shape complementarity were selected. Next, molecular dynamics simulations and MM-PBSA analysis were employed to understand the dynamic, structural features of the complexes and measure the binding affinity of the final designs. Our results suggest that binding sites 1, 3 and 6 on PD-1 and binding sites 9 and 11 on PD-L1 can be regarded as the most appropriate sites for the inhibition of PD-1-PD-L1 interaction by the designed antibodies. This study provides comprehensive information regarding the potential binding epitopes on PD-1 which could be considered as hotspots for designing potential biopharmaceuticals. We also showed that mutations in the CDRs regions will rearrange the interaction pattern between the designed antibodies and targets (PD-1 and PD-L1) with improved affinity to effectively inhibit protein-protein interaction and block the immune checkpoint.
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Affiliation(s)
- Sarah Abdolmaleki
- Department of Cell and Molecular Biology & Microbiology, University of Isfahan, Isfahan, Iran
| | - Mazdak Ganjalikhani hakemi
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
- Department of Immunology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Idyahia A, Redouan S, Amalou G, Charoute H, Harmak H, Bonnet C, Petit C, Benrahma H, Barakat A. Exome sequencing reveals pathogenic mutations in the LARS2 and HSD17B4 genes associated with Perrault syndrome and D-bifunctional protein deficiency in Moroccan families. Mol Biol Rep 2024; 51:850. [PMID: 39052101 DOI: 10.1007/s11033-024-09740-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: 04/25/2024] [Accepted: 06/19/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Syndromic hearing loss (SHL) is characterized by hearing impairment accompanied by other clinical manifestations, reaching over 400 syndromes. Early and accurate diagnosis is essential to understand the progression of hearing loss and associated systemic complications. METHODS AND RESULTS In this study, we investigated the genetic etiology of sensorineural hearing loss in three Moroccan patients using whole exome sequencing (WES). The results revealed in two families Perrault syndrome caused by LARS2, p. Asn153His; p. Thr629Met compound heterozygous variants in two siblings in one family; and p. Thr522Asn, a homozygous variant in two sisters in another. The patient in the third family was diagnosed with D-bifunctional protein deficiency (D-BPD), linked to compound heterozygous mutations p. Asn457Tyr and p. Val643Argfs*5 in HSD17B4. Molecular dynamic simulation results showed that Val643Argfs*5 does not prevent HSD17B4 protein from binding to the PEX5 receptor, but further studies are recommended to verify its effect on HSD17B4 protein functionality. CONCLUSION These results highlight the effectiveness of WES in identifying pathogenic mutations involved in heterogeneous disorders and the usefulness of bioinformatics in predicting their effects on protein structure.
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Affiliation(s)
- Assia Idyahia
- Genomics and Human Genetics Laboratory, Institut Pasteur du Maroc, 1 Place Louis Pasteur, Casablanca, 20360, Morocco
- Interdisciplinary Laboratory of Biotechnology and Health, Mohammed VI Higher Institute of Biosciences and Biotechnology, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Salaheddine Redouan
- Genomics and Human Genetics Laboratory, Institut Pasteur du Maroc, 1 Place Louis Pasteur, Casablanca, 20360, Morocco
| | - Ghita Amalou
- Genomics and Human Genetics Laboratory, Institut Pasteur du Maroc, 1 Place Louis Pasteur, Casablanca, 20360, Morocco
| | - Hicham Charoute
- Research unit of epidemiology, biostatistics and bioinformatics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Houda Harmak
- Genomics and Human Genetics Laboratory, Institut Pasteur du Maroc, 1 Place Louis Pasteur, Casablanca, 20360, Morocco
| | - Crystel Bonnet
- Université Paris Cité, Institut Pasteur, AP-HP, Inserm, Fondation pour l'Audition, Institut de l'Audition, IHU reConnect, Paris, F-75012, France
| | - Christine Petit
- Université Paris Cité, Institut Pasteur, AP-HP, Inserm, Fondation pour l'Audition, Institut de l'Audition, IHU reConnect, Paris, F-75012, France
- Collège de France, Paris, F-75005, France
| | - Houda Benrahma
- Interdisciplinary Laboratory of Biotechnology and Health, Mohammed VI Higher Institute of Biosciences and Biotechnology, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Abdelhamid Barakat
- Genomics and Human Genetics Laboratory, Institut Pasteur du Maroc, 1 Place Louis Pasteur, Casablanca, 20360, Morocco.
