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Sabuakham S, Nasoontorn S, Kongtaworn N, Rungrotmongkol T, Silsirivanit A, Pingaew R, Mahalapbutr P. Anilino-1,4-naphthoquinones as potent mushroom tyrosinase inhibitors: in vitro and in silico studies. J Enzyme Inhib Med Chem 2024; 39:2357174. [PMID: 38814149 PMCID: PMC11141316 DOI: 10.1080/14756366.2024.2357174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/14/2024] [Indexed: 05/31/2024] Open
Abstract
Tyrosinase, a pivotal enzyme in melanin synthesis, is a primary target for the development of depigmenting agents. In this work, in vitro and in silico techniques were employed to identify novel tyrosinase inhibitors from a set of 12 anilino-1,4-naphthoquinone derivatives. Results from the mushroom tyrosinase activity assay indicated that, among the 12 derivatives, three compounds (1, 5, and 10) demonstrated the most significant inhibitory activity against mushroom tyrosinase, surpassing the effectiveness of the kojic acid. Molecular docking revealed that all studied derivatives interacted with copper ions and amino acid residues at the enzyme active site. Molecular dynamics simulations provided insights into the stability of enzyme-inhibitor complexes, in which compounds 1, 5, and particularly 10 displayed greater stability, atomic contacts, and structural compactness than kojic acid. Drug likeness prediction further strengthens the potential of anilino-1,4-naphthoquinones as promising candidates for the development of novel tyrosinase inhibitors for the treatment of hyperpigmentation disorders.
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Affiliation(s)
- Sahachai Sabuakham
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sutita Nasoontorn
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Napat Kongtaworn
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Atit Silsirivanit
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Ratchanok Pingaew
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand
| | - Panupong Mahalapbutr
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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Zhao F, Zhang K, Ma L, Huang Y. Identification of epithelial-related artificial neural network prognostic models for the prediction of bladder cancer prognosis through comprehensive analysis of single-cell and bulk RNA sequencing. Heliyon 2024; 10:e34632. [PMID: 39157397 PMCID: PMC11328080 DOI: 10.1016/j.heliyon.2024.e34632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/03/2024] [Accepted: 07/12/2024] [Indexed: 08/20/2024] Open
Abstract
Background Bladder cancer (BLCA) presents as a heterogeneous epithelial malignancy. Progress in the early detection and effective treatment of BLCA relies heavily on the identification of novel biomarkers. Therefore, the primary goal of this study is to pinpoint potential biomarkers for BLCA through the fusion of single-cell RNA sequencing and RNA sequencing assessments. Furthermore, the aim is to establish practical clinical prognostic models that can facilitate accurate categorization and individualized therapy for patients. Methods In this research, training sets were acquired from the TCGA database, whereas validation sets (GSE32894) and single-cell datasets (GSE135337) were extracted from the GEO database. Single-cell analysis was utilized to obtain characteristic subpopulations along with their associated marker genes. Subsequently, a novel BLCA subtype was identified within TCGA-BLCA. Furthermore, an artificial neural network prognostic model was constructed within the TCGA-BLCA cohort and subsequently verified utilizing a validation set. Two machine learning algorithms were employed to screen hub genes. QRT-qPCR was performed to detect the gene expression levels utilized in the construction of prognostic models across various cell lines. Additionally, the cMAP database and molecular docking were utilized for searching small molecule drugs. Results The results of single-cell analysis revealed the presence of epithelial cells in multiple subpopulations, with 1579 marker genes selected for subsequent investigations. Subsequently, four epithelial cell subtypes were identified within the TCGA-BLCA cohort. Notably, cluster A exhibited a significant survival advantage. Concurrently, an artificial neural network prognostic model comprising 17 feature genes was constructed, accurately stratifying patient risk. Patients categorized in the low-risk group demonstrated a considerable survival advantage. The ROC analysis suggested that the model has strong prognostic ability. Furthermore, the findings of the validation group align consistently with those from the training group. Two types of machine learning algorithms screened NFIC as hub genes. Forskolin, a small molecule drug that binds to NFIC, was identified by employing a cMAP database and molecular docking. Conclusion The analysis results supplement the research on the role of epithelial cells in BLCA. An artificial neural network prognostic model containing 17 characteristic genes demonstrates the capability to accurately stratify patient risk, thereby potentially improving clinical decision-making and optimizing personalized therapeutic approaches.
