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Nie J, Jiang X, Wang G, Xu Y, Pan R, Yu W, Li Y, Wang J. Yu-Ping-Feng-San alleviates inflammation in atopic dermatitis mice by TLR4/MyD88/NF-κB pathway. J Ethnopharmacol 2024; 329:118092. [PMID: 38604509 DOI: 10.1016/j.jep.2024.118092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/11/2024] [Accepted: 03/20/2024] [Indexed: 04/13/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Yu-Ping-Feng-San (YPF) is a traditional Chinese medicine formula that has therapeutic effects on allergic diseases such as allergic rhinitis and asthma. However, its potential efficacy and mechanism in the treatment of atopic dermatitis (AD) has not been extensively illustrated. AIM OF THE STUDY The purpose of this study was to investigate the efficacy and possible mechanisms of YPF in AD pathogenesis. METHODS Network pharmacology and GEO data mining were adopted to firstly identify the potential mechanisms of YPF on AD. Then DNCB induced-AD murine model was established to test the efficacy of YPF and verify its effects on inflammatory cytokines and NF-κB pathway. In addition, molecular docking was performed to detect the binding affinity of YPF's active components with NF-κB pathway related molecules. RESULTS Network pharmacology and human data mining suggested that YPF may act on the NF-κB pathway in AD pathogenesis. With DNCB mice model, we found that YPF significantly improved AD symptoms, reduced SCORAD scores, and alleviated skin tissue inflammation in mice. At the same time, the expression of inflammatory cytokines, TNF-α, sPLA2-IIA and IL-6, was down-regulated. Moreover, YPF suppressed TLR4/MyD88/NF-κB pathway in situ in a dose-dependent manner. Molecular docking further confirmed that seven compounds in YPF had exceptional binding properties with TNF-α, IL-6 and TLR4. CONCLUSION YPF may help the recovery of AD by inhibiting the TLR4/MyD88/NF-κB pathway, which provides novel insights for the treatment of AD by YPF.
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Affiliation(s)
- Jing Nie
- Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China; Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, China.
| | - Xiaoyuan Jiang
- FangShan Hospital, Beijing University of Chinese Medicine, Beijing, China.
| | - Guomi Wang
- Shanghai Skin Disease Hospital, Institute of Dermatology, School of Medicine, Tongji University, Shanghai, China.
| | - Yanan Xu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China.
| | - Rui Pan
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China.
| | - Wantao Yu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China.
| | - Yuanwen Li
- Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China.
| | - Jingxiao Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China.
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Sultana T, Mou SI, Chatterjee D, Faruk MO, Hosen MI. Computational exploration of SLC14A1 genetic variants through structure modeling, protein-ligand docking, and molecular dynamics simulation. Biochem Biophys Rep 2024; 38:101703. [PMID: 38596408 PMCID: PMC11001776 DOI: 10.1016/j.bbrep.2024.101703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024] Open
Abstract
The urea transporter UT-B1, encoded by the SLC14A1 gene, has been hypothesized to be a significant protein whose deficiency and dysfunction contribute to the pathogenesis of bladder cancer and many other diseases. Several studies reported the association of genetic alterations in the SLC14A1 (UT-B1) gene with bladder carcinogenesis, suggesting a need for thorough characterization of the UT-B1 protein's coding and non-coding variants. This study used various computational techniques to investigate the commonly occurring germ-line missense and non-coding SNPs (ncSNPs) of the SLC14A1 gene (UT-B1) for their structural, functional, and molecular implications for disease susceptibility and dysfunctionality. SLC14A1 missense variants, primarily identified from the ENSEMBL genome browser, were screened through twelve functionality prediction tools leading to two variants D280Y (predicted detrimental by maximum tools) and D280N (high global MAF) for rs1058396. Subsequently, the ConSurf and NetSurf tools revealed the D280 residue to be in a variable site and exposed on the protein surface. According to I-Mutant2.0 and MUpro, both variants are predicted to cause a significant effect on protein stability. Analysis of molecular docking anticipated these two variants to decrease the binding affinity of UT-B1 protein for the examined ligands to a significant extent. Molecular dynamics also disclosed the possible destabilization of the UT-B1 protein due to single nucleotide polymorphism compared to wild-type protein which may result in impaired protein function. Furthermore, several non-coding SNPs were estimated to affect transcription factor binding and regulation of SLC14A1 gene expression. Additionally, two ncSNPs were found to affect miRNA-based post-transcriptional regulation by creating new seed regions for miRNA binding. This comprehensive in-silico study of SLC14A1 gene variants may serve as a springboard for future large-scale investigations examining SLC14A1 polymorphisms.
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Affiliation(s)
- Tamanna Sultana
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Sadia Islam Mou
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Dipankor Chatterjee
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Md. Omar Faruk
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Md. Ismail Hosen
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
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Shahzadi Z, Yousaf Z, Anjum I, Bilal M, Yasin H, Aftab A, Booker A, Ullah R, Bari A. Network pharmacology and molecular docking: combined computational approaches to explore the antihypertensive potential of Fabaceae species. BIORESOUR BIOPROCESS 2024; 11:53. [PMID: 38767701 PMCID: PMC11106056 DOI: 10.1186/s40643-024-00764-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/26/2024] [Indexed: 05/22/2024] Open
Abstract
Hypertension is a major global public health issue, affecting quarter of adults worldwide. Numerous synthetic drugs are available for treating hypertension; however, they often come with a higher risk of side effects and long-term therapy. Modern formulations with active phytoconstituents are gaining popularity, addressing some of these issues. This study aims to discover novel antihypertensive compounds in Cassia fistula, Senna alexandrina, and Cassia occidentalis from family Fabaceae and understand their interaction mechanism with hypertension targeted genes, using network pharmacology and molecular docking. Total 414 compounds were identified; initial screening was conducted based on their pharmacokinetic and ADMET properties, with a particular emphasis on adherence to Lipinski's rules. 6 compounds, namely Germichrysone, Benzeneacetic acid, Flavan-3-ol, 5,7,3',4'-Tetrahydroxy-6, 8-dimethoxyflavon, Dihydrokaempferol, and Epiafzelechin, were identified as effective agents. Most of the compounds found non-toxic against various indicators with greater bioactivity score. 161 common targets were obtained against these compounds and hypertension followed by compound-target network construction and protein-protein interaction, which showed their role in diverse biological system. Top hub genes identified were TLR4, MMP9, MAPK14, AKT1, VEGFA and HSP90AA1 with their respective associates. Higher binding affinities was found with three compounds Dihydrokaempferol, Flavan-3-ol and Germichrysone, -7.1, -9.0 and -8.0 kcal/mol, respectively. The MD simulation results validate the structural flexibility of two complexes Flavan-MMP9 and Germich-TLR4 based on no. of hydrogen bonds, root mean square deviations and interaction energies. This study concluded that C. fistula (Dihydrokaempferol, Flavan-3-ol) and C. occidentalis (Germichrysone) have potential therapeutic active constituents to treat hypertension and in future novel drug formulation.
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Affiliation(s)
- Zainab Shahzadi
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Zubaida Yousaf
- Department of Botany, Lahore College for Women University, Lahore, Pakistan.
| | - Irfan Anjum
- Department of Basic Medical Sciences, Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Muhammad Bilal
- Centers for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Hamna Yasin
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Arusa Aftab
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Anthony Booker
- Research Centre for Optimal Health, School of Life Sciences, College of Liberal Arts and Sciences, University of Westminster, 115 New Cavendish Street, London, W1W 6UW, UK.
- Research Group 'Pharmacognosy and Phytotherapy', UCL School of Pharmacy, Univ. London, 29 - 39 Brunswick Sq., London, WC1N 1AX, UK.
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy King, Saud University, Riyadh, Saudi Arabia
| | - Ahmed Bari
- Department of Pharmaceutical Chemistry, College of Pharmacy King, Saud University, Riyadh, Saudi Arabia
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Cao J, Xiang B, Dou B, Hu J, Zhang L, Kang X, Lyu M, Wang S. Novel Angiotensin-Converting Enzyme-Inhibitory Peptides Obtained from Trichiurus lepturus: Preparation, Identification and Potential Antihypertensive Mechanism. Biomolecules 2024; 14:581. [PMID: 38785988 DOI: 10.3390/biom14050581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Peptides possessing antihypertensive attributes via inhibiting the angiotensin-converting enzyme (ACE) were derived through the enzymatic degradation of Trichiurus lepturus (ribbonfish) using alkaline protease. The resulting mixture underwent filtration using centrifugation, ultrafiltration tubes, and Sephadex G-25 gels. Peptides exhibiting ACE-inhibitory properties and DPPH free-radical-scavenging abilities were isolated and subsequently purified via LC/MS-MS, leading to the identification of over 100 peptide components. In silico screening yielded five ACE inhibitory peptides: FAGDDAPR, QGPIGPR, IFPRNPP, AGFAGDDAPR, and GPTGPAGPR. Among these, IFPRNPP and AGFAGDDAPR were found to be allergenic, while FAGDDAPRR, QGPIGPR, and GPTGPAGP showed good ACE-inhibitory effects. IC50 values for the latter peptides were obtained from HUVEC cells: FAGDDAPRR (IC50 = 262.98 μM), QGPIGPR (IC50 = 81.09 μM), and GPTGPAGP (IC50 = 168.11 μM). Peptide constituents derived from ribbonfish proteins effectively modulated ACE activity, thus underscoring their therapeutic potential. Molecular docking and modeling corroborated these findings, emphasizing the utility of functional foods as a promising avenue for the treatment and prevention of hypertension, with potential ancillary health benefits and applications as substitutes for synthetic drugs.