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Safarzadeh Kozani P, Safarzadeh Kozani P, Rahbarizadeh F. Humanization of the antigen-recognition domain does not impinge on the antigen-binding, cytokine secretion, and antitumor reactivity of humanized nanobody-based CD19-redirected CAR-T cells. J Transl Med 2024; 22:679. [PMID: 39054481 PMCID: PMC11271212 DOI: 10.1186/s12967-024-05461-8] [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] [Received: 03/22/2024] [Accepted: 07/01/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND The immunogenicity of the antigen-recognition domains of chimeric antigen receptor (CAR)-T cells leads to immune responses that may compromise the antitumor effects of the adoptively transferred T cells. Herein, we attempt to humanize a CD19-specific VHH (named H85) using in silico techniques and investigate the impact of antigen-recognition domain humanization on CAR expression and density, cytokine secretion, and cytolytic reactivity of CAR-T cells based on the humanized VHH. METHODS H85 was humanized (named HuH85), and then HuH85 was compared with H85 in terms of conformational structure, physicochemical properties, antigenicity and immunogenicity, solubility, flexibility, stability, and CD19-binding capacity using in silico techniques. Next, H85CAR-T cells and HuH85CAR-T cells were developed and CAR expression and surface density were assessed via flow cytometry. Ultimately, the antitumor reactivity and secreted levels of IFN-γ, IL-2, and TNF-α were assessed following the co-cultivation of the CAR-T cells with Ramos, Namalwa, and K562 cells. RESULTS In silico findings demonstrated no negative impacts on HuH85 as a result of humanization. Ultimately, H85CAR and HuH85CAR could be surface-expressed on transduced T cells at comparable levels as assessed via mean fluorescence intensity. Moreover, H85CAR-T cells and HuH85CAR-T cells mediated comparable antitumor effects against Ramos and Namalwa cells and secreted comparable levels of IFN-γ, IL-2, and TNF-α following co-cultivation. CONCLUSION HuH85 can be used to develop immunotherapeutics against CD19-associated hematologic malignancies. Moreover, HuH85CAR-T cells must be further investigated in vitro and in preclinical xenograft models of CD19+ leukemias and lymphomas before advancing into clinical trials.
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Affiliation(s)
- Pooria Safarzadeh Kozani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran
| | - Pouya Safarzadeh Kozani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran.
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Guan Y, Mei J, Gao X, Wang C, Jia M, Ahmad S, Muhammad FN, Ai H. Prediction of the 3D conformation of a small peptide vaccine targeting Aβ42 oligomers. Phys Chem Chem Phys 2024; 26:20087-20102. [PMID: 39007924 DOI: 10.1039/d4cp02078b] [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: 07/16/2024]
Abstract
The original etiology of Alzheimer's disease (AD) is the deposition of amyloid-beta (Aβ) proteins, which starts from the aggregation of the Aβ oligomers. The optimal therapeutic strategy targeting Aβ oligomer aggregation is the development of AD vaccines. Despite the fact that positive progress has been made for experimental attempts at AD vaccines, the physicochemical and even structural properties of these AD vaccines remain unclear. In this study, through immunoinformatic and molecular dynamics (MD) simulations, we first designed and simulated an alternative of vaccine TAPAS and found that the structure of the alternative can reproduce the 3D conformation of TAPAS determined experimentally. Meanwhile, immunoinformatic methods were used to analyze the physicochemical properties of TAPAS, including immunogenicity, antigenicity, thermal stability, and solubility, which confirm well the efficacy and safety of the vaccine, and validate the scheme reliability of immunoinformatic and MD simulations in designing and simulating the TAPAS vaccine. Using the same scheme, we predicted the 3D conformation of the optimized ACI-24 peptide vaccine, an Aβ peptide with the first 15 residues of Aβ42 (Aβ1-15). The vaccine was verified once to be effective against both full-length Aβ1-42 and truncated Aβ4-42 aggregates, but an experimental 3D structure was absent. We have also explored the immune mechanism of the vaccine at the molecular level and found that the optimized ACI-24 and its analogues can block the growth of either full-length Aβ1-42 or truncated Aβ4-42 pentamer by contacting the hydrophobic residues within the N-terminus and β1 region on the contact surface of either pentamer. Additionally, residues (D1, D7, S8, H13, and Q15) were identified as the key residues of the vaccine to contact either of the two Aβ oligomers. This work provides a feasible implementation scheme of immunoinformatic and MD simulations for the development of AD small peptide vaccines, validating the power of the scheme as a parallel tool to the experimental approaches and injecting molecular-level information into the understanding and design of anti-AD vaccines.
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Affiliation(s)
- Yvning Guan
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China.
| | - Jinfei Mei
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China.
| | - Xvzhi Gao
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China.
| | - Chuanbo Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China.
| | - Mengke Jia
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China.
| | - Sajjad Ahmad
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China.
| | - Fahad Nouman Muhammad
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China.
| | - Hongqi Ai
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China.
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Sirirungruang S, Blay V, Scott YF, Pereira JH, Hammel M, Barnum CR, Adams PD, Shih PM. Structural and biochemical basis for regiospecificity of the flavonoid glycosyltransferase UGT95A1. J Biol Chem 2024:107602. [PMID: 39059496 DOI: 10.1016/j.jbc.2024.107602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/02/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Glycosylation is a predominant strategy plants employ to fine-tune the properties of small molecule metabolites to affect their bioactivity, transport, and storage. It is also important in biotechnology and medicine as many glycosides are utilized in human health. Small molecule glycosylation is largely carried out by family 1 glycosyltransferases. Here, we report a structural and biochemical investigation of UGT95A1, a family 1 GT enzyme from Pilosella officinarum that exhibits a strong, unusual regiospecificity for the 3'-O position of flavonoid acceptor substrate luteolin. We obtained an apo crystal structure to help drive the analyses of a series of binding site mutants, revealing that while most residues are tolerant to mutations, key residues M145 and D464 are important for overall glycosylation activity. Interestingly, E347 is crucial for maintaining the strong preference for 3'-O glycosylation, while R462 can be mutated to increase regioselectivity. The structural determinants of regioselectivity were further confirmed in homologous enzymes. Our study also suggests that the enzyme contains large, highly dynamic, disordered regions. We showed that while most disordered regions of the protein have little to no implication in catalysis, the disordered regions conserved among investigated homologues are important to both the overall efficiency and regiospecificity of the enzyme. This report represents a comprehensive in-depth analysis of a family 1 GT enzyme with a unique substrate regiospecificity and may provide a basis for enzyme functional prediction and engineering.
