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Walesch S, Garcia R, Mahmoud AB, Panter F, Bollenbach S, Mäser P, Kaiser M, Krug D, Müller R. New myxobacteria of the Myxococcaceae clade produce angiolams with antiparasitic activities. Microbiol Spectr 2024; 12:e0368923. [PMID: 38298128 PMCID: PMC10913735 DOI: 10.1128/spectrum.03689-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024] Open
Abstract
In the past century, microbial natural products have proven themselves to be substantial and fruitful sources of anti-infectives. In addition to the well-studied Actinobacteria, understudied bacterial taxa like the Gram-negative myxobacteria have increasingly gained attention in the ongoing search for novel and biologically active natural products. In the course of a regional sampling campaign to source novel myxobacteria, we recently uncovered new myxobacterial strains MCy12716 and MCy12733 belonging to the Myxococcaceae clade. Early bioactivity screens of the bacterial extracts revealed the presence of bioactive natural products that were identified as angiolam A and several novel derivatives. Sequencing of the corresponding producer strains allowed the identification of the angiolam biosynthetic gene cluster, which was verified by targeted gene inactivation. Based on bioinformatic analysis of the biosynthetic gene cluster, a concise biosynthesis model was devised to explain angiolam biosynthesis. Importantly, novel angiolam derivatives uncovered in this study named angiolams B, C, and D were found to display promising antiparasitic activities against the malaria pathogen Plasmodium falciparum in the 0.3-0.8 µM range.IMPORTANCEThe COVID-19 pandemic and continuously emerging antimicrobial resistance (AMR) have recently raised awareness about limited treatment options against infectious diseases. However, the shortage of treatment options against protozoal parasitic infections, like malaria, is much more severe, especially for the treatment of so-called neglected tropical diseases. The detection of anti-parasitic bioactivities of angiolams produced by MCy12716 and MCy12733 displays the hidden potential of scarcely studied natural products to have promising biological activities in understudied indications. Furthermore, the improved biological activities of novel angiolam derivatives against Plasmodium falciparum and the evaluation of its biosynthesis display the opportunities of the angiolam scaffold on route to treat protozoal parasitic infections as well as possible ways to increase the production of derivatives with improved bioactivities.
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Affiliation(s)
- Sebastian Walesch
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- DZIF-German Center for Infection Research, partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Ronald Garcia
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- DZIF-German Center for Infection Research, partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Abdelhalim B. Mahmoud
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- DZIF-German Center for Infection Research, partner site Hannover-Braunschweig, Braunschweig, Germany
- Faculty of Pharmacy, University of Khartoum, Khartoum, Sudan
| | - Fabian Panter
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- DZIF-German Center for Infection Research, partner site Hannover-Braunschweig, Braunschweig, Germany
- Helmholtz International Lab for Anti-Infectives, Saarbrücken, Germany
| | - Sophie Bollenbach
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- DZIF-German Center for Infection Research, partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Pascal Mäser
- Parasite Chemotherapy Unit, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Marcel Kaiser
- Parasite Chemotherapy Unit, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Daniel Krug
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- DZIF-German Center for Infection Research, partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- DZIF-German Center for Infection Research, partner site Hannover-Braunschweig, Braunschweig, Germany
- Helmholtz International Lab for Anti-Infectives, Saarbrücken, Germany
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Hao L, Zhong X, Yu R, Chen J, Li W, Chen Y, Lu W, Wu J, Wang P. Integrating Network Pharmacology and Experimental Validation to Decipher the Anti-Inflammatory Effects of Magnolol on LPS-induced RAW264.7 Cells. Comb Chem High Throughput Screen 2024; 27:462-478. [PMID: 37818577 DOI: 10.2174/0113862073255964230927105959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/11/2023] [Accepted: 08/11/2023] [Indexed: 10/12/2023]