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Affiliation(s)
- Jiaming Cao
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Boyuan Xiang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Baojie Dou
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Jingfei Hu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Lei Zhang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xinxin Kang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Mingsheng Lyu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Shujun Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
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Singha S, Das Gupta B, Sarkar A, Jana S, Bharadwaj PK, Sharma N, Haldar PK, Mukherjee PK, Kar A. Chemo-profiling and exploring therapeutic potential of Momordica dioica Roxb. ex Willd. for managing metabolic related disorders: In-vitro studies, and docking based approach. J Ethnopharmacol 2024; 331:118351. [PMID: 38759763 DOI: 10.1016/j.jep.2024.118351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/22/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Momordica dioica Roxb. ex Willd. (M. dioica Roxb.) a nutritious and therapeutic property rich crop of Cucurbitaceae plant family. In various folklore medicine including Ayurveda fruits are used to treat several metabolic related disorders i.e., hyperglycemia, hyperlipidemia, diabetes, obesity etc. Furthermore, traditionally it is used to treat fever, inflammation, ulcer, skin diseases, haemorrhoids, hypertension and also employed as cardioprotective, hepatoprotective, analgesic, diuretic. AIM OF THE STUDY This study focuses to explore the therapeutic potential of Momordica dioica Roxb. ex Willd. through in-vitro and in-silico approach for managing hyperlipidemia, hyperglycemia and related metabolic disorders along with its phytochemical profiling for quality evaluation and validation of traditional claim. MATERIALS AND METHODS The present study was carried out on hydroalcohol extract of dried leaf and fruit of Momordica dioica. In-vitro antioxidant potential using DPPH and Nitric oxide scavenging assay along with in-vitro enzyme inhibitory potential against α-amylase, α-glucosidase, and pancreatic lipase enzymes was studied. The bioactive metabolites were identified from the most potent bioactive extract by analysis with LC-QTOF-MS and also studied their role to lessen the metabolic related disorder through in-silico approaches. RESULTS The results confirmed that the fruit extract is more active to possess antioxidant and prominent enzyme inhibition potential compared to the leaf. Sixteen identified metabolites in M. dioica Roxb. fruits may be responsible for the therapeutic potential related to metabolic related disorder. The in-silico study of the identified phytomolecules against α-amylase, α-glucosidase and pancreatic lipase showed significant docking scores ranging from -9.8 to -5.5, -8.3 to -4.8 and -8.3 to -6 respectively. CONCLUSION The current study illustrated that M. dioica Roxb., a traditionally important plant is potential against metabolic related disorders. Phytocomponents present in the fruit extract may be responsible for antioxidant as well as the enzymes' inhibitory potential. Thus, fruits of M. dioica Roxb. will be useful as alternative therapeutics for treatment of hyperlipidemia, hyperglycemia and related metabolic disorders.
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Affiliation(s)
- Seha Singha
- School of Natural Product Studies, Jadavpur University, Kolkata, 700 032, India.
| | - Barun Das Gupta
- School of Natural Product Studies, Jadavpur University, Kolkata, 700 032, India.
| | - Arnab Sarkar
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700 032, India.
| | - Sandipan Jana
- School of Natural Product Studies, Jadavpur University, Kolkata, 700 032, India.
| | - Pardeep K Bharadwaj
- Institute of Bioresources and Sustainable Development, Dept. of Biotechnology, Govt. of India, Imphal, Manipur, 795001, India.
| | - Nanaocha Sharma
- Institute of Bioresources and Sustainable Development, Dept. of Biotechnology, Govt. of India, Imphal, Manipur, 795001, India.
| | - Pallab K Haldar
- School of Natural Product Studies, Jadavpur University, Kolkata, 700 032, India.
| | - Pulok Kumar Mukherjee
- School of Natural Product Studies, Jadavpur University, Kolkata, 700 032, India; Institute of Bioresources and Sustainable Development, Dept. of Biotechnology, Govt. of India, Imphal, Manipur, 795001, India.
| | - Amit Kar
- Institute of Bioresources and Sustainable Development, Dept. of Biotechnology, Govt. of India, Imphal, Manipur, 795001, India.
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Mohammed YHI, Shamkh IM, Shntaif AH, Sufyan M, Rehman MT, AlAjmi MF, Shahwan M, Alghamdi S, Abd El-Lateef AE, Khidir EB, Abouzied AS, Khalifa NE, A Khojali WM, Huwaimel B, Al Farraj DA, Almutairi SM. Synthesis and evaluation of pyridine-3-carboxamide analogs as effective agents against bacterial wilt in tomatoes. Sci Rep 2024; 14:11118. [PMID: 38750062 PMCID: PMC11096348 DOI: 10.1038/s41598-024-59609-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 04/12/2024] [Indexed: 05/18/2024] Open
Abstract
This study focused on developing novel pyridine-3-carboxamide analogs to treat bacterial wilt in tomatoes caused by Ralstonia solanacearum. The analogs were synthesized through a multistep process and their structures confirmed using spectroscopy. Molecular docking studies identified the most potent analog from the series. A specific analog, compound 4a, was found to significantly enhance disease resistance in tomato plants infected with R. solanacearum. The structure-activity relationship analysis showed the positions and types of substituents on the aromatic rings of compounds 4a-i strongly influenced their biological activity. Compound 4a, with a chloro group at the para position on ring C and hydroxyl group at the ortho position on ring A, was exceptionally effective against R. solanacearum. When used to treat seeds, the analogs displayed remarkable efficacy, especially compound 4a which had specific activity against bacterial wilt pathogens. Compound 4a also promoted vegetative and reproductive growth of tomato plants, increasing seed germination and seedling vigor. In plants mechanically infected with bacteria, compound 4a substantially reduced the percentage of infection, pathogen quantity in young tissue, and disease progression. The analogs were highly potent due to their amide linkage. Molecular docking identified the best compounds with strong binding affinities. Overall, the strategic design and synthesis of these pyridine-3-carboxamide analogs offers an effective approach to targeting and controlling R. solanacearum and bacterial wilt in tomatoes.
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Affiliation(s)
- Yasser Hussein Issa Mohammed
- Department of Biochemistry, Faculty of Applied Science, University of Hajjah, Hajjah, Yemen.
- Department of Pharmacy, Faculty of Medicine and Medical Science, University of Al-Razi, Al-Razi, Yemen.
| | - Israa M Shamkh
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, Egypt
- Chemo and Bioinformatics Lab, Bio Search Research Institution, BSRI, Giza, Egypt
| | - Ahmed Hassen Shntaif
- Department of Chemistry, College of Science for Women, University of Babylon, Alhilla, 51002, Iraq
| | - Muhammad Sufyan
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Moayad Shahwan
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Saad Alghamdi
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | | | - Elshiekh B Khidir
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Amr S Abouzied
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
- Department of Pharmaceutical Chemistry, National Organization for Drug Control and Research (NODCAR), Giza, 12553, Egypt
| | - Nasrin E Khalifa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
- Department of Pharmaceutics, Faculty of Pharmacy, University of Khartoum, Khartoum, Sudan
| | - Weam M A Khojali
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Omdurman Islamic University, Omdurman, Sudan
| | - Bader Huwaimel
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
| | - Dunia A Al Farraj
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, 11451, Riyadh, Saudi Arabia
| | - Saeedah Musaed Almutairi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, 11451, Riyadh, Saudi Arabia
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Vergoten G, Bailly C. Interaction of Norsecurinine-Type Oligomeric Alkaloids with α-Tubulin: A Molecular Docking Study. Plants (Basel) 2024; 13:1269. [PMID: 38732484 PMCID: PMC11085049 DOI: 10.3390/plants13091269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024]
Abstract
The medicinal plant Securinega virosa (Roxb ex. Willd) Baill., also known as Flueggea virosa (Roxb. ex Willd.) Royle, is commonly used in traditional medicine in Africa and Asia for the management of diverse pathologies, such as parasite infections, diabetes, and gastrointestinal diseases. Numerous alkaloids have been isolated from the twigs and leaves of the plant, notably a variety of oligomeric indolizidine alkaloids derived from the monomers securinine and norsecurinine which both display anticancer properties. The recent discovery that securinine can bind to tubulin and inhibit microtubule assembly prompted us to investigate the potential binding of two series of alkaloids, fluevirosines A-H and fluevirosinine A-J, with the tubulin dimer by means of molecular modeling. These natural products are rare high-order alkaloids with tri-, tetra-, and pentameric norsecurinine motifs. Despite their large size (up to 2500 Å3), these alkaloids can bind easily to the large drug-binding cavity (about 4800 Å3) on α-tubulin facing the β-tubulin unit. The molecular docking analysis suggests that these hydrophobic macro-alkaloids can form stable complexes with α/β-tubulin. The tubulin-binding capacity varies depending on the alkaloid size and structure. Structure-binding relationships are discussed. The docking analysis identifies the trimer fluevirosine D, tetramer fluevirosinine D, and pentamer fluevirosinine H as the most interesting tubulin ligands in the series. This study is the first to propose a molecular target for these atypical oligomeric Securinega alkaloids.
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Affiliation(s)
- Gérard Vergoten
- U1286—INFINITE, Lille Inflammation Research International Center, Institut de Chimie Pharmaceutique Albert Lespagnol (ICPAL), Faculté de Pharmacie, University of Lille, 3 rue du Professeur Laguesse, 59006 Lille, France
| | - Christian Bailly
- CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, OncoLille Institut, University of Lille, 59000 Lille, France
- Institute of Pharmaceutical Chemistry Albert Lespagnol (ICPAL), Faculty of Pharmacy, University of Lille, 59006 Lille, France
- OncoWitan, Scientific Consulting Office, 59290 Lille, France
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Ncube NB, Tukulula M, Govender KG. Leveraging computational tools to combat malaria: assessment and development of new therapeutics. J Cheminform 2024; 16:50. [PMID: 38698437 PMCID: PMC11064327 DOI: 10.1186/s13321-024-00842-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/12/2024] [Indexed: 05/05/2024] Open
Abstract
As the world grapples with the relentless challenges posed by diseases like malaria, the advent of sophisticated computational tools has emerged as a beacon of hope in the quest for effective treatments. In this study we delve into the strategies behind computational tools encompassing virtual screening, molecular docking, artificial intelligence (AI), and machine learning (ML). We assess their effectiveness and contribution to the progress of malaria treatment. The convergence of these computational strategies, coupled with the ever-increasing power of computing systems, has ushered in a new era of drug discovery, holding immense promise for the eradication of malaria. SCIENTIFIC CONTRIBUTION: Computational tools remain pivotal in drug design and development. They provide a platform for researchers to explore various treatment options and save both time and money in the drug development pipeline. It is imperative to assess computational techniques and monitor their effectiveness in disease control. In this study we examine renown computational tools that have been employed in the battle against malaria, the benefits and challenges these tools have presented, and the potential they hold in the future eradication of the disease.
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Affiliation(s)
- Nomagugu B Ncube
- School of Chemistry and Physics, College of Agriculture, Engineering and Science (CAES), University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Matshawandile Tukulula
- School of Chemistry and Physics, College of Agriculture, Engineering and Science (CAES), University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
| | - Krishna G Govender
- Department of Chemical Sciences, University of Johannesburg, Johannesburg, 2028, South Africa.
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9
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Mei Y, Chang L, Ji Y, Yang B, Zhao J, Chen H, Chen W. Biomolecular investigations into BBI reveal an enzymatic mechanism for PUFA isomerisation in bifidobacterium CFA bioconversion strains. Int J Biol Macromol 2024; 268:131836. [PMID: 38692553 DOI: 10.1016/j.ijbiomac.2024.131836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024]
Abstract
Multiple species of Bifidobacterium exhibit the ability to bioconvert conjugated fatty acids (CFAs), which is considered an important pathway for these strains to promote host health. However, there has been limited progress in understanding the enzymatic mechanism of CFA bioconversion by bifidobacteria, despite the increasing number of studies identifying CFA-producing strains. The protein responsible for polyunsaturated fatty acid (PUFA) isomerization in B. breve CCFM683 has recently been discovered and named BBI, providing a starting point for exploring Bifidobacterium isomerases (BIs). This study presents the sequence classification of membrane-bound isomerases from four common Bifidobacterium species that produce CFA. Heterologous expression, purification, and enzymatic studies of the typical sequences revealed that all possess a single c9, t11 isomer as the product and share common features in terms of enzymatic properties and catalytic kinetics. Using molecular docking and alanine scanning, Lys84, Tyr198, Asn202, and Leu245 located in the binding pocket were identified as critical to the catalytic activity, a finding further confirmed by site-directed mutagenesis-based screening assays. Overall, these findings provide insightful knowledge concerning the molecular mechanisms of BIs. This will open up additional opportunities for the use of bifidobacteria and CFAs in probiotic foods and precision nutrition.