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Affiliation(s)
- Sasilada Sirirungruang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Vincent Blay
- Biofuels and Bioproducts Division, Joint BioEnergy Institute, Emeryville, CA, USA
| | - Yasmine F Scott
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Jose H Pereira
- Technology Division, Joint BioEnergy Institute, Emeryville, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Collin R Barnum
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, CA, University of California, Davis, CA, USA
| | - Paul D Adams
- Technology Division, Joint BioEnergy Institute, Emeryville, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Patrick M Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, CA, USA.
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Sharma N, Gupta M, Anand P, Akhter Y, Al-Dayan N, Majed HA, Biswas S, Ali S, Sarwat M. Mechanistic Insight into the Autophagic and Apoptotic Activity of Kaempferol on Liver Cancer Cells. Onco Targets Ther 2024; 17:579-601. [PMID: 39071955 PMCID: PMC11283267 DOI: 10.2147/ott.s460359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 07/08/2024] [Indexed: 07/30/2024] Open
Abstract
Background The accumulation of poorly folded protein in the endoplasmic reticulum (ER) promotes ER stress and contributes to the pathogenesis of hepatocellular carcinoma (HCC). Current therapies have various adverse effects, therefore, laying the need for an alternative approach. Kaempferol (KP), a naturally occurring flavonoid, possesses potent anti-proliferative properties against various cancer cells. Nevertheless, its involvement in HCC remains relatively unexplored, particularly regarding its influence on apoptosis and autophagy pathways. Methods The effect of KP on cell viability, and motility of Hep3B cells was evaluated by MTT, and scratch assay, respectively. Hoechst staining and FACS analysis were done to check the effect of KP on apoptosis and cell cycle progression. qRTPCR was used to evaluate the expression of several apoptosis and autophagy-related genes. KP was docked with several ER stress-related proteins involved in HCC to gain further insights into molecular mechanisms. The results of docking studies were validated with MD simulation and in vitro studies. Results Treatment with KP at different time intervals showed dose- and time-dependent growth inhibition of liver cancer cells. KP decreased motility and arrested the cell cycle at the G0/G1 phase in Hep3B cells. Additionally, in the context of HCC, the relationship between KP, apoptosis, and autophagy is significant. It induced apoptosis and autophagy in Hep3B cells by downregulating the expression of Bcl-2 and upregulated Bax and Bid, Caspase-3, Beclin-1, and LC3. KP showed a better binding affinity with Nrf2, PERK, and IRE1α among all selected proteins. Further, it reversed the protective effect of 4-PBA (ER Stress inhibitor) by inducing apoptosis and autophagy in Hep3B cells. Conclusion The study suggested KP as a potential chemopreventive agent for managing HCC by effectively inducing apoptosis and autophagy in Hep3B cells.
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Affiliation(s)
- Nidhi Sharma
- Amity Institute of Pharmacy, Amity University, Noida, Uttar Pradesh, 201301, India
| | - Meenakshi Gupta
- Amity Institute of Pharmacy, Amity University, Noida, Uttar Pradesh, 201301, India
| | - Pragya Anand
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Noura Al-Dayan
- Department of Medical Laboratory, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Hind Abdul Majed
- Department of Clinical Microbiology and Immunology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Subhrajit Biswas
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, Uttar Pradesh, 201301, India
| | - Sher Ali
- VC Office, Era University, Lucknow, Uttar Pradesh, 226003, India
| | - Maryam Sarwat
- Amity Institute of Pharmacy, Amity University, Noida, Uttar Pradesh, 201301, India
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Uribe C, Nery MF, Zavala K, Mardones GA, Riadi G, Opazo JC. Evolution of ion channels in cetaceans: a natural experiment in the tree of life. Sci Rep 2024; 14:17024. [PMID: 39043711 PMCID: PMC11266680 DOI: 10.1038/s41598-024-66082-1] [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: 05/08/2024] [Accepted: 06/26/2024] [Indexed: 07/25/2024] Open
Abstract
Cetaceans represent a natural experiment within the tree of life in which a lineage changed from terrestrial to aquatic habitats. This shift involved phenotypic modifications, representing an opportunity to explore the genetic bases of phenotypic diversity. Among the different molecular systems that maintain cellular homeostasis, ion channels are crucial for the proper physiological functioning of all living species. This study aims to explore the evolution of ion channels during the evolutionary history of cetaceans. To do so, we created a bioinformatic pipeline to annotate the repertoire of ion channels in the genome of the species included in our sampling. Our main results show that cetaceans have, on average, fewer protein-coding genes and a higher percentage of annotated ion channels than non-cetacean mammals. Signals of positive selection were detected in ion channels related to the heart, locomotion, visual and neurological phenotypes. Interestingly, we predict that the NaV1.5 ion channel of most toothed whales (odontocetes) is sensitive to tetrodotoxin, similar to NaV1.7, given the presence of tyrosine instead of cysteine, in a specific position of the ion channel. Finally, the gene turnover rate of the cetacean crown group is more than three times faster than that of non-cetacean mammals.