Abstract
INTRODUCTION Magnolol is beneficial against inflammation-mediated damage. However, the underlying mechanisms by which magnolol exerts anti-inflammatory effects on macrophages remain unclear. OBJECTIVE In this study, network pharmacology and experimental validation were used to assess the effect of magnolol on inflammation caused by lipopolysaccharide (LPS) in RAW264.7 cells. MATERIALS AND METHODS Genes related to magnolol were identified in the PubChem and Swiss Target Prediction databases, and gene information about macrophage polarization was retrieved from the GeneCards, OMIM, and PharmGKB databases. Analysis of protein-protein interactions was performed with STRING, and Cytoscape was used to construct a component-target-disease network. GO and KEGG enrichment analyses were performed to ascertain significant molecular biological processes and signaling pathways. LPS was used to construct the inflammatory cell model. ELISA and qRT.PCR were used to examine the expression levels of inflammationassociated factors, immunofluorescence was used to examine macrophage markers (CD86 and CD206), and western blotting was used to examine protein expression levels. RESULTS The hub target genes of magnolol that act on macrophage polarization were MDM2, MMP9, IL-6, TNF, EGFR, AKT1, and ERBB2. The experimental validation results showed that magnolol treatment decreased the levels of proinflammatory factors (TNF-α, IL-1β, and IL-6). Moreover, the levels of anti-inflammatory factors (IL-10 and IL-4) were increased. In addition, magnolol upregulated the expression of M2 markers (Agr-1, Fizzl, and CD206) and downregulated M1 markers (CD86). The cell experiment results supported the network pharmacological results and demonstrated that magnolol alleviated inflammation by modulating the PI3k-Akt and P62/keap1/Nrf2 signaling pathways. CONCLUSION According to network pharmacology and experimental validation, magnolol attenuated inflammation in LPS-induced RAW264.7 cells mainly by inhibiting M1 polarization and enhancing M2 polarization by activating the PI3K/Akt and P62/keap1/Nrf2 signaling pathways.
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Affiliation(s)
- Lei Hao
- Department of Surgery Two, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaoying Zhong
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Runjia Yu
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiahui Chen
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wei Li
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuzhong Chen
- Department of Surgery Two, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Weiqi Lu
- Department of Surgery Two, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jianyu Wu
- Department of Surgery Two, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Peizong Wang
- State Key Laboratory of Oncology in South China, Department of Anesthesiology, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P.R. China
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Quimque MTJ, Go AD, Lim JAK, Vidar WS, Macabeo APG. Mycobacterium tuberculosis Inhibitors Based on Arylated Quinoline Carboxylic Acid Backbones with Anti- Mtb Gyrase Activity. Int J Mol Sci 2023; 24:11632. [PMID: 37511390 PMCID: PMC10380224 DOI: 10.3390/ijms241411632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
New antitubercular agents with either a novel mode of action or novel mode of inhibition are urgently needed to overcome the threat of drug-resistant tuberculosis (TB). The present study profiles new arylated quinoline carboxylic acids (QCAs) having activity against replicating and non-replicating Mycobacterium tuberculosis (Mtb), the causative agent of TB. Thus, the synthesis, characterization, and in vitro screening (MABA and LORA) of 48 QCAs modified with alkyl, aryl, alkoxy, halogens, and nitro groups in the quinoline ring led to the discovery of two QCA derivatives, 7i and 7m, adorned with C-2 2-(naphthalen-2-yl)/C-6 1-butyl and C-2 22-(phenanthren-3-yl)/C-6 isopropyl, respectively, as the best Mtb inhibitors. DNA gyrase inhibition was shown to be exhibited by both, with QCA 7m illustrating better activity up to a 1 μM test concentration. Finally, a docking model for both compounds with Mtb DNA gyrase was developed, and it showed a good correlation with in vitro results.