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Affiliation(s)
- Fan Zhao
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Kun Zhang
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Limin Ma
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Yeqing Huang
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, 226001, China
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Vaithiyalingam M, Mohan Kumar R, Khagar P, Sabarathinam S, Alghazwani Y, Chidambaram K. Isolation of 6-gingerol and semi-synthesis of 1,4-benzodiazepines derivatives: An in-situ pharmacokinetics properties, molecular docking and molecular dynamics simulation assessments. Saudi J Biol Sci 2024; 31:104048. [PMID: 38988339 PMCID: PMC11234153 DOI: 10.1016/j.sjbs.2024.104048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/31/2024] [Accepted: 06/07/2024] [Indexed: 07/12/2024] Open
Abstract
This paper outlines a methodical approach for isolating 6-gingerol (1a) from Zingiber officinale Roscoe rhizomes on a gram-scale, resulting in a product of high purity and significant yield. Further, 6-gingerol (1a) [SSG1] derivatives, including 1-(4-hydroxy-3-methoxyphenyl)decane-3,5-dione (1ab), were synthesized via a semi-synthetic pathway involving DMP-mediated fast oxidation and replication. Subsequently, a new series of 1,4-benzodiazepines (3a-c) was synthesized quantitatively using a basic technique. This synthesis necessitated the interaction of 1ab with various o-phenylenediamine (2a-c) compounds. Spectroscopic methods were employed to characterize the synthesized 1,4-benzodiazepines (3a-c)[SSG2, SSG3 & SSG4]. Despite extensive investments by pharmaceutical companies in traditional drug research and development for diseases like type 2 diabetes (T2D), successful treatments remain elusive. Medication repurposing has gained traction as a strategy to address not only diabetes but also other disorders. Leveraging existing molecular pharmacology data accelerates the development of new medications. This paper underscores the importance of repurposing traditional medicines to combat a range of communicable and non-communicable diseases, offering a promising avenue for therapeutic advancement. Additionally, molecular docking studies suggested that one derivative (SSG2) exhibited stronger binding affinity compared to the reference standards. Overall, the findings of this study highlight the potential of semi-synthetic gingerol derivatives for the development of novel therapeutic agents.
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Affiliation(s)
- Mariyappan Vaithiyalingam
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu 603 203, India
| | - Ramasamy Mohan Kumar
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu 603 203, India
- Interdisciplinary Institute of Indian System of Medicine, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu 603 203, India
| | - Prerna Khagar
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur 440010 MS India
| | - Sarvesh Sabarathinam
- Interdisciplinary Institute of Indian System of Medicine, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu 603 203, India
| | - Yahia Alghazwani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Al-Qara, Asir Province, Saudi Arabia
| | - Kumarappan Chidambaram
- Department of Pharmacology & Toxicology, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia
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Singh D, Mittal N, Mittal P, Tiwari N, Khan SUD, Ali MAM, Chaudhary AA, Siddiqui MH. In silico molecular screening of bioactive natural compounds of rosemary essential oil and extracts for pharmacological potentials against rhinoviruses. Sci Rep 2024; 14:17426. [PMID: 39075176 PMCID: PMC11286848 DOI: 10.1038/s41598-024-68450-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 07/23/2024] [Indexed: 07/31/2024] Open
Abstract
Rhinoviruses (RVs) cause upper respiratory tract infections and pneumonia in children and adults. These non-enveloped viruses contain viral coats of four capsid proteins: VP1, VP2, VP3, and VP4. The canyon on VP1 used cell surface receptor ICAM-1 as the site of attachment and for the internalization of viruses. To date, there has been no drug or vaccine available against RVs. In this study, bioactive natural compounds of rosemary (Salvia rosmarinus L.), which are known for their pharmacological potential, were considered to target the VP1 protein. A total of 30 bioactive natural compounds of rosemary were taken as ligands to target viral proteins. The PkCSM tool was used to detect their adherence to Lipinski's rule of five and the ADMET properties of the selected ligands. Further, the CB-Dock tool was used for molecular docking studies between the VP1 protein and ligands. Based on the molecular docking and ADMET profiling results, phenethyl amine (4 methoxy benzyl) was selected as the lead compound. A comparative study was performed between the lead compound and two antiviral drugs, Placonaril and Nitazoxanide, to investigate the higher potential of natural compounds over synthetic drugs. Placonaril also targets VP1 but failed in clinical trials while Nitazoxanide was examined in clinical trials against rhinoviruses. It was discovered from this study that the (4 methoxy benzyl) phenethyl amine exhibited less toxicity in comparison to other tested drugs against RVs. More research is needed to determine its potential and make it a good medication against RVs.
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Affiliation(s)
- Dhananjay Singh
- Department of Biosciences, Integral University, Kursi Road, Lucknow, 226026, India
| | - Nishu Mittal
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, 225003, India
| | - Pooja Mittal
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, 140401, India
| | - Neeraj Tiwari
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, 225003, India
| | - Salah Ud-Din Khan
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), 11623, Riyadh, Saudi Arabia
| | - Mohamed A M Ali
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), 11623, Riyadh, Saudi Arabia
- Department of Biochemistry, Faculty of Science, Ain Shams University, Abbassia, Cairo, 11566, Egypt
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), 11623, Riyadh, Saudi Arabia.
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Wang R, Zhang L, Li X, Zhu L, Xiang Z, Xu J, Xue D, Deng Z, Su X, Zou M. High-Performance Aluminum Fuels Induced by Monolayer Self-Assembly of Nano-Sized Energetic Fluoride Vesicles on the Surface. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401564. [PMID: 38704734 PMCID: PMC11234408 DOI: 10.1002/advs.202401564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/17/2024] [Indexed: 05/07/2024]
Abstract
Surface modification is frequently used to solve the problems of low combustion properties and agglomeration for aluminum-based fuels. However, due to the intrinsic incompatibility between the aluminum powder and the organic modifiers, the surface coating is usually uneven and disordered, which significantly deteriorates the uniformity and performances of the Al-based fuels. Herein, a new approach of monolayer nano-vesicular self-assembly is proposed to prepare high-performance Al fuels. Triblock copolymer G-F-G is produced by glycidyl azide polymer (GAP) and 2,2'-(2,2,3,3,4,5,5-Octafluorohexane-1,6-diyl) bis (oxirane) (fluoride) ring-open addition reaction. By utilizing G-F-G vesicular self-assembly in a special solvent, the nano-sized vesicles are firmly adhered to the surface of Al powder through the long-range attraction between the fluorine segments and Al. Meanwhile, the electrostatic repulsion between vesicles ensures an extremely thin coating thickness (≈15 nm), maintaining the monolayer coating structure. Nice ignition, combustion, anti-agglomeration, and water-proof properties of Al@G-F-G(DMF) are achieved, which are superior among the existing Al-based fuels. The derived Al-based fuel has excellent comprehensive properties, which can not only inspire the development of new-generation energetic materials but also provide facile but exquisite strategies for exquisite surface nanostructure construction via ordered self-assembly for many other applications.