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Affiliation(s)
- Cristóbal Uribe
- Department of Bioinformatics, Program in Sciences Mention Modeling of Chemical and Biological Systems, School of Bioinformatics Engineering, Center for Bioinformatics, Simulation and Modeling, CBSM, Faculty of Engineering, University of Talca, Campus Talca, Talca, Chile
| | - Mariana F Nery
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas-UNICAMP, Cidade Universitária, Campinas, Brazil
| | - Kattina Zavala
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile
| | - Gonzalo A Mardones
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile
- Integrative Biology Group, Valdivia, Chile
| | - Gonzalo Riadi
- Department of Bioinformatics, Center for Bioinformatics, Simulation and Modeling, Faculty of Engineering, CBSM, University of Talca, Talca, Chile.
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile.
| | - Juan C Opazo
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile.
- Integrative Biology Group, Valdivia, Chile.
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile.
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Khanal M, Acharya A, Maharjan R, Gyawali K, Adhikari R, Mulmi DD, Lamichhane TR, Lamichhane HP. Identification of potent inhibitors of HDAC2 from herbal products for the treatment of colon cancer: Molecular docking, molecular dynamics simulation, MM/GBSA calculations, DFT studies, and pharmacokinetic analysis. PLoS One 2024; 19:e0307501. [PMID: 39037973 PMCID: PMC11262678 DOI: 10.1371/journal.pone.0307501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 07/06/2024] [Indexed: 07/24/2024] Open
Abstract
The histone deacetylase 2 (HDAC2), an enzyme involved in gene regulation, is a potent drug target for the treatment of colon cancer. Phytocompounds having anticancer properties show the ability to interact with HDAC2 enzyme. Among the compounds, docking scores of caffeic acid (CA) and p-coumaric acid (pCA) with HDAC2 showed good binding efficacy of -5.46 kcal/mol and -5.16 kcal/mol, respectively, with small inhibition constants. The higher binding efficacy of CA compared to pCA can be credited to the presence of an extra oxygen atom in the CA molecule, which forms an additional hydrogen bond with Tyr297. The HDAC2 in complex with these molecules was found to be stable by analyzing RMSD, RMSF, Rg, and SASA values obtained through MD simulations. Furthermore, CA and pCA exhibited low MM/GBSA free energies of -16.32 ± 2.62 kcal/mol and -17.01 ± 2.87 kcal/mol, respectively. The HOMO and LUMO energy gaps, dipole moments, global reactivity descriptor values, and MEP surfaces showed the reactivity of the molecules. The favourable physicochemical and pharmacokinetic properties, along with absence of toxicity of the molecules determined using ADMET analysis, suggested both the acids to be regarded as effective drugs in the treatment of colon cancer.
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Affiliation(s)
- Madan Khanal
- Central Department of Physics, Tribhuvan University, Kathmandu, Nepal
| | - Arjun Acharya
- Central Department of Physics, Tribhuvan University, Kathmandu, Nepal
| | - Rajesh Maharjan
- Central Department of Physics, Tribhuvan University, Kathmandu, Nepal
| | - Kalpana Gyawali
- Central Department of Physics, Tribhuvan University, Kathmandu, Nepal
| | - Rameshwar Adhikari
- Central Department of Chemistry, Tribhuvan University, Kathmandu, Nepal
- Research Center for Applied Science and Technology (RECAST), Tribhuvan University, Kathmandu, Nepal
| | - Deependra Das Mulmi
- Nanomaterials Research Laboratory, Nepal Academy of Science and Technology (NAST), Lalitpur, Nepal
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Varlı M, Kim E, Oh S, Pulat S, Zhou R, Gamage CDB, Gökalsın B, Sesal NC, Kim KK, Paik MJ, Kim H. Chrysophanol inhibits of colorectal cancer cell motility and energy metabolism by targeting the KITENIN/ErbB4 oncogenic complex. Cancer Cell Int 2024; 24:253. [PMID: 39030594 PMCID: PMC11264950 DOI: 10.1186/s12935-024-03434-x] [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: 01/24/2024] [Accepted: 07/04/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Expression of the KITENIN/ErbB4 oncogenic complex is associated with metastasis of colorectal cancer to distant organs and lymph nodes and is linked with poor prognosis and poor survival. METHODS Here, we used in vitro and in silico methods to test the ability of chrysophanol, a molecule of natural origin, to suppress the progression of colorectal cancer by targeting the KITENIN/ErbB4 complex. RESULTS Chrysophanol binds to ErbB4, disrupting the ErbB4/KITENIN complex and causing autophagic degradation of KITENIN. We demonstrated that chrysophanol binds to ErbB4 according to a molecular docking model. Chrysophanol reversed KITENIN-mediated effects on cell motility, aerobic glycolysis, and expression of downstream effector genes. Moreover, under conditions of KITENIN overexpression, chrysophanol suppressed the production of onco-metabolites. CONCLUSION Chrysophanol suppresses oncogenic activities by targeting the KITENIN/ErbB4 complex.