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Affiliation(s)
- Mark Tristan J Quimque
- The Graduate School, University of Santo Tomas, España Blvd., Manila 1015, Philippines
- Laboratory for Organic Reactivity, Discovery and Synthesis (Rm. 410), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Espana Blvd., Manila 1015, Philippines
- Chemistry Department, College of Science and Mathematics, Mindanao State University-Iligan Institute of Technology, Tibanga, Iligan City 9200, Philippines
| | - Adrian D Go
- Laboratory for Organic Reactivity, Discovery and Synthesis (Rm. 410), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Espana Blvd., Manila 1015, Philippines
| | - Justin Allen K Lim
- Laboratory for Organic Reactivity, Discovery and Synthesis (Rm. 410), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Espana Blvd., Manila 1015, Philippines
| | - Warren S Vidar
- Laboratory for Organic Reactivity, Discovery and Synthesis (Rm. 410), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Espana Blvd., Manila 1015, Philippines
| | - Allan Patrick G Macabeo
- Laboratory for Organic Reactivity, Discovery and Synthesis (Rm. 410), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Espana Blvd., Manila 1015, Philippines
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Aziz S, Waqas M, Mohanta TK, Halim SA, Iqbal A, Ali A, Khalid A, Abdalla AN, Khan A, Al-Harrasi A. Identifying non-nucleoside inhibitors of RNA-dependent RNA-polymerase of SARS-CoV-2 through per-residue energy decomposition-based pharmacophore modeling, molecular docking, and molecular dynamics simulation. J Infect Public Health 2023; 16:501-519. [PMID: 36801630 PMCID: PMC9927802 DOI: 10.1016/j.jiph.2023.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND AND OBJECTIVE The current coronavirus disease-2019 (COVID-19) pandemic has triggered a worldwide health and economic crisis. The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes the disease and completes its life cycle using the RNA-dependent RNA-polymerase (RdRp) enzyme, a prominent target for antivirals. In this study, we have computationally screened ∼690 million compounds from the ZINC20 database and 11,698 small molecule inhibitors from DrugBank to find existing and novel non-nucleoside inhibitors for SARS-CoV-2 RdRp. METHODS Herein, a combination of the structure-based pharmacophore modeling and hybrid virtual screening methods, including per-residue energy decomposition-based pharmacophore screening, molecular docking, pharmacokinetics, and toxicity evaluation were employed to retrieve novel as well as existing RdRp non-nucleoside inhibitors from large chemical databases. Besides, molecular dynamics simulation and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) method were used to investigate the binding stability and calculate the binding free energy of RdRp-inhibitor complexes. RESULTS Based on docking scores and significant binding interactions with crucial residues (Lys553, Arg557, Lys623, Cys815, and Ser816) in the RNA binding site of RdRp, three existing drugs, ZINC285540154, ZINC98208626, ZINC28467879, and five compounds from ZINC20 (ZINC739681614, ZINC1166211307, ZINC611516532, ZINC1602963057, and ZINC1398350200) were selected, and the conformational stability of RdRp due to their binding was confirmed through molecular dynamics simulation. The free energy calculations revealed these compounds possess strong binding affinities for RdRp. In addition, these novel inhibitors exhibited drug-like features, good absorption, distribution, metabolism, and excretion profile and were found to be non-toxic. CONCLUSION The compounds identified in the study by multifold computational strategy can be validated in vitro as potential non-nucleoside inhibitors of SARS-CoV-2 RdRp and holds promise for the discovery of novel drugs against COVID-19 in future.
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Affiliation(s)
- Shahkaar Aziz
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25000, Pakistan
| | - Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, 2100, Pakistan; Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Aqib Iqbal
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25000, Pakistan; Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan.
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, 2100, Pakistan
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, Jazan 45142, Saudi Arabia; Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, P. O. Box 2404, Khartoum, Sudan
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman.