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Affiliation(s)
- Ruibin Wang
- School of Materials Science and EngineeringBeijing Institute of TechnologyNo. 5 South Zhongguancun Street, HaidianBeijing100081China
| | - Lichen Zhang
- School of Materials Science and EngineeringBeijing Institute of TechnologyNo. 5 South Zhongguancun Street, HaidianBeijing100081China
| | - Xiaodong Li
- School of Materials Science and EngineeringBeijing Institute of TechnologyNo. 5 South Zhongguancun Street, HaidianBeijing100081China
| | - Lixiang Zhu
- School of Materials Science and EngineeringBeijing Institute of TechnologyNo. 5 South Zhongguancun Street, HaidianBeijing100081China
| | - Zilong Xiang
- School of Materials Science and EngineeringBeijing Institute of TechnologyNo. 5 South Zhongguancun Street, HaidianBeijing100081China
| | - Jin Xu
- School of Materials Science and EngineeringBeijing Institute of TechnologyNo. 5 South Zhongguancun Street, HaidianBeijing100081China
| | - Dichang Xue
- School of Materials Science and EngineeringBeijing Institute of TechnologyNo. 5 South Zhongguancun Street, HaidianBeijing100081China
| | - Zitong Deng
- School of Materials Science and EngineeringBeijing Institute of TechnologyNo. 5 South Zhongguancun Street, HaidianBeijing100081China
| | - Xing Su
- School of Materials Science and EngineeringBeijing Institute of TechnologyNo. 5 South Zhongguancun Street, HaidianBeijing100081China
| | - Meishuai Zou
- School of Materials Science and EngineeringBeijing Institute of TechnologyNo. 5 South Zhongguancun Street, HaidianBeijing100081China
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Dubinin MV, Chulkov AV, Igoshkina AD, Cherepanova AA, Mikina NV. Effect of 2-aminoethoxydiphenyl borate on the functions of mouse skeletal muscle mitochondria. Biochem Biophys Res Commun 2024; 712-713:149944. [PMID: 38636302 DOI: 10.1016/j.bbrc.2024.149944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/10/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024]
Abstract
This work examined the effect of 2-aminoethoxydiphenyl borate (2-APB) on the functioning of isolated mouse skeletal muscle mitochondria and modeled its putative interaction with mitochondrial proteins. We have shown that 2-APB is able to dose-dependently suppress mitochondrial respiration in state 3 and 3UDNP driven by substrates of complex I and II. This effect of 2-APB was accompanied by a slight dose-dependent decrease in mitochondrial membrane potential and appears to be due to inhibition of complex I and complex III of the electron transport chain (ETC) with IC50 values of 200 and 120 μM, respectively. The results of molecular docking identified putative 2-APB interaction sites in these ETC complexes. 2-APB was shown to dose-dependently inhibit both mitochondrial Ca2+ uptake and Ca2+ efflux, which seems to be caused by a decrease in the membrane potential of the organelles. We have found that 2-APB has no significant effect on mitochondrial calcium retention capacity. On the other hand, 2-APB exhibited antioxidant effect by reducing mitochondrial hydrogen peroxide production but without affecting superoxide generation. It is concluded that the effect of 2-APB on mitochondrial targets should be taken into account when interpreting the results of cell and in vivo experiments.
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Affiliation(s)
- Mikhail V Dubinin
- Mari State University, pl. Lenina 1, Yoshkar-Ola, Mari El, 424001, Russia.