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Affiliation(s)
- Mücahit Varlı
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam, 57922, Republic of Korea
| | - Eunae Kim
- College of Pharmacy, Chosun University, 146 Chosundae-gil, Gwangju, 61452, Republic of Korea
| | - Songjin Oh
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam, 57922, Republic of Korea
| | - Sultan Pulat
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam, 57922, Republic of Korea
| | - Rui Zhou
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam, 57922, Republic of Korea
| | - Chathurika D B Gamage
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam, 57922, Republic of Korea
| | - Barış Gökalsın
- Faculty of Arts and Sciences, Department of Biology, Marmara University, Istanbul, Türkiye
| | - Nüzhet Cenk Sesal
- Faculty of Arts and Sciences, Department of Biology, Marmara University, Istanbul, Türkiye
| | - Kyung Keun Kim
- Department of Pharmacology, Chonnam National University Medical School, 160 Baekseoro, Gwangju, 61469, Republic of Korea
| | - Man-Jeong Paik
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam, 57922, Republic of Korea
| | - Hangun Kim
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam, 57922, Republic of Korea.
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Sklenicka J, Tran T, Ramirez MS, Donow HM, Magaña AJ, LaVoi T, Mamun Y, Jimenez V, Chapagain P, Santos R, Pinilla C, Giulianotti MA, Tolmasky ME. Structure-Activity Relationship of Pyrrolidine Pentamine Derivatives as Inhibitors of the Aminoglycoside 6'- N-Acetyltransferase Type Ib. Antibiotics (Basel) 2024; 13:672. [PMID: 39061354 PMCID: PMC11274322 DOI: 10.3390/antibiotics13070672] [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: 05/20/2024] [Revised: 07/09/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Resistance to amikacin and other major aminoglycosides is commonly due to enzymatic acetylation by the aminoglycoside 6'-N-acetyltransferase type I enzyme, of which type Ib [AAC(6')-Ib] is the most widespread among Gram-negative pathogens. Finding enzymatic inhibitors could be an effective way to overcome resistance and extend the useful life of amikacin. Small molecules possess multiple properties that make them attractive for drug development. Mixture-based combinatorial libraries and positional scanning strategy have led to the identification of a chemical scaffold, pyrrolidine pentamine, that, when substituted with the appropriate functionalities at five locations (R1-R5), inhibits AAC(6')-Ib-mediated inactivation of amikacin. Structure-activity relationship studies have shown that while truncations to the molecule result in loss of inhibitory activity, modifications of functionalities and stereochemistry have different effects on the inhibitory properties. In this study, we show that alterations at position R1 of the two most active compounds, 2700.001 and 2700.003, reduced inhibition levels, demonstrating the essential nature not only of the presence of an S-phenyl moiety at this location but also the distance to the scaffold. On the other hand, modifications on the R3, R4, and R5 positions had varied effects, demonstrating the potential for optimization. A correlation analysis between molecular docking values (ΔG) and the dose required for two-fold potentiation of the compounds described in this and the previous studies showed a significant correlation between ΔG values and inhibitory activity.
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Affiliation(s)
- Jan Sklenicka
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (J.S.); (T.T.); (M.S.R.); (A.J.M.); (V.J.)
| | - Tung Tran
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (J.S.); (T.T.); (M.S.R.); (A.J.M.); (V.J.)
| | - Maria S. Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (J.S.); (T.T.); (M.S.R.); (A.J.M.); (V.J.)
| | - Haley M. Donow
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA; (H.M.D.); (T.L.)
| | - Angel J. Magaña
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (J.S.); (T.T.); (M.S.R.); (A.J.M.); (V.J.)
| | - Travis LaVoi
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA; (H.M.D.); (T.L.)
| | - Yasir Mamun
- Department of Physics, Florida International University, Miami, FL 33199, USA; (Y.M.); (P.C.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Verónica Jimenez
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (J.S.); (T.T.); (M.S.R.); (A.J.M.); (V.J.)
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA; (Y.M.); (P.C.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Radleigh Santos
- Department of Mathematics, Nova Southeastern University, Fort Lauderdale, FL 33314, USA;
| | - Clemencia Pinilla
- Department of Medicinal Chemistry and Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA; (C.P.); (M.A.G.)
| | - Marc A. Giulianotti
- Department of Medicinal Chemistry and Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA; (C.P.); (M.A.G.)
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (J.S.); (T.T.); (M.S.R.); (A.J.M.); (V.J.)
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Pham C, Stogios PJ, Savchenko A, Mahadevan R. Design and Characterization of a Generalist Biosensor for Indole Derivatives. ACS Synth Biol 2024; 13:2246-2252. [PMID: 38875315 DOI: 10.1021/acssynbio.3c00736] [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] [Indexed: 06/16/2024]
Abstract
Transcription factor (TF)-based biosensors are useful synthetic biology tools for applications in a variety of areas of biotechnology. A major challenge of biosensor circuits is the limited repertoire of identified and well-characterized TFs for applications of interest, in addition to the challenge of optimizing selected biosensors. In this work, we implement the IclR family repressor TF TtgV from Pseudomonas putida DOT-T1E as an indole-derivative biosensor in Escherichia coli. We optimize the genetic circuit utilizing different components, providing insights into biosensor design and expanding on previous studies investigating this TF. We discover novel physiologically relevant ligands of TtgV, such as skatole. The broad specificity of TtgV makes it a useful target for directed evolution and protein engineering toward desired specificity. TtgV, as an indole-derivative biosensor, is a promising genetic component for the detection of compounds with biological activities relevant to health and the gut microbiome.