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Affiliation(s)
- Yongchao Mei
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Lulu Chang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Yibin Ji
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Bo Yang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China
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10
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Touaibia M, Chiasson AI, Robichaud S, Doiron JA, Hébert MPA, Surette ME. Single and multiple inhibitors of the biosynthesis of 5-, 12-, 15-lipoxygenase products derived from cinnamyl-3,4-dihydroxy-α-cyanocinnamate: Synthesis and structure-activity relationship. Drug Dev Res 2024; 85:e22181. [PMID: 38619209 DOI: 10.1002/ddr.22181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/18/2024] [Accepted: 03/21/2024] [Indexed: 04/16/2024]
Abstract
The involvement of lipoxygenases in various pathologies, combined with the unavailability of safe and effective inhibitors of the biosynthesis of their products, is a source of inspiration for the development of new inhibitors. Based on a structural analysis of known inhibitors of lipoxygenase products biosynthesis, a comprehensive structure-activity study was carried out, which led to the discovery of several novel compounds (16a-c, 17a) demonstrating promising potency to inhibit the biosynthesis of products of 5-, 12- and 15-LO. Compounds 16b and 16c outperformed zileuton (1), the only FDA-approved 5-LO inhibitor, as well as known inhibitors such as caffeic acid phenethyl ester (CAPE (2)) and cinnamyl-3,4-dihydroxy-α-cyanocinnamate (CDC (4)). However, the introduction of a cyano group at the α-position of the carbonyl abolished the activity. Compounds 16a and 17a also inhibited the biosynthesis of 12- and 15-LO products. Compounds 16a, 17a far surpassed baicalein, a known 12-LO inhibitor, as inhibitors of 12-LO products biosynthesis. Compound 17a and CDC (4) showed equivalent inhibition of LO products, proposing that the double bond in the ester moiety is not necessary for the inhibitory activity. The introduction of the cyano group, as in compound 17a, at the α-position of the carbonyl in compound 16a significantly reduced the inhibitory activity against the biosynthesis of 15-LO products. In addition to the interactions with residues His372 and Phe421 also found with zileuton and CAPE, compounds 16a and 16c each interact with residue His367 as shown by molecular docking. This new interaction may explain their high affinity with the 5-LO active site.
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Affiliation(s)
- Mohamed Touaibia
- Chemistry and Biochemistry Department, Université de Moncton, Moncton, New Brunswick, Canada
| | - Audrey Isabel Chiasson
- Chemistry and Biochemistry Department, Université de Moncton, Moncton, New Brunswick, Canada
| | - Samuel Robichaud
- Chemistry and Biochemistry Department, Université de Moncton, Moncton, New Brunswick, Canada
| | - Jérémie A Doiron
- Chemistry and Biochemistry Department, Université de Moncton, Moncton, New Brunswick, Canada
- New Brunswick Center for Precision Medicine, Université de Moncton, Moncton, New Brunswick, Canada
| | - Mathieu P A Hébert
- Chemistry and Biochemistry Department, Université de Moncton, Moncton, New Brunswick, Canada
- New Brunswick Center for Precision Medicine, Université de Moncton, Moncton, New Brunswick, Canada
| | - Marc E Surette
- Chemistry and Biochemistry Department, Université de Moncton, Moncton, New Brunswick, Canada
- New Brunswick Center for Precision Medicine, Université de Moncton, Moncton, New Brunswick, Canada
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Yasmeen N, Chaudhary AA, Khan S, Ayyar PV, Lakhawat SS, Sharma PK, Kumar V. Antiangiogenic potential of phytochemicals from Clerodendrum inerme (L.) Gaertn investigated through in silico and quantum computational methods. Mol Divers 2024:10.1007/s11030-024-10846-4. [PMID: 38678137 DOI: 10.1007/s11030-024-10846-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 03/12/2024] [Indexed: 04/29/2024]
Abstract
Suppressing vascular endothelial growth factor (VEGF), its receptor (VEGFR2), and the VEGF/VEGFR2 signaling cascade system to inhibit angiogenesis has emerged as a possible cancer therapeutic target. The present work was designed to discover and evaluate bioactive phytochemicals from the Clerodendrum inerme (L.) Gaertn plant for their anti-angiogenic potential. Molecular docking of twenty-one phytochemicals against the VEGFR-2 (PDB ID: 3VHE) protein was performed, followed by ADMET profiling and molecular docking simulations. These investigations unveiled two hit compounds, cirsimaritin (- 12.29 kcal/mol) and salvigenin (- 12.14 kcal/mol), with the highest binding energy values when compared to the reference drug, Sorafenib (- 15.14 kcal/mol). Furthermore, only nine phytochemicals (cirsimaritin and salvigenin included) obeyed Lipinski's rule of five and passed ADMET filters. Molecular dynamics simulations run over 100 ns revealed that the protein-ligand complexes remained stable with minimal backbone fluctuations. The binding free energy values of cirsimaritin (- 52.35 kcal/mol) and salvigenin (- 55.89 kcal/mol), deciphered by MM-GBSA analyses, further corroborated the docking interactions. The HOMO-LUMO band energy gap (ΔE) was calculated using density-functional theory (DFT) and substantiated using density of state (DOS) spectra. The chemical reactivity analyses revealed that salvigenin exhibited the highest chemical softness value (6.384 eV), the lowest hardness value (0.07831 eV), and the lowest ΔE value (0.1566 eV), which implies salvigenin was less stable and chemically more reactive than cirsimaritin and sorafenib. These findings provide further evidence that cirsimaritin and salvigenin have the ability to prevent angiogenesis and the development of cancer. Nevertheless, more in vitro and in vivo confirmation is necessary.
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Affiliation(s)
- Nusrath Yasmeen
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, Rajasthan, India
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Salauddin Khan
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Priya Vijay Ayyar
- School of Life Science, Punyashlok Ahilyadevi Holkar Solapur University, Solapur, Maharashtra, India
| | - Sudarshan S Lakhawat
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, Rajasthan, India
| | - Pushpender K Sharma
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, Rajasthan, India
| | - Vikram Kumar
- Amity Institute of Pharmacy, Amity University Rajasthan, Jaipur, Rajasthan, India.
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12
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Xu C, Zhang X, Zhao L, Verkhivker GM, Bai F. Accurate Characterization of Binding Kinetics and Allosteric Mechanisms for the HSP90 Chaperone Inhibitors Using AI-Augmented Integrative Biophysical Studies. JACS Au 2024; 4:1632-1645. [PMID: 38665669 PMCID: PMC11040708 DOI: 10.1021/jacsau.4c00123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024]
Abstract
The binding kinetics of drugs to their targets are gradually being recognized as a crucial indicator of the efficacy of drugs in vivo, leading to the development of various computational methods for predicting the binding kinetics in recent years. However, compared with the prediction of binding affinity, the underlying structure and dynamic determinants of binding kinetics are more complicated. Efficient and accurate methods for predicting binding kinetics are still lacking. In this study, quantitative structure-kinetics relationship (QSKR) models were developed using 132 inhibitors targeting the ATP binding domain of heat shock protein 90α (HSP90α) to predict the dissociation rate constant (koff), enabling a direct assessment of the drug-target residence time. These models demonstrated good predictive performance, where hydrophobic and hydrogen bond interactions significantly influence the koff prediction. In subsequent applications, our models were used to assist in the discovery of new inhibitors for the N-terminal domain of HSP90α (N-HSP90α), demonstrating predictive capabilities on an experimental validation set with a new scaffold. In X-ray crystallography experiments, the loop-middle conformation of apo N-HSP90α was observed for the first time (previously, the loop-middle conformation had only been observed in holo-N-HSP90α structures). Interestingly, we observed different conformations of apo N-HSP90α simultaneously in an asymmetric unit, which was also observed in a holo-N-HSP90α structure, suggesting an equilibrium of conformations between different states in solution, which could be one of the determinants affecting the binding kinetics of the ligand. Different ligands can undergo conformational selection or alter the equilibrium of conformations, inducing conformational rearrangements and resulting in different effects on binding kinetics. We then used molecular dynamics simulations to describe conformational changes of apo N-HSP90α in different conformational states. In summary, the study of the binding kinetics and molecular mechanisms of N-HSP90α provides valuable information for the development of more targeted therapeutic approaches.
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Affiliation(s)
- Chao Xu
- Shanghai
Institute for Advanced Immunochemical Studies and School of Life Science
and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Xianglei Zhang
- Shanghai
Institute for Advanced Immunochemical Studies and School of Life Science
and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Lianghao Zhao
- Shanghai
Institute for Advanced Immunochemical Studies and School of Life Science
and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Gennady M. Verkhivker
- Keck
Center for Science and Engineering, Graduate Program in Computational
and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
- Department
of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
| | - Fang Bai
- Shanghai
Institute for Advanced Immunochemical Studies and School of Life Science
and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
- School
of Information Science and Technology, ShanghaiTech
University, 393 Middle Huaxia Road, Shanghai 201210, China
- Shanghai
Clinical Research and Trial Center, Shanghai 201210, China
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Mhaidat I, Banidomi S, Wedian F, Badarneh R, Tashtoush H, Almomani W, Al-Mazaideh GM, Alharbi NS, Thiruvengadam M. Antioxidant and antibacterial activities of 5-mercapto(substitutedthio)-4-substituted-1,2,4-triazol based on nalidixic acid: A comprehensive study on its synthesis, characterization, and In silico evaluation. Heliyon 2024; 10:e28204. [PMID: 38571635 PMCID: PMC10987910 DOI: 10.1016/j.heliyon.2024.e28204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 04/05/2024] Open
Abstract
This study introduces a series of novel Alkyl thio-1,2,4-triazole (4a-p) and mercapto-1,2,4-triazole (3a-d) compounds derived from nalidixic acid. The synthesis was streamlined, involving interactions between nalidixic acid hydrazide and various isothiocyanates to yield cyclic and alkyl(aryl) sulfide compounds, characterized using 1H NMR, 13C NMR, IR, and elemental analysis. Antioxidant capabilities were quantified through DPPH and ABTS assays, highlighting significant potential, especially for compound 3d, which demonstrated an ABTS IC50 value of 0.397 μM, on par with ascorbic acid (IC50 = 0.87 μM). Antibacterial efficacy was established through MIC assessments against a broad spectrum of Gram-positive and Gram-negative bacteria, including Candida albicans. Compounds 3b, 4e, 4h, 4j, 4i, 4m, and 4o showed broad-spectrum activity, with 4k and 4m exhibiting pronounced potency against E. coli. Molecular docking studies validated the antibacterial potential, with compounds 4f and 4h showing high binding affinities (docking scores of -9.8 and -9.6 kcal/mol, respectively), indicating robust interactions with the bacterial enzyme targets. These scores underscore the compounds' mechanistic basis for their antibacterial action and support their therapeutic promise. Furthermore, compounds 3b, 4i, and 4m, identified through drug-likeness and toxicity predictions, were highlighted for their favorable profiles, suggesting their suitability for oral antibiotic therapies. This comprehensive study, blending synthetic, in vitro, and in silico approaches, emphasizes the triazole derivatives' potential as future candidates for antibiotic and antioxidant applications, particularly spotlighting compounds 3b, 4i, and 4m due to their promising efficacy and safety profiles.