| | | | | | | | - Natalia V Mikina
- Mari State University, pl. Lenina 1, Yoshkar-Ola, Mari El, 424001, Russia
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Quispe-Díaz IM, Ybañez-Julca RO, Pino-Ríos R, Quispe-Rodríguez JD, Asunción-Alvarez D, Mantilla-Rodríguez E, Rengifo-Penadillos RA, Vásquez-Corales E, de Albuquerque RDDG, Gutiérrez-Alvarado WO, Benites J. Chemical Composition, Antioxidant Activities, Antidepressant Effect, and Lipid Peroxidation of Peruvian Blueberry: Molecular Docking Studies on Targets Involved in Oxidative Stress and Depression. PLANTS (BASEL, SWITZERLAND) 2024; 13:1643. [PMID: 38931078 PMCID: PMC11207408 DOI: 10.3390/plants13121643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
Blueberries (Vaccinium corymbosum L.) are cultivated worldwide and are among the best dietary sources of bioactive compounds with beneficial health effects. This study aimed to investigate the components of Peruvian blueberry using high-performance liquid chromatography coupled to electrospray ionization and quadrupole time-of-flight mass spectrometry (HPLC-ESI-QTOF-MS/MS), identifying 11 compounds. Furthermore, we assessed in vitro the antioxidant activity and in vivo the antidepressant effect using a rat model and protective effect on lipid peroxidation (in the serum, brain, liver, and stomach). We also conducted molecular docking simulations with proteins involved in oxidative stress and depression for the identified compounds. Antioxidant activity was assessed by measuring total phenolic and flavonoid contents, as well as using 1,1-diphenyl-2-picrylhydrazin (DPPH), 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonic) acid (ABTS•+), and ferric-reducing antioxidant power (FRAP) assays. Peruvian blueberries demonstrated higher antioxidant activity than Vaccinium corymbosum fruits from Chile, Brazil, the United States, Turkey, Portugal, and China. The results showed that oral administration of Peruvian blueberries (10 and 20 mg/kg) for 28 days significantly (p < 0.001) increased swimming and reduced immobility in the forced swimming test (FST). Additionally, at doses of 40 and 80 mg/kg, oxidative stress was reduced in vivo (p < 0.001) by decreasing lipid peroxidation in brain, liver, stomach, and serum. Molecular docking and absorption, distribution, metabolism, excretion, and toxicity (ADMET) predictions were performed. In the molecular docking studies, quercitrin and 3,5-di-O-caffeoylquinic acid showed the best docking scores for nicotinamide adenine dinucleotide phosphate (NADPH) oxidase, superoxide dismutase, and xanthine oxidase; while 3,5-dicaffeoylquinic acid methyl ester and caffeoyl coumaroylquinic acid had the best docking scores for monoamine oxidase and serotonin receptor 5-HT2. In summary, our results suggest that the antidepressant and protective effects against lipid peroxidation might be related to the antioxidant activity of Peruvian Vaccinium corymbosum L.
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Affiliation(s)
- Iván M. Quispe-Díaz
- Facultad de Farmacia y Bioquímica, Universidad Nacional de Trujillo, Trujillo 13011, Peru; (I.M.Q.-D.); (J.D.Q.-R.); (D.A.-A.); (E.M.-R.); (R.A.R.-P.); (R.D.D.G.d.A.)
| | - Roberto O. Ybañez-Julca
- Facultad de Farmacia y Bioquímica, Universidad Nacional de Trujillo, Trujillo 13011, Peru; (I.M.Q.-D.); (J.D.Q.-R.); (D.A.-A.); (E.M.-R.); (R.A.R.-P.); (R.D.D.G.d.A.)
| | - Ricardo Pino-Ríos
- Laboratorio de Química Medicinal, Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile;
- Instituto de Química Medicinal, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile
| | - José D. Quispe-Rodríguez
- Facultad de Farmacia y Bioquímica, Universidad Nacional de Trujillo, Trujillo 13011, Peru; (I.M.Q.-D.); (J.D.Q.-R.); (D.A.-A.); (E.M.-R.); (R.A.R.-P.); (R.D.D.G.d.A.)
| | - Daniel Asunción-Alvarez
- Facultad de Farmacia y Bioquímica, Universidad Nacional de Trujillo, Trujillo 13011, Peru; (I.M.Q.-D.); (J.D.Q.-R.); (D.A.-A.); (E.M.-R.); (R.A.R.-P.); (R.D.D.G.d.A.)
| | - Elena Mantilla-Rodríguez
- Facultad de Farmacia y Bioquímica, Universidad Nacional de Trujillo, Trujillo 13011, Peru; (I.M.Q.-D.); (J.D.Q.-R.); (D.A.-A.); (E.M.-R.); (R.A.R.-P.); (R.D.D.G.d.A.)
| | - Roger A. Rengifo-Penadillos
- Facultad de Farmacia y Bioquímica, Universidad Nacional de Trujillo, Trujillo 13011, Peru; (I.M.Q.-D.); (J.D.Q.-R.); (D.A.-A.); (E.M.-R.); (R.A.R.-P.); (R.D.D.G.d.A.)
| | - Edison Vásquez-Corales
- Escuela de Farmacia y Bioquímica, Universidad Católica Los Ángeles de Chimbote, Chimbote 02801, Peru;
| | - Ricardo D. D. G. de Albuquerque
- Facultad de Farmacia y Bioquímica, Universidad Nacional de Trujillo, Trujillo 13011, Peru; (I.M.Q.-D.); (J.D.Q.-R.); (D.A.-A.); (E.M.-R.); (R.A.R.-P.); (R.D.D.G.d.A.)
| | | | - Julio Benites
- Laboratorio de Química Medicinal, Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile;
- Instituto de Química Medicinal, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile
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Belosludtsev KN, Ilzorkina AI, Matveeva LA, Chulkov AV, Semenova AA, Dubinin MV, Belosludtseva NV. Effect of VBIT-4 on the functional activity of isolated mitochondria and cell viability. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184329. [PMID: 38679309 DOI: 10.1016/j.bbamem.2024.184329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 04/11/2024] [Accepted: 04/23/2024] [Indexed: 05/01/2024]
Abstract
VBIT-4 is a new inhibitor of the oligomerization of VDAC proteins of the outer mitochondrial membrane preventing the development of oxidative stress, mitochondrial dysfunction, and cell death in various pathologies. However, as a VDAC inhibitor, VBIT-4 may itself cause mitochondrial dysfunction in healthy cells. The article examines the effect of VBIT-4 on the functional activity of rat liver mitochondria and cell cultures. We have demonstrated that high concentrations of VBIT-4 (15-30 μM) suppressed mitochondrial respiration in state 3 and 3UDNP driven by substrates of complex I and II. VBIT-4 induced depolarization of organelles fueled by substrates of complex I but not complex II of the respiratory chain. VBIT-4 has been found to inhibit the activity of complexes I, III, and IV of the respiratory chain. Molecular docking demonstrated that VBIT-4 interacts with the rotenone-binding site in complex I with similar affinity. 15-30 μM VBIT-4 caused an increase in H2O2 production in mitochondria, decreased the Ca2+ retention capacity, but increased the time of Ca2+-dependent mitochondrial swelling. We have found that the incubation of breast adenocarcinoma (MCF-7) with 30 μM VBIT-4 for 48 h led to the decrease of the mitochondrial membrane potential, an increase in ROS production and death of MCF-7 cells. The mechanism of action of VBIT-4 on mitochondria and cells is discussed.