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Sabzian-Molaei F, Hosseini S, Alipour A, Ghaderi H, Fotouhi-Chahouki F, Hadi A, Shahsavarani H. Urtica dioica agglutinin (UDA) as a potential candidate for inhibition of SARS-CoV-2 Omicron variants: In silico prediction and experimental validation. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 111:154648. [PMID: 36681052 PMCID: PMC9815882 DOI: 10.1016/j.phymed.2023.154648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/27/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND The high number of mutations and consequent structure modifications in a Receptor-Binding Domain (RBD) of the spike protein of the Omicron variant of SARS-CoV-2 increased concerns about evading neutralization by antibodies induced by previous infection or vaccination. Thus, developing novel drugs with potent inhibitory activity can be considered an alternative for treating this highly transmissible variant. Considering that Urtica dioica agglutinin (UDA) displays antiviral activity against SARS-CoV-2, the potency of this lectin to inhibit the Receptor Binding Domain of the Omicron variant (RBDOmic) was examined in this study. PURPOSE This study examines how UDA inhibits the Omicron variant of SARS-CoV-2 by blocking its RBD, using a combination of in silico and experimental methods. METHODS To investigate the interaction between UDA and RBDOmic, the CLUSPRO 2.0 web server was used to dock the RBDOmic-UDA complex, and molecular dynamics simulations were performed by the Gromacs 2020.2 software to confirm the stability of the selected docked complex. Finally, the binding affinity (ΔG) of the simulation was calculated using MM-PBSA. In addition, ELISA and Western blot tests were used to examine UDA's binding to RBDOmic. RESULTS Based on the docking results, UDA forms five hydrogen bonds with the RBDOmic active site, which contains mutated residues Tyr501, Arg498, Arg493, and His505. According to MD simulations, the UDA-RBDOmic complex is stable over 100 ns, and its average binding energy during the simulation is -87.201 kJ/mol. Also, the ELISA test showed that UDA significantly binds to RBDOmic, and by increasing the concentration of UDA protein, the attachment to RBDOmic became stronger. In Western blotting, RBDOmic was able to attach to and detect UDA. CONCLUSION This study indicates that UDA interaction with RBDOmic prevents virus attachment to Angiotensin-converting enzyme 2 (ACE2) and, therefore, its entry into the host cell. Altogether, UDA exhibited a significant suppression effect on the Omicron variant and can be considered a new candidate to improve protection against severe infection of this variant.
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Affiliation(s)
- Fatemeh Sabzian-Molaei
- Laboratory of Regenerative Medicine & Biomedical Innovations, Pasteur Institute of Iran, Tehran, Iran
| | | | - Atefeh Alipour
- Department of Nanobiotechnology, Pasteur Institute of Iran, Tehran, Iran.
| | - Hajarossadat Ghaderi
- Laboratory of Regenerative Medicine & Biomedical Innovations, Pasteur Institute of Iran, Tehran, Iran
| | | | - Amin Hadi
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran.
| | - Hosein Shahsavarani
- Laboratory of Regenerative Medicine & Biomedical Innovations, Pasteur Institute of Iran, Tehran, Iran; Department of Cell and Molecular Biology, Faculty of Life science and Biotechnology, Shahid Beheshti University, Tehran, Iran.