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Affiliation(s)
- Ibrahim Mhaidat
- Department of Chemistry, Faculty of Sciences, Yarmouk University, Irbid, 21163, Jordan
| | - Sojoud Banidomi
- Department of Chemistry, Faculty of Sciences, Yarmouk University, Irbid, 21163, Jordan
| | - Fadel Wedian
- Department of Chemistry, Faculty of Sciences, Yarmouk University, Irbid, 21163, Jordan
| | - Rahaf Badarneh
- Department of Chemistry, Faculty of Sciences, Yarmouk University, Irbid, 21163, Jordan
| | - Hasan Tashtoush
- Department of Chemistry, Faculty of Sciences, Yarmouk University, Irbid, 21163, Jordan
| | - Waleed Almomani
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid, 21163, Jordan
| | - Ghassab M. Al-Mazaideh
- Department of Chemistry and Chemical Technology, Tafila Technical University, Tafila, Jordan
| | - Naiyf S. Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Sciences, Konkuk University, Seoul, 05029, South Korea
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Bailly C, Bedart C, Vergoten G. A molecular docking exploration of the large extracellular loop of tetraspanin CD81 with small molecules. In Silico Pharmacol 2024; 12:24. [PMID: 38584777 PMCID: PMC10997574 DOI: 10.1007/s40203-024-00203-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 03/13/2024] [Indexed: 04/09/2024] Open
Abstract
Tetraspanin CD81 is a transmembrane protein used as a co-receptor by different viruses and implicated in some cancer and inflammatory diseases. The design of therapeutic small molecules targeting CD81 lags behind monoclonal antibodies and peptides but different synthetic and natural products binding to CD81 have been identified. We have investigated the interaction between synthetic compounds and CD81, considering both the cholesterol-bound full-length receptor and a truncated protein corresponding to the large extracellular loop (LEL) of the tetraspanin. They represent the closed and open conformations of the protein, respectively. Stable complexes were characterized with bi-aryl compounds (notably the quinolinone-benzothiazole 6) and atypical molecules bearing a 1-amino-boraadamantane scaffold well adapted to interact with CD81 (5a-d). In each case, the mode of binding to CD81 was analyzed, the binding sites identified and the molecular contacts determined. The narrow intra-LEL binding site of CD81 can accommodate the elongated bi-aryl 6 but not a series of isosteric compounds with a bis(bicyclic) scaffold. The bora-adamantane derivatives appeared to bind well to CD81, but essentially to the external surface of the protein loop. The binding selectivity of the compounds was assessed comparing binding to the LEL of tetraspanins CD81, CD9 and Tspan15. A net preference for CD81 over CD9 was evidenced, but the LEL of Tspan15 also provided a suitable binding site for the compounds, notably for the bora-adamantane derivatives. This work provides an aid to the identification and design of tetraspanin-binding small molecules, underlining the distinct behavior of the open and closed conformation of the protein for drug binding. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00203-6.
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Affiliation(s)
- Christian Bailly
- OncoWitan, Scientific Consulting Office, 59290 Lille, Wasquehal, France
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277, CANTHER, Cancer Heterogeneity Plasticity and Resistance to Therapies, 59000 Lille, France
| | - Corentin Bedart
- University of Lille, Inserm, U1286, INFINITE, Lille Inflammation Research International Center, Institut de Chimie Pharmaceutique Albert Lespagnol (ICPAL)Faculté de Pharmacie, 3 rue du Professeur Laguesse, 59,000 Lille, France
| | - Gérard Vergoten
- University of Lille, Inserm, U1286, INFINITE, Lille Inflammation Research International Center, Institut de Chimie Pharmaceutique Albert Lespagnol (ICPAL)Faculté de Pharmacie, 3 rue du Professeur Laguesse, 59,000 Lille, France
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15
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Agu PC, Obulose CN. Piquing artificial intelligence towards drug discovery: Tools, techniques, and applications. Drug Dev Res 2024; 85:e22159. [PMID: 38375772 DOI: 10.1002/ddr.22159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/12/2024] [Accepted: 01/29/2024] [Indexed: 02/21/2024]
Abstract
The purpose of this study was to discuss how artificial intelligence (AI) methods have affected the field of drug development. It looks at how AI models and data resources are reshaping the drug development process by offering more affordable and expedient options to conventional approaches. The paper opens with an overview of well-known information sources for drug development. The discussion then moves on to molecular representation techniques that make it possible to convert data into representations that computers can understand. The paper also gives a general overview of the algorithms used in the creation of drug discovery models based on AI. In particular, the paper looks at how AI algorithms might be used to forecast drug toxicity, drug bioactivity, and drug physicochemical properties. De novo drug design, binding affinity prediction, and other AI-based models for drug-target interaction were covered in deeper detail. Modern applications of AI in nanomedicine design and pharmacological synergism/antagonism prediction were also covered. The potential advantages of AI in drug development are highlighted as the evaluation comes to a close. It underlines how AI may greatly speed up and improve the efficiency of drug discovery, resulting in the creation of new and better medicines. To fully realize the promise of AI in drug discovery, the review acknowledges the difficulties that come with its uses in this field and advocates for more study and development.
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Affiliation(s)
- Peter Chinedu Agu
- Department of Biochemistry, College of Science, Evangel University, Akaeze, Ebonyi State, Nigeria
| | - Chidiebere Nwiboko Obulose
- Department of Computer Sciences, Our Savior Institute of Science, Agriculture, and Technology (OSISATECH Polytechnic), Enugu, Nigeria
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Nandi S, Bhaduri S, Das D, Ghosh P, Mandal M, Mitra P. Deciphering the Lexicon of Protein Targets: A Review on Multifaceted Drug Discovery in the Era of Artificial Intelligence. Mol Pharm 2024; 21:1563-1590. [PMID: 38466810 DOI: 10.1021/acs.molpharmaceut.3c01161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Understanding protein sequence and structure is essential for understanding protein-protein interactions (PPIs), which are essential for many biological processes and diseases. Targeting protein binding hot spots, which regulate signaling and growth, with rational drug design is promising. Rational drug design uses structural data and computational tools to study protein binding sites and protein interfaces to design inhibitors that can change these interactions, thereby potentially leading to therapeutic approaches. Artificial intelligence (AI), such as machine learning (ML) and deep learning (DL), has advanced drug discovery and design by providing computational resources and methods. Quantum chemistry is essential for drug reactivity, toxicology, drug screening, and quantitative structure-activity relationship (QSAR) properties. This review discusses the methodologies and challenges of identifying and characterizing hot spots and binding sites. It also explores the strategies and applications of artificial-intelligence-based rational drug design technologies that target proteins and protein-protein interaction (PPI) binding hot spots. It provides valuable insights for drug design with therapeutic implications. We have also demonstrated the pathological conditions of heat shock protein 27 (HSP27) and matrix metallopoproteinases (MMP2 and MMP9) and designed inhibitors of these proteins using the drug discovery paradigm in a case study on the discovery of drug molecules for cancer treatment. Additionally, the implications of benzothiazole derivatives for anticancer drug design and discovery are deliberated.
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Affiliation(s)
- Suvendu Nandi
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Soumyadeep Bhaduri
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Debraj Das
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Priya Ghosh
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Mahitosh Mandal
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Pralay Mitra
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
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Prasad M, Tamil Selvan S, Shanmugam R, Murugan R, Fareed M. Analysing the Anticancer Properties of Pterostilbene Through Absorption, Distribution, Metabolism, and Excretion (ADME) and Molecular Docking Studies. Cureus 2024; 16:e58425. [PMID: 38756274 PMCID: PMC11097614 DOI: 10.7759/cureus.58425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/16/2024] [Indexed: 05/18/2024] Open
Abstract
Aim The aim of this study is to examine the possible therapeutic effect of pterostilbene (PTS), a chemical present in grapes and blueberries, in the treatment of liver cancer by analysing its interactions with important proteins linked to the wingless/integrated (Wnt) signaling system. Objective Using computational techniques like molecular docking and absorption, distribution, metabolism, and excretion (ADME) studies, this research focuses on examining the pharmacokinetics and molecular interactions of PTS with proteins such as vimentin (Vim), glycogen synthase kinase 3 beta (GSK3-β), epithelial cadherin (E-cadherin), interleukin-6 (IL-6), interleukin-1 beta (IL-1β), c-Jun N-terminal kinase (JNK), and Wnt, all of which are connected to the Wnt signaling pathway in liver cancer. Methods The study includes the synthesis of proteins and ligands, ADME investigations for PTS, and AutoDock Vina molecular docking simulations to evaluate binding affinities and interactions. PTS is obtained from PubChem, while protein structures are obtained from the Protein Data Bank. Results Strong binding affinities between PTS and essential proteins in the Wnt signaling cascade are shown by molecular docking, which also highlights noteworthy hydrogen bonds, hydrophobic interactions, and electrostatic contacts. According to an ADME study, PTS has advantageous pharmacokinetic properties, such as moderate solubility, membrane permeability, and a minimal chance of drug interactions. Conclusion The extensive study highlights PTS's potential as a viable treatment option for liver cancer. The study promotes its investigation in cutting-edge liver cancer therapy approaches and urges more investigation into the molecular mechanisms, underpinning its anticancer properties. This paper sheds important light on the role of natural chemicals in cancer therapy and emphasizes the need for computational methods in drug discovery.