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Affiliation(s)
| | - Anna I Ilzorkina
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya 3, Pushchino, Moscow region 142290, Russia
| | | | | | - Alena A Semenova
- Mari State University, pl. Lenina 1, Yoshkar-Ola, Mari El 424001, Russia
| | - Mikhail V Dubinin
- Mari State University, pl. Lenina 1, Yoshkar-Ola, Mari El 424001, Russia
| | - Natalia V Belosludtseva
- Mari State University, pl. Lenina 1, Yoshkar-Ola, Mari El 424001, Russia; Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya 3, Pushchino, Moscow region 142290, Russia
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9
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Harahap U, Syahputra RA, Ahmed A, Nasution A, Wisely W, Sirait ML, Dalimunthe A, Zainalabidin S, Taslim NA, Nurkolis F, Kim B. Current insights and future perspectives of flavonoids: A promising antihypertensive approach. Phytother Res 2024; 38:3146-3168. [PMID: 38616386 DOI: 10.1002/ptr.8199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/27/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
Hypertension, or high blood pressure (BP), is a complex disease influenced by various risk factors. It is characterized by persistent elevation of BP levels, typically exceeding 140/90 mmHg. Endothelial dysfunction and reduced nitric oxide (NO) bioavailability play crucial roles in hypertension development. L-NG-nitro arginine methyl ester (L-NAME), an analog of L-arginine, inhibits endothelial NO synthase (eNOS) enzymes, leading to decreased NO production and increased BP. Animal models exposed to L-NAME manifest hypertension, making it a useful design for studying the hypertension condition. Natural products have gained interest as alternative approaches for managing hypertension. Flavonoids, abundant in fruits, vegetables, and other plant sources, have potential cardiovascular benefits, including antihypertensive effects. Flavonoids have been extensively studied in cell cultures, animal models, and, to lesser extent, in human trials to evaluate their effectiveness against L-NAME-induced hypertension. This comprehensive review summarizes the antihypertensive activity of specific flavonoids, including quercetin, luteolin, rutin, troxerutin, apigenin, and chrysin, in L-NAME-induced hypertension models. Flavonoids possess antioxidant properties that mitigate oxidative stress, a major contributor to endothelial dysfunction and hypertension. They enhance endothelial function by promoting NO bioavailability, vasodilation, and the preservation of vascular homeostasis. Flavonoids also modulate vasoactive factors involved in BP regulation, such as angiotensin-converting enzyme (ACE) and endothelin-1. Moreover, they exhibit anti-inflammatory effects, attenuating inflammation-mediated hypertension. This review provides compelling evidence for the antihypertensive potential of flavonoids against L-NAME-induced hypertension. Their multifaceted mechanisms of action suggest their ability to target multiple pathways involved in hypertension development. Nonetheless, the reviewed studies contribute to the evidence supporting the useful of flavonoids for hypertension prevention and treatment. In conclusion, flavonoids represent a promising class of natural compounds for combating hypertension. This comprehensive review serves as a valuable resource summarizing the current knowledge on the antihypertensive effects of specific flavonoids, facilitating further investigation and guiding the development of novel therapeutic strategies for hypertension management.