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Affiliation(s)
- Chester Pham
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
- The Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3H7, Canada
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Muñoz Sosa CJ, Lenz C, Hamann A, Farges F, Dopfer J, Krämer A, Cherkashyna V, Tarnovskiy A, Moroz YS, Proschak E, Němec V, Müller S, Saxena K, Knapp S. A C-Degron Structure-Based Approach for the Development of Ligands Targeting the E3 Ligase TRIM7. ACS Chem Biol 2024; 19:1638-1647. [PMID: 38934237 DOI: 10.1021/acschembio.4c00301] [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: 06/28/2024]
Abstract
TRIM7 is a ubiquitin E3 ligase with key regulatory functions, mediating viral infection, tumor biology, innate immunity, and cellular processes, such as autophagy and ferroptosis. It contains a PRYSPRY domain that specifically recognizes degron sequences containing C-terminal glutamine. Ligands that bind to the TRIM7 PRYSPRY domain may have applications in the treatment of viral infections, as modulators of inflammation, and in the design of a new class of PROTACs (PROteolysis TArgeting Chimeras) that mediate the selective degradation of therapeutically relevant proteins (POIs). Here, we developed an assay toolbox for the comprehensive evaluation of TRIM7 ligands. Using TRIM7 degron sequences together with a structure-based design, we developed the first series of peptidomimetic ligands with low micromolar affinity. The terminal carboxylate moiety was required for ligand activity but prevented cell penetration. A prodrug strategy using an ethyl ester resulted in enhanced permeability, which was evaluated using confocal imaging.
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Affiliation(s)
- Christian J Muñoz Sosa
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences (BMLS), Johann Wolfgang Goethe-University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Christopher Lenz
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences (BMLS), Johann Wolfgang Goethe-University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Anton Hamann
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences (BMLS), Johann Wolfgang Goethe-University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Frederic Farges
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences (BMLS), Johann Wolfgang Goethe-University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Johannes Dopfer
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences (BMLS), Johann Wolfgang Goethe-University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Andreas Krämer
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences (BMLS), Johann Wolfgang Goethe-University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | | | | | - Yurii S Moroz
- Enamine Ltd., Winston Churchill Street 78, 02094 Kyïv, Ukraine
- Taras Shevchenko National University of Kyïv, Volodymyrska Street 60, Kyïv 01601, Ukraine
| | - Ewgenij Proschak
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Václav Němec
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences (BMLS), Johann Wolfgang Goethe-University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences (BMLS), Johann Wolfgang Goethe-University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Krishna Saxena
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences (BMLS), Johann Wolfgang Goethe-University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences (BMLS), Johann Wolfgang Goethe-University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
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Tak H, Anirudh J, Chattopadhyay A, Naick BH. Argonaute protein assisted drug discovery for miRNA-181c-5p and target gene ATM translation repression: a computational approach. Mol Divers 2024:10.1007/s11030-024-10855-3. [PMID: 39026118 DOI: 10.1007/s11030-024-10855-3] [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: 12/26/2023] [Accepted: 03/21/2024] [Indexed: 07/20/2024]
Abstract
The miRNA binds to AGO's seed region, prompting the exploration of small molecules that can offset miRNA repression of target mRNA. This miRNA-181c-5p was found to be upregulated in the chronic traumatic encephalopathy, a prevalent neurodegenerative disease in contact sports and military personals. The research aimed to identify compounds that disrupt the AGO-assisted loop formation between miRNA-181c-5p and ATM, consequently repressing the translation of ATM. Target genes from commonly three databases (DIANA-microT-CDS, miRDB, RNA22 and TargetScan) were subjected to functional annotation and clustering analysis using DAVID bioinformatics tool. Haddock server were employed to make miRNA-181c-5p:ATM-AGO complex. A total of 2594 small molecules were screened using Glide XP based on their highest binding affinity towards the complex, through a three-phase docking approach. The top 5 compounds (DB00674-Galantamine, DB00371-Meprobamate, DB00694-Daunorubicin, DB00837-Progabide, and DB00851-Dacarbazine) were further analyzed for stability in the miRNA-181c-5p:ATM-AGO-ligand complex interaction using GROMACS (version 2023.2). Hence, these findings suggest that these molecules hold potential for facilitating AGO-assisted repression of ATM gene translation.
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Affiliation(s)
- Harshita Tak
- Department of Sports Biosciences, School of Sports Science, Central University of Rajasthan, Ajmer, India
| | - Jivanage Anirudh
- Department of Sports Biosciences, School of Sports Science, Central University of Rajasthan, Ajmer, India
| | - Arpan Chattopadhyay
- Department of Sports Biosciences, School of Sports Science, Central University of Rajasthan, Ajmer, India
| | - B Hemanth Naick
- Department of Sports Biosciences, School of Sports Science, Central University of Rajasthan, Ajmer, India.