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Affiliation(s)
- Monisha Prasad
- Centre for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
| | - Silambarasan Tamil Selvan
- Centre for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
| | - Rajeshkumar Shanmugam
- Nanobiomedicine Lab, Centre for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
| | - Ramadurai Murugan
- Centre for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
| | - Mohammad Fareed
- Centre for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
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18
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Nikitha R, Afeeza K, Suresh V, Dilipan E. Molecular Docking of Seaweed-Derived Drug Fucoxanthin Against the Monkeypox Virus. Cureus 2024; 16:e58730. [PMID: 38779278 PMCID: PMC11110489 DOI: 10.7759/cureus.58730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Background The monkeypox virus (MPXV) is classified as a zoonotic virus of the Poxviridae family, resulting from the MPXV strain of the Orthopoxvirus genus. Seaweeds, or marine macroalgae, are abundant reservoirs of bioactive compounds that demonstrate diverse biological properties, such as antiviral actions. In the field of computational analysis, in silico analysis refers to the use of computer-based methods to study and assess biological systems and processes. To forecast the binding affinity and interaction between the discovered chemical and the target proteins of the MPXV, a molecular docking analysis was conducted. Aim The research aims to conduct an in silico examination of a protein-ligand interaction of a drug produced from seaweed that targets the MPXV. Methodology Protein Data Bank (PDB) and PubChem databases provided MPXV methyltransferase and fucoxanthin ligand compounds. AutoDockTools 1.5.7 calculated the molecular docking using the Lamarckian genetic algorithm. Autogrid created a grid box around target 8B07 active site hotspot residues. Each docked molecule's docking parameters were obtained from 100 docking experiments with a maximum of 2.5 × 106 energy evaluations, a 0.02 mutation rate, and a 0.8 crossover rate. The population comprised 250 randomly selected volunteers. PyMOL was utilized to observe ligand fragment interactions. Results The binding energy of the ligand fucoxanthin was -5.46 kcal/mol. Fucoxanthin interacts with receptor molecules via hydrogen bonding at the amino acid level: Chain A: PHE188 and TYR189; and Chain B: LYS33, GLN37, GLY38, GLY96, ARG97, PHE115, PRO202, and SER203. The higher the negative docking score, the stronger the binding affinity between the receptor and ligand molecules, indicating that bioactive substances are more effective. Conclusion The findings of this study indicate that fucoxanthin, a pharmaceutical derivative generated from seaweed, had antiviral activity against the MPXV. This conclusion was reached based on protein-ligand interactions.
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Affiliation(s)
- Ramakrishnan Nikitha
- Physiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
| | - Klg Afeeza
- Physiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
| | - Vasugi Suresh
- Medical Physiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
| | - Elangovan Dilipan
- Physiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
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Huangfu B, Yang M, Xu J, Gao R, Hu Y, Zhao Y, Huang K, He X. Coreopsis tinctoria improves energy metabolism in obese hyperglycemic mice. Heliyon 2024; 10:e27449. [PMID: 38496841 PMCID: PMC10944243 DOI: 10.1016/j.heliyon.2024.e27449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/20/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Coreopsis tinctoria (CT) improves energy metabolism. However, the role of CT in alleviating obesity-induced hyperglycemia by targeting the liver remains unknown. Therefore, this article aims to explore the mechanism by which CT improves energy metabolism and resists hyperglycemia. The water and ethanol extracts of CT were administered to high-fat diet-induced (HFD) obese C57BL/6J mice at a dose of 4 g/kg.bw (low-dose water extract, WL; low-dose ethanol extract, EL) or 10 g/kg.bw (high-dose water extract, WH; high-dose ethanol extract, EH). Mice that consumed a maintenance diet (LFD) were included as blank controls. Network pharmacology, liquid chromatography-mass spectrometry (LC-MS), L02 cell cultivation, and liver transcriptomics were used to examine the mechanism and functional components of CT against obesity-induced hyperglycemia. The results indicated that WL significantly (p < 0.05) alleviated glucose intolerance and insulin resistance in obesity-induced hyperglycemia. Kaempferol is the main active compound of CT, which demonstrated significant (p < 0.05) anti-hyperglycemic effects in obese mice and L02 cells. Finally, kaempferol significantly (p < 0.05; fold change >1.2) shifted the genes involved in carbon metabolism, glycolysis/gluconeogenesis, and the mitogen-activated protein kinase (MAPK) pathways toward the trend of LFD, indicating that it exerts an anti-hyperglycemic effect through these molecular mechanisms. Overall, oral intake of CT lowers blood glucose and improves insulin sensitivity in mice with obesity-induced hyperglycemia. Kaempferol is the primary functional component of CT.
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Affiliation(s)
- Bingxin Huangfu
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Minglan Yang
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Department of Clinical Nutrition, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Jia Xu
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Ruxin Gao
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yanzhou Hu
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yijia Zhao
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), The Ministry of Agriculture and Rural Affairs of the PR China, Beijing, 100083, China
| | - Kunlun Huang
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), The Ministry of Agriculture and Rural Affairs of the PR China, Beijing, 100083, China
| | - Xiaoyun He
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), The Ministry of Agriculture and Rural Affairs of the PR China, Beijing, 100083, China
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Bapat RA, Mak KK, Pichika MR, Pang JC, Lin SL, Khoo SP, Daood U. Newly discovered clouting interplay between matrix metalloproteinases structures and novel quaternary Ammonium K21: computational and in-vivo testing. BMC Oral Health 2024; 24:382. [PMID: 38528501 DOI: 10.1186/s12903-024-04069-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/24/2024] [Indexed: 03/27/2024] Open
Abstract
AIMS AND OBJECTIVES To analyze anti-MMP mode of action of Quaternary Ammonium Silane (QAS, codenamed as k21) by binding onto specific MMP site using computational molecular simulation and Anti-Sortase A (SrtA) mode of action by binding onto specific site using computational molecular simulation. MATERIALS AND METHODS In silico Molecular Dynamics (MD) was used to determine the interactions of K21 inside the pocket of the targeted protein (crystal structure of fibroblast collagenase-1 complexed to a diphenyl-ether sulphone based hydroxamic acid; PDB ID: 966C; Crystal structure of MMP-2 active site mutant in complex with APP-derived decapeptide inhibitor. MD simulations were accomplished with the Desmond package in Schrödinger Drug Discovery Suite. Blood samples (~ 0.5 mL) collected into K2EDTA were immediately transferred for further processing using the Litron MicroFlow® PLUS micronucleus analysis kit for mouse blood according to the manufacturer's instructions. Bacterial Reverse Mutation Test of K21 Molecule was performed to evaluate K21 and any possible metabolites for their potential to induce point mutations in amino acid-requiring strains of Escherichia coli (E. coli) (WP2 uvrA (tryptophan-deficient)). RESULTS Molecular Simulation depicted that K21 has a specific pocket binding on various MMPs and SrtA surfaces producing a classical clouting effect. K21 did not induce micronuclei, which are the result of chromosomal damage or damage to the mitotic apparatus, in the peripheral blood reticulocytes of male and female CD-1 mice when administered by oral gavage up to the maximum recommended dose of 2000 mg/kg. The test item, K21, was not mutagenic to Salmonella typhimurium (S. typhimurium) strains TA98, TA100, TA1535 and TA1537 and E. coli strain WP2 uvrA in the absence and presence of metabolic activation when tested up to the limit of cytotoxicity or solubility under the conditions of the test. CONCLUSION K21 could serve as a potent protease inhibitor maintaining the physical and biochemical properties of dental structures.
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Affiliation(s)
- Ranjeet Ajit Bapat
- Restorative Dentistry Division, School of Dentistry, International Medical University Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Kit-Kay Mak
- School of Pharmacy, International Medical University Kuala Lumpur, 126, Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Mallikarjuna Rao Pichika
- School of Pharmacy, International Medical University Kuala Lumpur, 126, Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Jia Chern Pang
- School of Postgraduate Studies, International Medical University, 57000, Kuala Lumpur, Malaysia
| | - Seow Liang Lin
- Restorative Dentistry Division, School of Dentistry, International Medical University Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Suan Phaik Khoo
- Division of Clinical Oral Health, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
| | - Umer Daood
- Restorative Dentistry Division, School of Dentistry, International Medical University Kuala Lumpur, Kuala Lumpur, Malaysia.
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Vergoten G, Bailly C. Insights into the Mechanism of Action of the Degraded Limonoid Prieurianin. Int J Mol Sci 2024; 25:3597. [PMID: 38612409 PMCID: PMC11011620 DOI: 10.3390/ijms25073597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/12/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
Limonoids are extremely diversified in plants, with many categories of products bearing an intact, rearranged or fragmented oxygenated scaffold. A specific subgroup of fragmented or degraded limonoids derives from the tetranortriterpenoid prieurianin, initially isolated from the tree Trichilia prieuriana but also found in other plants of the Meliaceae family, including the more abundant species Aphanamixis polystachya. Prieurianin-type limonoids include about seventy compounds, among which are dregeanin and rohitukin. Prieurianin and analogs exhibit insecticidal, antimicrobial, antiadipogenic and/or antiparasitic properties but their mechanism of action remains ill-defined at present. Previous studies have shown that prieurianin, initially known as endosidin 1, stabilizes the actin cytoskeleton in plant and mammalian cells via the modulation of the architecture and dynamic of the actin network, most likely via interference with actin-binding proteins. A new mechanistic hypothesis is advanced here based on the recent discovery of the targeting of the chaperone protein Hsp47 by the fragmented limonoid fraxinellone. Molecular modeling suggested that prieurianin and, to a lesser extent dregeanin, can form very stable complexes with Hsp47 at the protein-collagen interface. Hsp-binding may account for the insecticidal action of the product. The present review draws up a new mechanistic portrait of prieurianin and provides an overview of the pharmacological properties of this atypical limonoid and its chemical family.
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Affiliation(s)
- Gérard Vergoten
- U1286—INFINITE, Lille Inflammation Research International Center, Institut de Chimie Pharmaceutique Albert Lespagnol (ICPAL), Faculté de Pharmacie, University of Lille, 3 Rue du Professeur Laguesse, 59006 Lille, France
| | - Christian Bailly
- CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, OncoLille Institut, University of Lille, 59000 Lille, France
- Institute of Pharmaceutical Chemistry Albert Lespagnol (ICPAL), Faculty of Pharmacy, University of Lille, 59006 Lille, France
- OncoWitan, Scientific Consulting Office, 59290 Lille, France
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Tadesse K, Benhamou RI. Targeting MicroRNAs with Small Molecules. Noncoding RNA 2024; 10:17. [PMID: 38525736 PMCID: PMC10961812 DOI: 10.3390/ncrna10020017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/07/2024] [Accepted: 03/10/2024] [Indexed: 03/26/2024] Open
Abstract
MicroRNAs (miRs) have been implicated in numerous diseases, presenting an attractive target for the development of novel therapeutics. The various regulatory roles of miRs in cellular processes underscore the need for precise strategies. Recent advances in RNA research offer hope by enabling the identification of small molecules capable of selectively targeting specific disease-associated miRs. This understanding paves the way for developing small molecules that can modulate the activity of disease-associated miRs. Herein, we discuss the progress made in the field of drug discovery processes, transforming the landscape of miR-targeted therapeutics by small molecules. By leveraging various approaches, researchers can systematically identify compounds to modulate miR function, providing a more potent intervention either by inhibiting or degrading miRs. The implementation of these multidisciplinary approaches bears the potential to revolutionize treatments for diverse diseases, signifying a significant stride towards the targeting of miRs by precision medicine.