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Affiliation(s)
- Urip Harahap
- Department of Pharmacology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan, Indonesia
| | - Rony Abdi Syahputra
- Department of Pharmacology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan, Indonesia
| | - Amer Ahmed
- Department of Bioscience, Biotechnology and Environment, University of Bari, Bari, Italy
| | - Azhari Nasution
- Department of Pharmacology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan, Indonesia
| | - Wenny Wisely
- Department of Pharmacology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan, Indonesia
| | - Maureen Lazurit Sirait
- Department of Pharmacology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan, Indonesia
| | - Aminah Dalimunthe
- Department of Pharmacology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan, Indonesia
| | - Satirah Zainalabidin
- Biomedical Science, Centre of Toxicology and Health Risk Study, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nurpudji Astuti Taslim
- Division of Clinical Nutrition, Department of Nutrition, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
| | - Fahrul Nurkolis
- Department of Biological Sciences, State Islamic University of Sunan Kalijaga (UIN Sunan Kalijaga), Yogyakarta, Indonesia
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul, Republic of Korea
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul, Republic of Korea
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10
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Pandey P, Rao L, Shekhar BR, Das DK, Vavilala SL. Molecular insights into flavone-mediated quorum sensing interference: A novel strategy against Serratiamarcescens biofilm-induced antibiotic resistance". Chem Biol Interact 2024; 396:111027. [PMID: 38735452 DOI: 10.1016/j.cbi.2024.111027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 05/14/2024]
Abstract
Antibiotic resistance poses a significant challenge in modern medicine, urging the exploration of innovative approaches to combat bacterial infections. Biofilms, complex bacterial communities encased in a protective matrix, contribute to resistance by impeding antibiotic efficacy and promoting genetic exchange. Understanding biofilm dynamics is crucial for developing effective antimicrobial therapies against antibiotic resistance. This study explores the potential of flavone to combat biofilm-induced antibiotic resistance by employing in-vitro biochemical, cell biology, and Insilico (MD simulation), approaches. Flavone exhibited potent antibacterial effects with a low minimum inhibitory concentration by inducing intracellular reactive oxygen species. Flavones further inhibited the formation of biofilms by 50-60 % and disrupted the pre-formed biofilms by reducing the extracellular polysaccharide substance protective layer formed on the biofilm by 80 %. Quorum sensing (QS) plays a crucial role in bacterial pathogenicity and flavone significantly attenuated the production of QS-induced virulence factors like urease, protease, lipase, hemolysin and prodigiosin pigment in a dose-dependent manner. Further Insilico molecular docking studies along with molecular dynamic simulations run for 100 ns proved the stable binding affinity of flavone with QS-specific proteins which are crucial for biofilm formation. This study demonstrates the therapeutic potential of flavone to target QS-signaling pathway to combat S.marcescens biofilms.
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Affiliation(s)
- Pooja Pandey
- School of Biological Sciences, UM DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidyanagari, Kalina Campus, Mumbai, 400098, India.
| | - Lawanya Rao
- School of Biological Sciences, UM DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidyanagari, Kalina Campus, Mumbai, 400098, India.
| | - Bipin R Shekhar
- Stem Cell Biology, ICMR-National Institute for Research in Reproductive and Child Health, Jahangir Merwanji Street, Parel, Mumbai, India.
| | - Dhanjit K Das
- Stem Cell Biology, ICMR-National Institute for Research in Reproductive and Child Health, Jahangir Merwanji Street, Parel, Mumbai, India.
| | - Sirisha L Vavilala
- School of Biological Sciences, UM DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidyanagari, Kalina Campus, Mumbai, 400098, India.
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Moin AT, Robin TB, Patil RB, Rani NA, Prome AA, Sakif TI, Hossain M, Chowdhury DUS, Rashid SS, Mollah AKMM, Islam S, Uddin MH, Khalequzzaman M, Islam T, Islam NN. Antifungal plant flavonoids identified in silico with potential to control rice blast disease caused by Magnaporthe oryzae. PLoS One 2024; 19:e0301519. [PMID: 38578751 PMCID: PMC10997076 DOI: 10.1371/journal.pone.0301519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/14/2024] [Indexed: 04/07/2024] Open
Abstract
Rice blast disease, caused by the fungus Magnaporthe oryzae, poses a severe threat to rice production, particularly in Asia where rice is a staple food. Concerns over fungicide resistance and environmental impact have sparked interest in exploring natural fungicides as potential alternatives. This study aimed to identify highly potent natural fungicides against M. oryzae to combat rice blast disease, using advanced molecular dynamics techniques. Four key proteins (CATALASE PEROXIDASES 2, HYBRID PKS-NRPS SYNTHETASE TAS1, MANGANESE LIPOXYGENASE, and PRE-MRNA-SPLICING FACTOR CEF1) involved in M. oryzae's infection process were identified. A list of 30 plant metabolites with documented antifungal properties was compiled for evaluation as potential fungicides. Molecular docking studies revealed that 2-Coumaroylquinic acid, Myricetin, Rosmarinic Acid, and Quercetin exhibited superior binding affinities compared to reference fungicides (Azoxystrobin and Tricyclazole). High throughput molecular dynamics simulations were performed, analyzing parameters like RMSD, RMSF, Rg, SASA, hydrogen bonds, contact analysis, Gibbs free energy, and cluster analysis. The results revealed stable interactions between the selected metabolites and the target proteins, involving important hydrogen bonds and contacts. The SwissADME server analysis indicated that the metabolites possess fungicide properties, making them effective and safe fungicides with low toxicity to the environment and living beings. Additionally, bioactivity assays confirmed their biological activity as nuclear receptor ligands and enzyme inhibitors. Overall, this study offers valuable insights into potential natural fungicides for combating rice blast disease, with 2-Coumaroylquinic acid, Myricetin, Rosmarinic Acid, and Quercetin standing out as promising and environmentally friendly alternatives to conventional fungicides. These findings have significant implications for developing crop protection strategies and enhancing global food security, particularly in rice-dependent regions.