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Agbavor C, Zimnicka A, Kumar A, George JL, Torres M, Prehna G, Alonzo F, Durrant JD, Freitag NE, Cahoon LA. The chaperone PrsA2 regulates the secretion, stability, and folding of listeriolysin O during Listeria monocytogenes infection. mBio 2024; 15:e0074324. [PMID: 38809022 PMCID: PMC11253611 DOI: 10.1128/mbio.00743-24] [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: 03/10/2024] [Accepted: 04/22/2024] [Indexed: 05/30/2024] Open
Abstract
Pathogenic bacteria rely on secreted virulence factors to cause disease in susceptible hosts. However, in Gram-positive bacteria, the mechanisms underlying secreted protein activation and regulation post-membrane translocation remain largely unknown. Using proteomics, we identified several proteins that are dependent on the secreted chaperone PrsA2. We followed with phenotypic, biochemical, and biophysical assays and computational analyses to examine the regulation of a detected key secreted virulence factor, listeriolysin O (LLO), and its interaction with PrsA2 from the bacterial pathogen Listeria monocytogenes (Lm). Critical to Lm virulence is internalization by host cells and the subsequent action of the cholesterol-dependent pore-forming toxin, LLO, which enables bacterial escape from the host cell phagosome. Since Lm is a Gram-positive organism, the space between the cell membrane and wall is solvent exposed. Therefore, we hypothesized that the drop from neutral to acidic pH as the pathogen is internalized into a phagosome is critical to regulating the interaction of PrsA2 with LLO. Here, we demonstrate that PrsA2 directly interacts with LLO in a pH-dependent manner. We show that PrsA2 protects and sequesters LLO under neutral pH conditions where LLO can be observed to aggregate. In addition, we identify molecular features of PrsA2 that are required for interaction and ultimately the folding and activity of LLO. Moreover, protein-complex modeling suggests that PrsA2 interacts with LLO via its cholesterol-binding domain. These findings highlight a mechanism by which a Gram-positive secretion chaperone regulates the secretion, stability, and folding of a pore-forming toxin under conditions relevant to host cell infection. IMPORTANCE Lm is a ubiquitous food-borne pathogen that can cause severe disease to vulnerable populations. During infection, Lm relies on a wide repertoire of secreted virulence factors including the LLO that enables the bacterium to invade the host and spread from cell to cell. After membrane translocation, secreted factors must become active in the challenging bacterial cell membrane-wall interface. However, the mechanisms required for secreted protein folding and function are largely unknown. Lm encodes a chaperone, PrsA2, that is critical for the activity of secreted factors. Here, we show that PrsA2 directly associates and protects the major Lm virulence factor, LLO, under conditions corresponding to the host cytosol, where LLO undergoes irreversible denaturation. Additionally, we identify molecular features of PrsA2 that enable its interaction with LLO. Together, our results suggest that Lm and perhaps other Gram-positive bacteria utilize secreted chaperones to regulate the activity of pore-forming toxins during infection.
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Affiliation(s)
- Charles Agbavor
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Adriana Zimnicka
- Department of Pharmaceutical Sciences, University of Illinois Chicago, Chicago, Illinois, USA
| | - Allison Kumar
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jada L. George
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Madeline Torres
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Gerd Prehna
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Francis Alonzo
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Jacob D. Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Nancy E. Freitag
- Department of Pharmaceutical Sciences, University of Illinois Chicago, Chicago, Illinois, USA
| | - Laty A. Cahoon
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Gonçalves G, da Silva MS, dos Santos LA, Guimarães TZ, Taveira GB, Almeida FA, Ferreira SR, Amancio Oliveira AE, Nagano CS, Chaves RP, Silveira V, de Oliveira Carvalho A, Rodrigues R, Gomes VM. Structural and Functional Characterization of New Lipid Transfer Proteins with Chitin-Binding Properties: Insights from Protein Structure Prediction, Molecular Docking, and Antifungal Activity. Biochemistry 2024; 63:1824-1836. [PMID: 38968244 PMCID: PMC11256766 DOI: 10.1021/acs.biochem.4c00124] [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: 03/08/2024] [Revised: 06/07/2024] [Accepted: 06/20/2024] [Indexed: 07/07/2024]
Abstract
Faced with the emergence of multiresistant microorganisms that affect human health, microbial agents have become a serious global threat, affecting human health and plant crops. Antimicrobial peptides have attracted significant attention in research for the development of new microbial control agents. This work's goal was the structural characterization and analysis of antifungal activity of chitin-binding peptides from Capsicum baccatum and Capsicum frutescens seeds on the growth of Candida and Fusarium species. Proteins were initially submitted to extraction in phosphate buffer pH 5.4 and subjected to chitin column chromatography. Posteriorly, two fractions were obtained for each species, Cb-F1 and Cf-F1 and Cb-F2 and Cf-F2, respectively. The Cb-F1 (C. baccatum) and Cf-F1 (C. frutescens) fractions did not bind to the chitin column. The electrophoresis results obtained after chromatography showed two major protein bands between 3.4 and 14.2 kDa for Cb-F2. For Cf-F2, three major bands were identified between 6.5 and 14.2 kDa. One band from each species was subjected to mass spectrometry, and both bands showed similarity to nonspecific lipid transfer protein. Candida albicans and Candida tropicalis had their growth inhibited by Cb-F2. Cf-F2 inhibited the development of C. albicans but did not inhibit the growth of C. tropicalis. Both fractions were unable to inhibit the growth of Fusarium species. The toxicity of the fractions was tested in vivo on Galleria mellonella larvae, and both showed a low toxicity rate at high concentrations. As a result, the fractions have enormous promise for the creation of novel antifungal compounds.