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Affiliation(s)
| | - Raphael I. Benhamou
- The Institute for Drug Research of the School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
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23
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Ge Q, Zhang Z, Cao Z, Wu D, Xu C, Yao J, Gao J, Feng Y. Exploration of the in vitro Antiviral Effects and the Active Components of Changyanning Tablets Against Enterovirus 71. Drug Des Devel Ther 2024; 18:651-665. [PMID: 38450095 PMCID: PMC10916518 DOI: 10.2147/dddt.s444625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/15/2024] [Indexed: 03/08/2024] Open
Abstract
Purpose This study aims to investigate the in vitro antiviral effects of the aqueous solution of Changyanning (CYN) tablets on Enterovirus 71 (EV71), and to analyze its active components. Methods The in vitro anti-EV71 effects of CYN solution and its herbal ingredients were assessed by testing the relative viral RNA (vRNA) expression level and the cell viability rates. Material basis analysis was performed using HPLC-Q-TOF-MS/MS detection. Potential targets and active components were identified by network pharmacology and molecular docking. The screened components were verified by in vitro antiviral experiments. Results CYN solution exerted anti-EV71 activities as the vRNA is markedly reduced after treatment, with a half maximal inhibitory concentration (IC50) of 996.85 μg/mL. Of its five herbal ingredients, aqueous extract of Mosla chinensis (AEMC) and leaves of Liquidambar formosana Hance (AELLF) significantly inhibited the intracellular replication of EV71, and the IC50 was tested as 202.57 μg/mL and 174.77 μg/mL, respectively. Based on HPLC-Q-TOF-MS/MS results, as well as the comparison with the material basis of CYN solution, a total of 44 components were identified from AEMC and AELLF. Through network pharmacology, AKT1, ALB, and SRC were identified as core targets. Molecular docking performed between core targets and the components indicated that 21 components may have anti-EV71 effects. Of these, nine were selected for in vitro pharmacodynamic verification, and only rosmarinic acid manifested in vitro anti-EV71 activity, with an IC50 of 11.90 μg/mL. Moreover, rosmarinic acid can stably bind with three core targets by forming hydrogen bonds. Conclusion CYN solution has inhibitory effects on EV71 replication in vitro, and its active component was identified as rosmarinic acid. Our study provides a new approach for screening and confirmation of the effective components in Chinese herbal preparation.
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Affiliation(s)
- Qiong Ge
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310051, People’s Republic of China
| | - Zhewen Zhang
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, People’s Republic of China
| | - Zhiming Cao
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, People’s Republic of China
| | - Dan Wu
- Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine Pharmaceutical Technology, Zhejiang Conba Pharmaceutical Co., Ltd, Hangzhou, Zhejiang, 310057, People’s Republic of China
| | - Changping Xu
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310051, People’s Republic of China
| | - Jianbiao Yao
- Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine Pharmaceutical Technology, Zhejiang Conba Pharmaceutical Co., Ltd, Hangzhou, Zhejiang, 310057, People’s Republic of China
| | - Jian Gao
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310051, People’s Republic of China
| | - Yan Feng
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310051, People’s Republic of China
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Malar DS, Verma K, Prasanth MI, Tencomnao T, Brimson JM. Network analysis-guided drug repurposing strategies targeting LPAR receptor in the interplay of COVID, Alzheimer's, and diabetes. Sci Rep 2024; 14:4328. [PMID: 38383841 PMCID: PMC10882047 DOI: 10.1038/s41598-024-55013-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/19/2024] [Indexed: 02/23/2024] Open
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 virus has greatly affected global health. Emerging evidence suggests a complex interplay between Alzheimer's disease (AD), diabetes (DM), and COVID-19. Given COVID-19's involvement in the increased risk of other diseases, there is an urgent need to identify novel targets and drugs to combat these interconnected health challenges. Lysophosphatidic acid receptors (LPARs), belonging to the G protein-coupled receptor family, have been implicated in various pathological conditions, including inflammation. In this regard, the study aimed to investigate the involvement of LPARs (specifically LPAR1, 3, 6) in the tri-directional relationship between AD, DM, and COVID-19 through network analysis, as well as explore the therapeutic potential of selected anti-AD, anti-DM drugs as LPAR, SPIKE antagonists. We used the Coremine Medical database to identify genes related to DM, AD, and COVID-19. Furthermore, STRING analysis was used to identify the interacting partners of LPAR1, LPAR3, and LPAR6. Additionally, a literature search revealed 78 drugs on the market or in clinical studies that were used for treating either AD or DM. We carried out docking analysis of these drugs against the LPAR1, LPAR3, and LPAR6. Furthermore, we modeled the LPAR1, LPAR3, and LPAR6 in a complex with the COVID-19 spike protein and performed a docking study of selected drugs with the LPAR-Spike complex. The analysis revealed 177 common genes implicated in AD, DM, and COVID-19. Protein-protein docking analysis demonstrated that LPAR (1,3 & 6) efficiently binds with the viral SPIKE protein, suggesting them as targets for viral infection. Furthermore, docking analysis of the anti-AD and anti-DM drugs against LPARs, SPIKE protein, and the LPARs-SPIKE complex revealed promising candidates, including lupron, neflamapimod, and nilotinib, stating the importance of drug repurposing in the drug discovery process. These drugs exhibited the ability to bind and inhibit the LPAR receptor activity and the SPIKE protein and interfere with LPAR-SPIKE protein interaction. Through a combined network and targeted-based therapeutic intervention approach, this study has identified several drugs that could be repurposed for treating COVID-19 due to their expected interference with LPAR(1, 3, and 6) and spike protein complexes. In addition, it can also be hypothesized that the co-administration of these identified drugs during COVID-19 infection may not only help mitigate the impact of the virus but also potentially contribute to the prevention or management of post-COVID complications related to AD and DM.
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Affiliation(s)
- Dicson Sheeja Malar
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok, Thailand
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Kanika Verma
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok, Thailand.
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand.
- Department of Molecular Epidemiology, ICMR- National Institute of Malaria Research (NIMR), New Delhi, India.
| | - Mani Iyer Prasanth
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok, Thailand
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Tewin Tencomnao
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok, Thailand
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - James Michael Brimson
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok, Thailand.
- Research Unit for Innovation and International Affairs, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand.
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Di Paola A, Marrapodi MM, Pota E, Colucci Cante R, Rana D, Giliberti G, Di Feo G, Ahmed S, Roberti D, Nigro R, Rossi F, Argenziano M. Role of Nutraceuticals in Counteracting Inflammation in In Vitro Macrophages Obtained from Childhood Cancer Survivors. Cancers (Basel) 2024; 16:714. [PMID: 38398105 PMCID: PMC10886672 DOI: 10.3390/cancers16040714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
The advancement of anti-cancer therapies has markedly improved the survival rate of children with cancer, making them long-term childhood cancer survivors (CCS). Nevertheless, these treatments cause a low-grade inflammatory state, determining inflamm-aging and, thus, favoring the early onset of chronic diseases normally associated with old age. Identification of novel and safer therapeutic strategies is needed to counteract and prevent inflamm-aging. Macrophages are cells involved in immune and inflammatory responses, with a pivotal role in iron metabolism, which is related to inflammation. We obtained macrophages from CCS patients and evaluated their phenotype markers, inflammatory states, and iron metabolism by Western blotting, ELISA, and iron assays. We observed a strong increase in classically activated phenotype markers (M1) and iron metabolism alteration in CCS, with an increase in intracellular iron concentration and inflammatory markers. These results suggest that the prevalence of M1 macrophages and alteration of iron metabolism could be involved in the worsening of inflammation in CCS. Therefore, we propose macrophages and iron metabolism as novel therapeutic targets to counteract inflamm-aging. To avoid toxic regimens, we tested some nutraceuticals (resveratrol, curcumin, and oil-enriched lycopene), which are already known to exert anti-inflammatory properties. After their administration, we observed a macrophage switch towards the anti-inflammatory phenotype M2, as well as reductions in pro-inflammatory cytokines and the intracellular iron concentration. Therefore, we suggest-for the first time-that nutraceuticals reduce inflammation in CCS macrophages through a novel anti-inflammatory mechanism of action, modulating iron metabolism.
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Affiliation(s)
- Alessandra Di Paola
- Department of Woman, Child and General and Specialist Surgery, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.D.P.); (M.M.M.); (E.P.); (G.D.F.); (D.R.); (M.A.)
| | - Maria Maddalena Marrapodi
- Department of Woman, Child and General and Specialist Surgery, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.D.P.); (M.M.M.); (E.P.); (G.D.F.); (D.R.); (M.A.)
| | - Elvira Pota
- Department of Woman, Child and General and Specialist Surgery, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.D.P.); (M.M.M.); (E.P.); (G.D.F.); (D.R.); (M.A.)
| | - Rosa Colucci Cante
- Department of Industrial Engineering, University of Niccolò Cusano, 00166 Rome, Italy;
| | - Deeksha Rana
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (D.R.); (G.G.); (S.A.)
| | - Giulia Giliberti
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (D.R.); (G.G.); (S.A.)
| | - Giuseppe Di Feo
- Department of Woman, Child and General and Specialist Surgery, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.D.P.); (M.M.M.); (E.P.); (G.D.F.); (D.R.); (M.A.)
| | - Shakeel Ahmed
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (D.R.); (G.G.); (S.A.)
| | - Domenico Roberti
- Department of Woman, Child and General and Specialist Surgery, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.D.P.); (M.M.M.); (E.P.); (G.D.F.); (D.R.); (M.A.)
| | - Roberto Nigro
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, 80125 Naples, Italy;
| | - Francesca Rossi
- Department of Woman, Child and General and Specialist Surgery, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.D.P.); (M.M.M.); (E.P.); (G.D.F.); (D.R.); (M.A.)
| | - Maura Argenziano
- Department of Woman, Child and General and Specialist Surgery, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.D.P.); (M.M.M.); (E.P.); (G.D.F.); (D.R.); (M.A.)
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Zhang L, Kong H, Chitrakar B, Ban X, Gu Z, Hong Y, Cheng L, Li Z, Li C. The substitution sites of hydroxyl and galloyl groups determine the inhibitory activity of human pancreatic α-amylase in twelve tea polyphenol monomers. Int J Biol Macromol 2024; 259:129189. [PMID: 38181909 DOI: 10.1016/j.ijbiomac.2023.129189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/21/2023] [Accepted: 12/31/2023] [Indexed: 01/07/2024]
Abstract
Tea polyphenols have been reported as potential α-amylase inhibitors. However, the quantitative structure-activity relationship (QSAR) between tea polyphenols and human pancreas α-amylase (HPA) is not well understood. Herein, the inhibitory effect of twelve tea polyphenol monomers on HPA was investigated in terms of inhibitory activity, as well as QSAR analysis and interaction mechanism. The results revealed that the HPA inhibitory activity of theaflavins (TFs), especially theaflavin-3'-gallate (TF-3'-G, IC50: 0.313 mg/mL), was much stronger than that of catechins (IC50: 18.387-458.932 mg/mL). The QSAR analysis demonstrated that the determinant for the inhibitory activity of HPA was not the number of hydroxyl and galloyl groups in tea polyphenol monomers, while the substitution sites of these groups potentially might play a more important role in modulating the inhibitory activity. The inhibition kinetics and molecular docking revealed that TF-3'-G as a mixed-type inhibitor had the lowest inhibition constant and bound to the active sites of HPA with the lowest binding energy (-7.74 kcal/mol). These findings could provide valuable insights into the structures-activity relationships between tea polyphenols and the HPA inhibitors.