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Affiliation(s)
- Abu Tayab Moin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Tanjin Barketullah Robin
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Rajesh B. Patil
- Department of Pharmaceutical Chemistry, Sinhgad Technical Education Society’s, Sinhgad College of Pharmacy, Pune, Maharashtra, India
| | - Nurul Amin Rani
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Anindita Ash Prome
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Tahsin Islam Sakif
- Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, United States of America
| | - Mohabbat Hossain
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Dil Umme Salma Chowdhury
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Shah Samiur Rashid
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chattogram, Bangladesh
| | | | - Saiful Islam
- Chattogram Laboratories, Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram, Bangladesh
| | - Mohammad Helal Uddin
- Department of Applied Chemistry and Chemical Engineering, University of Chittagong, Chittagong, Bangladesh
| | | | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Nazneen Naher Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
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12
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Verma AK, Jaiswal G, Sultana KN, Srivastava SK. 'Computational studies on coumestrol-ArlR interaction to target ArlRS signaling cascade involved in MRSA virulence'. J Biomol Struct Dyn 2024; 42:3712-3730. [PMID: 37293938 DOI: 10.1080/07391102.2023.2220028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 05/10/2023] [Indexed: 06/10/2023]
Abstract
Two component signaling system ArlRS (Autolysis-related locus) regulates adhesion, biofilm formation and virulence in methicillin resistant Staphylococcus aureus. It consists of a histidine kinase ArlS and response regulator ArlR. ArlR is composed of a N-terminal receiver domain and DNA-binding effector domain at C-terminal. ArlR receiver domain dimerizes upon signal recognition and activates DNA binding by effector domain and subsequent virulence expression. In silico simulation and structural data suggest that coumestrol, a phytochemical found in Pueraria montana, forges a strong intermolecular interaction with residues involved in dimer formation and destabilizes ArlR dimerization, an essential conformational switch required for downstream effector domain to bind to virulent loci. Structural and energy profiles of simulated ArlR-coumestrol complexes suggest lower affinity between ArlR monomers due to structural rigidity at the dimer interface hindering the conformational rearrangements relevant for dimer formation. These analyses could be an attractive strategy to develop therapeutics and potent leads molecules response regulators of two component systems in which are involved in MRSA virulence as well as other drug-resistant pathogens.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abhishek Kumar Verma
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Jaipur, Rajasthan, India
| | - Grijesh Jaiswal
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Jaipur, Rajasthan, India
| | - Kazi Nasrin Sultana
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Jaipur, Rajasthan, India
| | - Sandeep Kumar Srivastava
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Jaipur, Rajasthan, India
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13
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Sudhakaran G, Kesavan D, Selvam M, Arasu A, Guru A, Arockiaraj J. Gonorrhea caused due to antimicrobial-resistant bacteria Neisseria gonorrhoeae treated using probiotic peptide. In Silico Pharmacol 2024; 12:17. [PMID: 38525049 PMCID: PMC10957827 DOI: 10.1007/s40203-023-00185-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/14/2023] [Indexed: 03/26/2024] Open
Abstract
Neisseria gonorrhea is a sexually transmitted disease from gonorrhea that lacks treatment; despite the urgency, the absence of adequate drugs, lack of human correlates of protection, and inadequate animal models of infection have delayed progress toward the prevention of gonococcal infection. Lactobacillus crispatus is a lactic acid bacterium typically found in the human vaginal microbiota. Peptides from L. crispatus have shown a potential therapeutic option for targetting N. gonorrhea. Bioinformatics analysis is important for speeding up drug target acquisition, screening refinement, and evaluating adverse effects and drug resistance prediction. Therefore, this study identified an antimicrobial peptide from the bacteriocin immunity protein (BIP) of L. crispatus using the bioinformatics tool and Collection of Antimicrobial Peptide (CAMPR3). Based on the AMP score and highest ADMET properties, the peptide SM20 was chosen for docking analysis. SM20 was docked against multiple proteins from the genome of the AMR bacterium N. gonorrhea using an online tool; protein-peptide interactions were established and visualized using the PyMol visualizing tool. Molecular docking was carried out using the CABSdock tool, and multiple conformations were obtained against the membrane proteins of N. gonorrhoea. The peptide SM20 exhibited higher docking scores and ADMET properties. Therefore, SM20 could be further encapsulated with cellulose; it can be applied topically to the genital tract to target N. gonorrhea infection. The controlled release of the antimicrobial peptide from the gel can provide sustained delivery of the treatment, increasing its efficacy and reducing the risk of resistance development.