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Affiliation(s)
- Gabriella
Rodrigues Gonçalves
- Laboratório
de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências
e Biotecnologia, Universidade Estadual do
Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Marciele Souza da Silva
- Laboratório
de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências
e Biotecnologia, Universidade Estadual do
Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Layrana Azevedo dos Santos
- Laboratório
de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências
e Biotecnologia, Universidade Estadual do
Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Thomas Zacarone
Afonso Guimarães
- Laboratório
de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências
e Biotecnologia, Universidade Estadual do
Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Gabriel Bonan Taveira
- Laboratório
de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências
e Biotecnologia, Universidade Estadual do
Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Felipe Astolpho Almeida
- Laboratório
de Química e Função de Proteínas e Peptídeos,
Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602 Campos
dos Goytacazes, RJ, Brazil
| | - Sarah Rodrigues Ferreira
- Laboratório
de Química e Função de Proteínas e Peptídeos,
Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602 Campos
dos Goytacazes, RJ, Brazil
| | - Antonia Elenir Amancio Oliveira
- Laboratório
de Química e Função de Proteínas e Peptídeos,
Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602 Campos
dos Goytacazes, RJ, Brazil
| | - Celso Shiniti Nagano
- Laboratório
de Bioquímica Marinha (BioMar-Lab), Departamento de Engenharia
de Pesca, Universidade Federal do Ceará
(UFC), 60455-900 Fortaleza, Ceará, Brazil
| | - Renata Pinheiro Chaves
- Laboratório
de Bioquímica Marinha (BioMar-Lab), Departamento de Engenharia
de Pesca, Universidade Federal do Ceará
(UFC), 60455-900 Fortaleza, Ceará, Brazil
| | - Vanildo Silveira
- Laboratório
de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, 28013-602 RJ, Brazil
| | - André de Oliveira Carvalho
- Laboratório
de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências
e Biotecnologia, Universidade Estadual do
Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Rosana Rodrigues
- Laboratório
de Melhoramento e Genética Vegetal, Centro de Ciências
e Tecnologias Agropecuárias, Universidade
Estadual do Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Valdirene Moreira Gomes
- Laboratório
de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências
e Biotecnologia, Universidade Estadual do
Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
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50
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Shrivastava S, Bahuguna T, Mondal S, Kumar S, Mathew B, Jeengar MK, Naidu VGM. Attenuation of adjuvant-induced arthritis with carnosic acid by inhibiting mPGES-1, COX-2, and bone loss in male SD rats. Immunopharmacol Immunotoxicol 2024:1-12. [PMID: 39013842 DOI: 10.1080/08923973.2024.2377984] [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: 01/10/2024] [Accepted: 07/04/2024] [Indexed: 07/18/2024]
Abstract
OBJECTIVE Rheumatoid arthritis (RA), a chronic inflammatory disease, is characterized by joint swelling, cartilage erosion, and bone destruction. This study investigated the therapeutic efficacy of Carnosic acid (CA), a natural compound with anti-inflammatory and antioxidant properties, in an adjuvant-induced arthritis model. METHODS Paw swelling and arthritis index were measured. Oxidative stress markers, including lipid peroxidation and antioxidant enzyme levels, were assessed. Synovial tissue was analyzed for pro-inflammatory markers using real-time Q-PCR and Western blotting. The expression of mPGES-1 was determined by Western blotting. Peripheral neuropathic pain was assessed using cold and mechanical allodynia tests. Bone loss was quantitatively assessed through microcomputed tomography (μCT) scanning of femurs and X-ray radiography. Indomethacin-induced gastric ulcers were evaluated. Molecular docking studies were conducted to analyze the binding affinity of CA to mPGES-1. RESULTS The CA treatment not only demonstrated a significant reduction in joint inflammation and paw swelling but also mitigated oxidative stress and improved the antioxidant defence system. CA inhibited microsomal prostaglandin E synthase-1 (mPGES-1) expression and the expression of pro-inflammatory molecules such as inducible nitric oxide synthase (iNOS) and cyclooxygenases-2 (COX-2), thus attenuating the arthritis symptoms without severe gastrointestinal side effects. Additionally, it inhibited the expression of pro-inflammatory molecules such as iNOS and COX-2, contributing to the reduction of arthritis symptoms. Notably, CA treatment prevented the common side effects of traditional RA treatments like corticosteroids and non-steroidal anti-inflammatory drugs (NSAIDs), including weight loss, bone degradation, and gastric ulcers. CONCLUSIONS These findings suggest that CA, through specific enzyme inhibition, offers a compelling alternative therapeutic approach for RA. Further research is warranted to explore the potential of CA in other arthritis models and its suitability for human RA treatment.
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Affiliation(s)
- Shweta Shrivastava
- School of Pharmacy, School of Health and Allied Sciences, ARKA JAIN University, Gamharia, Seraikela Kharsawan, Jharkhand, India
| | - Tribhuwan Bahuguna
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education & Research Institute (NIPER), Balanagar, Hyderabad, India
| | - Sudipto Mondal
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education & Research Institute (NIPER), Balanagar, Hyderabad, India
| | - Sunil Kumar
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
| | - Manish Kumar Jeengar
- Department of Pharmacology, Amrita School of Pharmacy, AIMS Health Sciences Campus, Kochi, Kerala, India
| | - V G M Naidu
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education & Research Institute (NIPER), Assam, India
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