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Affiliation(s)
- Lan Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Haocun Kong
- Key Laboratory of Synergetic and Biological Colloids, Ministry of Education, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Bimal Chitrakar
- College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Xiaofeng Ban
- Key Laboratory of Synergetic and Biological Colloids, Ministry of Education, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhengbiao Gu
- Key Laboratory of Synergetic and Biological Colloids, Ministry of Education, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yan Hong
- Key Laboratory of Synergetic and Biological Colloids, Ministry of Education, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Li Cheng
- Key Laboratory of Synergetic and Biological Colloids, Ministry of Education, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhaofeng Li
- Key Laboratory of Synergetic and Biological Colloids, Ministry of Education, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd., Yixing 214200, China.
| | - Caiming Li
- Key Laboratory of Synergetic and Biological Colloids, Ministry of Education, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd., Yixing 214200, China.
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27
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Vincenzi M, Mercurio FA, Leone M. Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools. Int J Mol Sci 2024; 25:1798. [PMID: 38339078 PMCID: PMC10855943 DOI: 10.3390/ijms25031798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Over the last few decades, we have witnessed growing interest from both academic and industrial laboratories in peptides as possible therapeutics. Bioactive peptides have a high potential to treat various diseases with specificity and biological safety. Compared to small molecules, peptides represent better candidates as inhibitors (or general modulators) of key protein-protein interactions. In fact, undruggable proteins containing large and smooth surfaces can be more easily targeted with the conformational plasticity of peptides. The discovery of bioactive peptides, working against disease-relevant protein targets, generally requires the high-throughput screening of large libraries, and in silico approaches are highly exploited for their low-cost incidence and efficiency. The present review reports on the potential challenges linked to the employment of peptides as therapeutics and describes computational approaches, mainly structure-based virtual screening (SBVS), to support the identification of novel peptides for therapeutic implementations. Cutting-edge SBVS strategies are reviewed along with examples of applications focused on diverse classes of bioactive peptides (i.e., anticancer, antimicrobial/antiviral peptides, peptides blocking amyloid fiber formation).
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Affiliation(s)
| | | | - Marilisa Leone
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy; (M.V.); (F.A.M.)
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Himtaş D, Yalçin E, Çavuşoğlu K, Acar A. In-vivo and in-silico studies to identify toxicity mechanisms of permethrin with the toxicity-reducing role of ginger. Environ Sci Pollut Res Int 2024; 31:9272-9287. [PMID: 38191734 PMCID: PMC10824804 DOI: 10.1007/s11356-023-31729-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 12/22/2023] [Indexed: 01/10/2024]
Abstract
In this study, the toxic effects of permethrin on Allium cepa L. and the protective role of Zingiber officinale rhizome extract (Zoex) were investigated. In this context, 6 different groups were formed. While the control group was treated with tap water, the groups II and III were treated with 10 µg/mL and 20 µg/mL Zoex, respectively, and the group IV was treated with 100 µg/L permethrin. The protective effect of Zoex against permethrin toxicity was studied as a function of dose, and groups V and VI formed for this purpose were treated with 10 µg/mL Zoex + 100 µg/L permethrin and 20 µg/mL Zoex + 100 µg/L permethrin, respectively. After 72 h of germination, cytogenetic, biochemical, physiological, and anatomical changes in meristematic cells of A. cepa were studied. As a result, permethrin application decreased the mitotic index (MI) and increased the frequency of micronuclei (MN), and chromosomal abnormalities. The increase in malondialdehyde (MDA), superoxide dismutase (SOD), and catalase (CAT) and the decrease in glutathione (GSH) indicate that permethrin causes oxidative damage. Compared to the control group, a 68.5% decrease in root elongation (p < 0.05) and an 81.8% decrease (p < 0.05) in weight gain were observed in the permethrin-treated group. It was found that the application of Zoex together with permethrin resulted in regression of all detected abnormalities, reduction in the incidence of anatomical damage, MN and chromosomal aberrations, and improvement in MI rates. The most significant improvement was observed in group VI treated with 20 µg/mL Zoex, and Zoex was also found to provide dose-dependent protection. The toxicity mechanism of permethrin was also elucidated by molecular docking and spectral studies. From the data obtained during the study, it was found that permethrin has toxic effects on A. cepa, a non-target organism, while Zoex plays a protective role by reducing these effects.
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Affiliation(s)
- Damla Himtaş
- Department of Biology, Institute of Natural Sciences, University of Giresun, 28200, Giresun, Turkey
| | - Emine Yalçin
- Department of Biology, Faculty of Science and Art, University of Giresun, 28200, Giresun, Turkey.
| | - Kültiğin Çavuşoğlu
- Department of Biology, Faculty of Science and Art, University of Giresun, 28200, Giresun, Turkey
| | - Ali Acar
- Department of Medical Services and Techniques, Vocational School of Health Services, University of Giresun, 28200, Giresun, Turkey
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Qian W, Lu J, Gao C, Liu Q, Yao W, Wang T, Wang X, Wang Z. Isobavachalcone exhibits antifungal and antibiofilm effects against C. albicans by disrupting cell wall/membrane integrity and inducing apoptosis and autophagy. Front Cell Infect Microbiol 2024; 14:1336773. [PMID: 38322671 PMCID: PMC10845358 DOI: 10.3389/fcimb.2024.1336773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 01/03/2024] [Indexed: 02/08/2024] Open
Abstract
Isobavachalcone (IBC) is a natural flavonoid with multiple pharmacological properties. This study aimed to evaluate the efficacy of IBC against planktonic growth and biofilms of Candida albicans (C. albicans) and the mechanisms underlying its antifungal action. The cell membrane integrity, cell metabolic viability, and cell morphology of C. albicans treated with IBC were evaluated using CLSM and FESEM analyses. Crystal violet staining, CLSM, and FESEM were used to assess the inhibition of biofilm formation, as well as dispersal and killing effects of IBC on mature biofilms. RNA-seq combined with apoptosis and autophagy assays was used to examine the mechanisms underlying the antifungal action of IBC. IBC exhibited excellent antifungal activity with 8 μg/mL of MIC for C. albicans. IBC disrupted the cell membrane integrity, and inhibited biofilm formation. IBC dispersed mature biofilms and damaged biofilm cells of C. albicans at 32 μg/mL. Moreover, IBC induced apoptosis and autophagy-associated cell death of C. albicans. The RNA-seq analysis revealed upregulation or downregulation of key genes involved in cell wall synthesis (Wsc1 and Fks1), ergosterol biosynthesis (Erg3, and Erg11), apoptisis (Hsp90 and Aif1), as well as autophagy pathways (Atg8, Atg13, and Atg17), and so forth, in response to IBC, as evidenced by the experiment-based phenotypic analysis. These results suggest that IBC inhibits C. albicans growth by disrupting the cell wall/membrane, caused by the altered expression of genes associated with β-1,3-glucan and ergosterol biosynthesis. IBC induces apoptosis and autophagy-associated cell death by upregulating the expression of Hsp90, and altering autophagy-related genes involved in the formation of the Atg1 complex and the pre-autophagosomal structure. Together, our findings provide important insights into the potential multifunctional mechanism of action of IBC.
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Affiliation(s)
- Weidong Qian
- School of Biological and Pharmaceutical Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | - Jiaxing Lu
- School of Biological and Pharmaceutical Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | - Chang Gao
- School of Biological and Pharmaceutical Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | - Qiming Liu
- School of Biological and Pharmaceutical Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | - Wendi Yao
- Department of Urology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Ting Wang
- School of Biological and Pharmaceutical Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | - Xiaobin Wang
- Department of Urology, Southern University of Science and Technology Hospital, Shenzhen, China
| | - Zhifeng Wang
- Department of Urology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
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Augustijn HE, Roseboom AM, Medema MH, van Wezel GP. Harnessing regulatory networks in Actinobacteria for natural product discovery. J Ind Microbiol Biotechnol 2024; 51:kuae011. [PMID: 38569653 PMCID: PMC10996143 DOI: 10.1093/jimb/kuae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/02/2024] [Indexed: 04/05/2024]
Abstract
Microbes typically live in complex habitats where they need to rapidly adapt to continuously changing growth conditions. To do so, they produce an astonishing array of natural products with diverse structures and functions. Actinobacteria stand out for their prolific production of bioactive molecules, including antibiotics, anticancer agents, antifungals, and immunosuppressants. Attention has been directed especially towards the identification of the compounds they produce and the mining of the large diversity of biosynthetic gene clusters (BGCs) in their genomes. However, the current return on investment in random screening for bioactive compounds is low, while it is hard to predict which of the millions of BGCs should be prioritized. Moreover, many of the BGCs for yet undiscovered natural products are silent or cryptic under laboratory growth conditions. To identify ways to prioritize and activate these BGCs, knowledge regarding the way their expression is controlled is crucial. Intricate regulatory networks control global gene expression in Actinobacteria, governed by a staggering number of up to 1000 transcription factors per strain. This review highlights recent advances in experimental and computational methods for characterizing and predicting transcription factor binding sites and their applications to guide natural product discovery. We propose that regulation-guided genome mining approaches will open new avenues toward eliciting the expression of BGCs, as well as prioritizing subsets of BGCs for expression using synthetic biology approaches. ONE-SENTENCE SUMMARY This review provides insights into advances in experimental and computational methods aimed at predicting transcription factor binding sites and their applications to guide natural product discovery.
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Affiliation(s)
- Hannah E Augustijn
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Anna M Roseboom
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
- Netherlands Institute for Ecology (NIOO-KNAW), Wageningen, The Netherlands
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Zayed A, Al-Saedi DA, Mensah EO, Kanwugu ON, Adadi P, Ulber R. Fucoidan's Molecular Targets: A Comprehensive Review of Its Unique and Multiple Targets Accounting for Promising Bioactivities Supported by In Silico Studies. Mar Drugs 2023; 22:29. [PMID: 38248653 PMCID: PMC10820140 DOI: 10.3390/md22010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
Fucoidan is a class of multifunctional polysaccharides derived from marine organisms. Its unique and diversified physicochemical and chemical properties have qualified them for potential and promising pharmacological uses in human diseases, including inflammation, tumors, immunity disorders, kidney diseases, and diabetes. Physicochemical and chemical properties are the main contributors to these bioactivities. The previous literature has attributed such activities to its ability to target key enzymes and receptors involved in potential disease pathways, either directly or indirectly, where the anionic sulfate ester groups are mainly involved in these interactions. These findings also confirm the advantageous pharmacological uses of sulfated versus non-sulfated polysaccharides. The current review shall highlight the molecular targets of fucoidans, especially enzymes, and the subsequent responses via either the upregulation or downregulation of mediators' expression in various tissue abnormalities. In addition, in silico studies will be applied to support the previous findings and show the significant contributors. The current review may help in understanding the molecular mechanisms of fucoidan. Also, the findings of this review may be utilized in the design of specific oligomers inspired by fucoidan with the purpose of treating life-threatening human diseases effectively.