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Notarte KI, Quimque MTJ, Macaranas IT, Khan A, Pastrana AM, Villaflores OB, Arturo HC, Pilapil IV DYH, Tan SMM, Wei DQ, Wenzel-Storjohann A, Tasdemir D, Yen CH, Ji SY, Kim GY, Choi YH, Macabeo APG. Attenuation of Lipopolysaccharide-Induced Inflammatory Responses through Inhibition of the NF-κB Pathway and the Increased NRF2 Level by a Flavonol-Enriched n-Butanol Fraction from Uvaria alba. ACS OMEGA 2023; 8:5377-5392. [PMID: 36816691 PMCID: PMC9933231 DOI: 10.1021/acsomega.2c06451] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/18/2023] [Indexed: 05/12/2023]
Abstract
Pathologic hyperreactive inflammatory responses occur when there is excessive activation of a proinflammatory NF-κB pathway and a reduced cytoprotective NRF2 cascade. The noncytotoxic, highly selective COX-2 inhibitory flavonol-enriched butanol fraction (UaB) from Uvaria alba (U. alba) was investigated for its inflammatory modulating potential by targeting NF-κB activation and NRF2 activity. Enzyme-linked immunosorbent assay was initially performed to measure levels of proinflammatory mediators [nitric oxide (NO), prostaglandin E2, and reactive oxygen species (ROS)] and cytokines [tumor necrosis factor-alpha (TNF-α), IL-1β, and IL-6], followed by reverse transcription-polymerase chain reaction and western blotting to determine mRNA and protein expression, respectively. Using immunofluorescence staining combined with western blot analysis, the activation of NF-κB was further investigated. NRF2 activity was also measured using a luciferase reporter assay. UaB abrogated protein and mRNA expressions of inducible nitric oxide synthase (iNOS), COX-2, TNF-α, IL-1β, and IL-6 in RAW 264.7 macrophages, thereby suppressing the production of proinflammatory mediators and cytokines. This was further validated when a concentration-dependent decrease in NO and ROS production was observed in zebrafish (Danio rerio) larvae. UaB also increased NRF2 activity in HaCaT/ARE cell line and attenuated NF-κB activation by inhibiting the nuclear translocation of transcription factor p65 in RAW 264.7 macrophages. Nontargeted LC-MS analysis of UaB revealed the presence of the flavonols quercitrin (1), quercetin (2), rutin (3), kaempferol (4), and kaempferol 3-O-rutinoside (5). Molecular docking indicates that major flavonol aglycones have high affinity toward COX-2 NSAID-binding sites, TNF-α, and TNF-α converting enzyme, while the glycosylated flavonoids showed strong binding toward iNOS and IKK-all possessing dynamic stability when performing molecular dynamics simulations at 140 ns. This is the first report to have elucidated the mechanistic anti-inflammatory potential of the Philippine endemic plant U. alba.
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Affiliation(s)
- Kin Israel
R. Notarte
- Laboratory
of Organic Reactivity, Discovery and Synthesis (LORDS), Research Center
for Natural and Applied Sciences, University
of Santo Tomas, España, 1015Manila, Philippines
- Department
of Pathology, Johns Hopkins University School
of Medicine, Baltimore, Maryland21218, United
States
| | - Mark Tristan J. Quimque
- Laboratory
of Organic Reactivity, Discovery and Synthesis (LORDS), Research Center
for Natural and Applied Sciences, University
of Santo Tomas, España, 1015Manila, Philippines
- Chemistry
Department, College of Science and Mathematics, Mindanao State University - Iligan Institute of Technology, Tibanga, 9200Iligan City, Philippines
| | - Imee T. Macaranas
- Faculty
of Medicine and Surgery, University of Santo
Tomas, España, 1008Manila, Philippines
| | - Abbas Khan
- Department
of Bioinformatics and Biostatistics, State Key Laboratory of Microbial
Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road Shanghai, Minhang
District, Shanghai200240, China
| | - Adriel M. Pastrana
- Faculty
of Medicine and Surgery, University of Santo
Tomas, España, 1008Manila, Philippines
| | - Oliver B. Villaflores
- Laboratory
of Phytochemistry, Research Center for Natural and Applied Sciences, University of Santo Tomas, España, 1015Manila, Philippines
| | - Hans Christian
P. Arturo
- Laboratory
of Organic Reactivity, Discovery and Synthesis (LORDS), Research Center
for Natural and Applied Sciences, University
of Santo Tomas, España, 1015Manila, Philippines
| | - Delfin Yñigo H. Pilapil IV
- Laboratory
of Organic Reactivity, Discovery and Synthesis (LORDS), Research Center
for Natural and Applied Sciences, University
of Santo Tomas, España, 1015Manila, Philippines
| | - Sophia Morgan M. Tan
- Laboratory
of Organic Reactivity, Discovery and Synthesis (LORDS), Research Center
for Natural and Applied Sciences, University
of Santo Tomas, España, 1015Manila, Philippines
| | - Dong-Qing Wei
- Department
of Bioinformatics and Biostatistics, State Key Laboratory of Microbial
Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road Shanghai, Minhang
District, Shanghai200240, China
| | - Arlette Wenzel-Storjohann
- GEOMAR
Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine
Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research
Kiel, 24106Kiel, Germany
| | - Deniz Tasdemir
- GEOMAR
Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine
Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research
Kiel, 24106Kiel, Germany
- Faculty
of Mathematics and Natural Sciences, Kiel
University, 24118Kiel, Germany
| | - Chia-Hung Yen
- National
Natural Product Libraries and High-Throughput Screening Core Facility, Kaohsiung Medical University, Kaohsiung80708, Taiwan
| | - Seon Yeong Ji
- Department
of Biochemistry, Dongeui University College
of Korean Medicine, 52-57,
Yangjeong-ro, Busanjin-gu, Busan47227Republic of Korea
| | - Gi-Young Kim
- Department
of Marine Life Science, Jeju National University, 102 Jejudaehak-ro, Jeju-si, Jeju Special Self-Governing Province63243, Republic of Korea
| | - Yung Hyun Choi
- Department
of Biochemistry, Dongeui University College
of Korean Medicine, 52-57,
Yangjeong-ro, Busanjin-gu, Busan47227Republic of Korea
| | - Allan Patrick G. Macabeo
- Laboratory
of Organic Reactivity, Discovery and Synthesis (LORDS), Research Center
for Natural and Applied Sciences, University
of Santo Tomas, España, 1015Manila, Philippines
- ;
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Indari O, Kumar Singh A, Tiwari D, Chandra Jha H, Nath Jha A. Deciphering antiviral efficacy of malaria box compounds against malaria exacerbating viral pathogens- Epstein Barr Virus and SARS-CoV-2, an in silico study. MEDICINE IN DRUG DISCOVERY 2022; 16:100146. [DOI: 10.1016/j.medidd.2022.100146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/18/2022] [Accepted: 09/04/2022] [Indexed: 11/10/2022] Open
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Elumalai E, Suresh Kumar M. Identification of neo-andrographolide compound targeting NS1 Lys14: an important residue in NS1 activity driving dengue pathogenesis. J Biomol Struct Dyn 2022:1-11. [DOI: 10.1080/07391102.2022.2068073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Elakkiya Elumalai
- Center for Bioinformatics, Pondicherry University, Pondicherry, India
| | - M. Suresh Kumar
- Center for Bioinformatics, Pondicherry University, Pondicherry, India
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de Jesus MSM, Macabeo APG, Ramos JDA, de Leon VNO, Asamitsu K, Okamoto T. Voacanga globosa Spirobisindole Alkaloids Exert Antiviral Activity in HIV Latently Infected Cell Lines by Targeting the NF-kB Cascade: In Vitro and In Silico Investigations. Molecules 2022; 27:1078. [PMID: 35164343 PMCID: PMC8840767 DOI: 10.3390/molecules27031078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 11/16/2022] Open
Abstract
Since the efficiency in the transcription of the HIV genome contributes to the success of viral replication and infectivity, we investigated the downregulating effects of the spirobisindole alkaloids globospiramine (1), deoxyvobtusine (2), and vobtusine lactone (3) from the endemic Philippine medicinal plant, Voacanga globosa, during HIV gene transcription. Alkaloids 1-3 were explored for their inhibitory activity on TNF-α-induced viral replication in two latently HIV-infected cell lines, OM10.1 and J-Lat. The induction of HIV replication from OM10.1 and J-Lat cells elicited by TNF-α was blocked by globospiramine (1) within noncytotoxic concentrations. Furthermore, globospiramine (1) was found to target the NF-ĸB activation cascade in a dose-dependent manner when the transcriptional step at which inhibitory activity is exerted was examined in TNF-α-induced 293 human cells using transient reporter (luciferase) gene expression systems (HIV LTR-luc, ĸB-luc, and mutant ĸB-luc). Interrogation through molecular docking against the NF-ĸB p50/p65 heterodimer and target sites of the subunits comprising the IKK complex revealed high binding affinities of globospiramine (1) against the S281 pocket of the p65 subunit (BE = -9.2 kcal/mol) and the IKKα activation loop (BE = -9.1 kcal/mol). These findings suggest globospiramine (1) as a molecular inspiration to discover new alkaloid-based anti-HIV derivatives.