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Affiliation(s)
- Ahmed Zayed
- Institute of Bioprocess Engineering, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Gottlieb-Daimler-Straße 49, 67663 Kaiserslautern, Germany
- Department of Pharmacognosy, College of Pharmacy, Tanta University, El-Guish Street (Medical Campus), Tanta 31527, Egypt
| | - Dalal A. Al-Saedi
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Emmanuel Ofosu Mensah
- Faculty of Ecotechnology, ITMO University, Lomonosova Street 9, Saint Petersburg 191002, Russia;
| | - Osman Nabayire Kanwugu
- Institute of Chemical Engineering, Ural Federal University, Mira Street 28, Yekaterinburg 620002, Russia;
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand;
| | - Roland Ulber
- Institute of Bioprocess Engineering, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Gottlieb-Daimler-Straße 49, 67663 Kaiserslautern, Germany
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Muthamil S, Muthuramalingam P, Kim HY, Jang HJ, Lyu JH, Shin UC, Go Y, Park SH, Lee HG, Shin H, Park JH. Unlocking Prognostic Genes and Multi-Targeted Therapeutic Bioactives from Herbal Medicines to Combat Cancer-Associated Cachexia: A Transcriptomics and Network Pharmacology Approach. Int J Mol Sci 2023; 25:156. [PMID: 38203330 PMCID: PMC10778733 DOI: 10.3390/ijms25010156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Cachexia is a devastating fat tissue and muscle wasting syndrome associated with every major chronic illness, including cancer, chronic obstructive pulmonary disease, kidney disease, AIDS, and heart failure. Despite two decades of intense research, cachexia remains under-recognized by oncologists. While numerous drug candidates have been proposed for cachexia treatment, none have achieved clinical success. Only a few drugs are approved by the FDA for cachexia therapy, but a very low success rate is observed among patients. Currently, the identification of drugs from herbal medicines is a frontier research area for many diseases. In this milieu, network pharmacology, transcriptomics, cheminformatics, and molecular docking approaches were used to identify potential bioactive compounds from herbal medicines for the treatment of cancer-related cachexia. The network pharmacology approach is used to select the 32 unique genes from 238 genes involved in cachexia-related pathways, which are targeted by 34 phytocompounds identified from 12 different herbal medicines used for the treatment of muscle wasting in many countries. Gene expression profiling and functional enrichment analysis are applied to decipher the role of unique genes in cancer-associated cachexia pathways. In addition, the pharmacological properties and molecular interactions of the phytocompounds were analyzed to find the target compounds for cachexia therapy. Altogether, combined omics and network pharmacology approaches were used in the current study to untangle the complex prognostic genes involved in cachexia and phytocompounds with anti-cachectic efficacy. However, further functional and experimental validations are required to confirm the efficacy of these phytocompounds as commercial drug candidates for cancer-associated cachexia.
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Affiliation(s)
- Subramanian Muthamil
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju 58245, Republic of Korea; (S.M.); (H.-Y.K.); (H.-J.J.); (J.-H.L.); (U.C.S.)
| | - Pandiyan Muthuramalingam
- Division of Horticultural Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52725, Republic of Korea; (P.M.); (H.S.)
| | - Hyun-Yong Kim
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju 58245, Republic of Korea; (S.M.); (H.-Y.K.); (H.-J.J.); (J.-H.L.); (U.C.S.)
| | - Hyun-Jun Jang
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju 58245, Republic of Korea; (S.M.); (H.-Y.K.); (H.-J.J.); (J.-H.L.); (U.C.S.)
| | - Ji-Hyo Lyu
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju 58245, Republic of Korea; (S.M.); (H.-Y.K.); (H.-J.J.); (J.-H.L.); (U.C.S.)
| | - Ung Cheol Shin
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju 58245, Republic of Korea; (S.M.); (H.-Y.K.); (H.-J.J.); (J.-H.L.); (U.C.S.)
| | - Younghoon Go
- Korean Medicine (KM)-Application Center, Korea Institute of Oriental Medicine, Daegu 41062, Republic of Korea;
| | - Seong-Hoon Park
- Genetic and Epigenetic Toxicology Research Group, Korea Institute of Toxicology, Daejeon 34141, Republic of Korea;
| | - Hee Gu Lee
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea;
| | - Hyunsuk Shin
- Division of Horticultural Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52725, Republic of Korea; (P.M.); (H.S.)
| | - Jun Hong Park
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju 58245, Republic of Korea; (S.M.); (H.-Y.K.); (H.-J.J.); (J.-H.L.); (U.C.S.)
- Korean Convergence Medicine Major, University of Science & Technology (UST), KIOM Campus, Daejeon 34054, Republic of Korea
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Liu L, Chen Y, Chen B, Xu M, Liu S, Su Y, Qiao K, Liu Z. Advances in Research on Marine-Derived Lipid-Lowering Active Substances and Their Molecular Mechanisms. Nutrients 2023; 15:5118. [PMID: 38140377 PMCID: PMC10745522 DOI: 10.3390/nu15245118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/09/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Hyperlipidemia (HLP) is a metabolic disorder caused by abnormal lipid metabolism. Recently, the prevalence of HLP caused by poor dietary habits in the population has been increasing year by year. In addition, lipid-lowering drugs currently in clinical use have shown significant improvement in blood lipid levels, but are accompanied by certain side effects. However, bioactive marine substances have been shown to possess a variety of physiological activities such as hypoglycemic, antioxidant, antithrombotic and effects on blood pressure. Therefore, the hypolipidemic efficacy of marine bioactive substances with complex and diverse structures has also attracted attention. This paper focuses on the therapeutic role of marine-derived polysaccharides, unsaturated fatty acids, and bioactive peptides in HLP, and briefly discusses the main mechanisms by which these substances exert their hypolipidemic activity in vivo.
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Affiliation(s)
- Lina Liu
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (Y.C.)
- Engineering Research Center of Fujian and Taiwan Characteristic Marine Food Processing and Nutrition and Health, Ministry of Education, Fuzhou 350002, China
| | - Yihui Chen
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (Y.C.)
- Engineering Research Center of Fujian and Taiwan Characteristic Marine Food Processing and Nutrition and Health, Ministry of Education, Fuzhou 350002, China
| | - Bei Chen
- Fisheries Research Institute of Fujian, Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Xiamen 361013, China; (B.C.); (M.X.); (S.L.); (Y.S.)
| | - Min Xu
- Fisheries Research Institute of Fujian, Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Xiamen 361013, China; (B.C.); (M.X.); (S.L.); (Y.S.)
| | - Shuji Liu
- Fisheries Research Institute of Fujian, Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Xiamen 361013, China; (B.C.); (M.X.); (S.L.); (Y.S.)
| | - Yongchang Su
- Fisheries Research Institute of Fujian, Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Xiamen 361013, China; (B.C.); (M.X.); (S.L.); (Y.S.)
| | - Kun Qiao
- Fisheries Research Institute of Fujian, Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Xiamen 361013, China; (B.C.); (M.X.); (S.L.); (Y.S.)
| | - Zhiyu Liu
- Fisheries Research Institute of Fujian, Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Xiamen 361013, China; (B.C.); (M.X.); (S.L.); (Y.S.)
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Song J, Zaidi SAA, He L, Zhang S, Zhou G. Integrative Analysis of Machine Learning and Molecule Docking Simulations for Ischemic Stroke Diagnosis and Therapy. Molecules 2023; 28:7704. [PMID: 38067435 PMCID: PMC10707570 DOI: 10.3390/molecules28237704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
Due to the narrow therapeutic window and high mortality of ischemic stroke, it is of great significance to investigate its diagnosis and therapy. We employed weighted gene coexpression network analysis (WGCNA) to ascertain gene modules related to stroke and used the maSigPro R package to seek the time-dependent genes in the progression of stroke. Three machine learning algorithms were further employed to identify the feature genes of stroke. A nomogram model was built and applied to evaluate the stroke patients. We analyzed single-cell RNA sequencing (scRNA-seq) data to discern microglia subclusters in ischemic stroke. The RNA velocity, pseudo time, and gene set enrichment analysis (GSEA) were performed to investigate the relationship of microglia subclusters. Connectivity map (CMap) analysis and molecule docking were used to screen a therapeutic agent for stroke. A nomogram model based on the feature genes showed a clinical net benefit and enabled an accurate evaluation of stroke patients. The RNA velocity and pseudo time analysis showed that microglia subcluster 0 would develop toward subcluster 2 within 24 h from stroke onset. The GSEA showed that the function of microglia subcluster 0 was opposite to that of subcluster 2. AZ_628, which screened from CMap analysis, was found to have lower binding energy with Mmp12, Lgals3, Fam20c, Capg, Pkm2, Sdc4, and Itga5 in microglia subcluster 2 and maybe a therapeutic agent for the poor development of microglia subcluster 2 after stroke. Our study presents a nomogram model for stroke diagnosis and provides a potential molecule agent for stroke therapy.
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Affiliation(s)
- Jingwei Song
- Department of Medical Cell Biology and Genetics, Guangdong Key Laboratory of Genomic Stability and Disease Prevention, Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine, and Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Sciences Center, Shenzhen University, Shenzhen 518060, China; (J.S.); (S.A.A.Z.); (L.H.)
| | - Syed Aqib Ali Zaidi
- Department of Medical Cell Biology and Genetics, Guangdong Key Laboratory of Genomic Stability and Disease Prevention, Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine, and Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Sciences Center, Shenzhen University, Shenzhen 518060, China; (J.S.); (S.A.A.Z.); (L.H.)
| | - Liangge He
- Department of Medical Cell Biology and Genetics, Guangdong Key Laboratory of Genomic Stability and Disease Prevention, Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine, and Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Sciences Center, Shenzhen University, Shenzhen 518060, China; (J.S.); (S.A.A.Z.); (L.H.)
| | - Shuai Zhang
- Brain Research Centre, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guangqian Zhou
- Department of Medical Cell Biology and Genetics, Guangdong Key Laboratory of Genomic Stability and Disease Prevention, Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine, and Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Sciences Center, Shenzhen University, Shenzhen 518060, China; (J.S.); (S.A.A.Z.); (L.H.)
- Lungene Biotech Ltd., Shenzhen 518060, China
- Senotherapeutics Ltd., Hangzhou 311100, China
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