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Affiliation(s)
- Ma. Sheila M. de Jesus
- The Graduate School, University of Santo Tomas, España Blvd., Manila 1015, Philippines;
- Department of Biological Sciences, College of Science, University of Santo Tomas, España Blvd., Manila 1015, Philippines;
| | - Allan Patrick G. Macabeo
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for Natural and Applied Sciences, University of Santo Tomas, España Blvd., Manila 1015, Philippines;
| | - John Donnie A. Ramos
- The Graduate School, University of Santo Tomas, España Blvd., Manila 1015, Philippines;
- Department of Biological Sciences, College of Science, University of Santo Tomas, España Blvd., Manila 1015, Philippines;
- Molecular Diagnostics and Therapeutics Laboratory, Research Center for Natural and Applied Sciences, University of Santo Tomas, España Blvd., Manila 1015, Philippines
| | - Von Novi O. de Leon
- Department of Biological Sciences, College of Science, University of Santo Tomas, España Blvd., Manila 1015, Philippines;
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for Natural and Applied Sciences, University of Santo Tomas, España Blvd., Manila 1015, Philippines;
| | - Kaori Asamitsu
- Department of Molecular and Cellular Biology, Graduate School of Medical Sciences, Nagoya City University, Nagoya 4678601, Japan; (K.A.); (T.O.)
| | - Takashi Okamoto
- Department of Molecular and Cellular Biology, Graduate School of Medical Sciences, Nagoya City University, Nagoya 4678601, Japan; (K.A.); (T.O.)
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Virtual Combinatorial Library Screening of Quinadoline B Derivatives against SARS-CoV-2 RNA-Dependent RNA Polymerase. COMPUTATION 2022. [DOI: 10.3390/computation10010007] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The unprecedented global health threat of SARS-CoV-2 has sparked a continued interest in discovering novel anti-COVID-19 agents. To this end, we present here a computer-based protocol for identifying potential compounds targeting RNA-dependent RNA polymerase (RdRp). Starting from our previous study wherein, using a virtual screening campaign, we identified a fumiquinazolinone alkaloid quinadoline B (Q3), an antiviral fungal metabolite with significant activity against SARS-CoV-2 RdRp, we applied in silico combinatorial methodologies for generating and screening a library of anti-SARS-CoV-2 candidates with strong in silico affinity for RdRp. For this study, the quinadoline pharmacophore was subjected to structural iteration, obtaining a Q3-focused library of over 900,000 unique structures. This chemical library was explored to identify binders of RdRp with greater affinity with respect to the starting compound Q3. Coupling this approach with the evaluation of physchem profile, we found 26 compounds with significant affinities for the RdRp binding site. Moreover, top-ranked compounds were submitted to molecular dynamics to evaluate the stability of the systems during a selected time, and to deeply investigate the binding mode of the most promising derivatives. Among the generated structures, five compounds, obtained by inserting nucleotide-like scaffolds (1, 2, and 5), heterocyclic thiazolyl benzamide moiety (compound 3), and a peptide residue (compound 4), exhibited enhanced binding affinity for SARS-CoV-2 RdRp, deserving further investigation as possible antiviral agents. Remarkably, the presented in silico procedure provides a useful computational procedure for hit-to-lead optimization, having implications in anti-SARS-CoV-2 drug discovery and in general in the drug optimization process.
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