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Affiliation(s)
- Gokul Sudhakaran
- Center for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, 600077 Tamil Nadu India
| | - D. Kesavan
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, 603203 Tamil Nadu India
| | - Madesh Selvam
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, 603203 Tamil Nadu India
| | - Abirami Arasu
- Department of Microbiology, SRM Arts and Science College, Kattankulathur, Chennai, 603203 Tamil Nadu India
| | - Ajay Guru
- Department of Cariology, Saveetha Dental College and Hospitals, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, 600077 Tamil Nadu India
| | - Jesu Arockiaraj
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, 603203 Tamil Nadu India
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Wang Y, Wang Y, Zhao T, Li M, Wang Y, Cao J, Liu Y, Wang Z, Cheng G. Protective Effect of Que Zui Tea on d-Galactose-Induced Oxidative Stress Damage in Mice via Regulating SIRT1/Nrf2 Signaling Pathway. Molecules 2024; 29:1384. [PMID: 38543018 PMCID: PMC10975416 DOI: 10.3390/molecules29061384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/01/2024] Open
Abstract
Que Zui tea (QT) is an important herbal tea in the diet of the 'Yi' people, an ethnic group in China, and it has shown significant antioxidant, anti-inflammatory, and hepatoprotective effects in vitro. This study aims to explore the protective effects of the aqueous-ethanol extract (QE) taken from QT against ᴅ-galactose (ᴅ-gal)-induced oxidative stress damage in mice and its potential mechanisms. QE was identified as UHPLC-HRMS/MS for its chemical composition and possible bioactive substances. Thus, QE is rich in phenolic and flavonoid compounds. Twelve compounds were identified, the main components of which were chlorogenic acid, quinic acid, and 6'-O-caffeoylarbutin. Histopathological and biochemical analysis revealed that QE significantly alleviated brain, liver, and kidney damage in ᴅ-gal-treated mice. Moreover, QE remarkably attenuated oxidative stress by activating the Nrf2/HO-1 pathway to increase the expression of antioxidant indexes, including GSH, GSH-Px, CAT, SOD, and T-AOC. In addition, QE administration could inhibit the IL-1β and IL-6 levels, which suppress the inflammatory response. QE could noticeably alleviate apoptosis by inhibiting the expressions of Caspase-3 and Bax proteins in the brains, livers, and kidneys of mice. The anti-apoptosis mechanism may be related to the upregulation of the SIRT1 protein and the downregulation of the p53 protein induced by QE in the brain, liver, and kidney tissues of mice. Molecular docking analysis demonstrated that the main components of QE, 6'-O-caffeoylarbutin, chlorogenic acid, quinic acid, and robustaside A, had good binding ability with Nrf2 and SIRT1 proteins. The present study indicated that QE could alleviate ᴅ-gal-induced brain, liver and kidney damage in mice by inhibiting the oxidative stress and cell apoptosis; additionally, the potential mechanism may be associated with the SIRT1/Nrf2 signaling pathway.
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Affiliation(s)
- Yongchao Wang
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China (Y.L.)
| | - Yongpeng Wang
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China (Y.L.)
| | - Tianrui Zhao
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China (Y.L.)
| | - Mengcheng Li
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China (Y.L.)
| | - Yudan Wang
- National and Local Joint Engineering Research Center for Green Preparation Technology of Biobased Materials, Yunnan Minzu University, Kunming 650500, China
| | - Jianxin Cao
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China (Y.L.)
| | - Yaping Liu
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China (Y.L.)
| | - Zhengxuan Wang
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China (Y.L.)
| | - Guiguang Cheng
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China (Y.L.)
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15
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Wu G, Ren Z, Hao Q, Wong Y, Zha D, Cao X, Liu R. The mechanism of Zhenzhu Pills treating intracerebral hemorrhage secondary injury based on network pharmacology and molecular docking. Medicine (Baltimore) 2024; 103:e36837. [PMID: 38363944 PMCID: PMC10869077 DOI: 10.1097/md.0000000000036837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 12/12/2023] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Intracerebral hemorrhage (ICH) secondary injury is serious and affects patient's prognosis. The Zhenzhu Pills used to treat subacute ICH in Tibet has shown to have a certain curative effect. Network pharmacology and molecular docking technology are employed to explore the potential mechanism of Zhenzhu Pills. The components and potential targets of Zhenzhu Pills were screened from the Traditional Chinese Medicine Systems Pharmacology database. The Gene Expression Omnibus Series 24265 was used to screen differentially expressed genes between perihematomal tissue and normal brain. METHODS The herbs-components-targets network was established, with weighted eigenvalue to identify the core components and targets of Zhenzhu Pills treatment of ICH secondary injury. Targets' bioinformatics enrichment was proceeded by gene ontology and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis. Finally, molecular docking was used to identify the hydrogen bonding activity between the key components and action targets. RESULTS Five herbal drugs were screened from Traditional Chinese Medicine Systems Pharmacology database, with a total of 48 components and 234 targets. The Gene Expression Omnibus Series 24265 dataset was evaluated and 920 differentially expressed genes were identified. A total of 29 intersection targets of Zhenzhu Pills were explored in the treatment of ICH secondary injury. Drugs-components-targets network analysis showed that the pivotal targets were prostaglandin G/H synthase 2, interleukin 6, heme oxygenase-1, vascular endothelial growth factor, and vascular cell adhesion molecule 1, and the core components were quercetin, luteolin, and kaempferol. Gene ontology and KEGG pathway enrichment analysis showed that biological processes such as cell chemotaxis, wound healing, leukocyte migration, and regulation of body fluid levels played an important role in the secondary injury of ICH. The results of KEGG pathway analysis were mainly related to advanced glycation end products-receptor for advanced glycation end products signal pathway and tumor necrosis factor signal pathway. Molecular docking of 3 flavonoids with 5 core targets with the results also showed active hydrogen bonding. CONCLUSIONS This study provides insights into the potential mechanisms of Zhenzhu Pills in the treatment of secondary injuries resulting from ICH and highlights specific components, targets, and molecular pathways involved in this therapeutic effect. These possible therapeutic mechanisms include inhibiting inflammation, edema, oxidative stress, and so on.
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Affiliation(s)
- Gang Wu
- Department of Neurosurgery, Peking University People’s Hospital, Beijing, P.R. China
| | - Zeng Ren
- Department of Neurosurgery, People’s Hospital of Tibet Autonomous Region, Lhasa, Tibet Autonomous Region, P.R. China
| | - Qingpei Hao
- Department of Neurosurgery, Peking University People’s Hospital, Beijing, P.R. China
| | - Yu Wong
- Department of Neurosurgery, People’s Hospital of Tibet Autonomous Region, Lhasa, Tibet Autonomous Region, P.R. China
| | - Duo Zha
- Department of Neurosurgery, People’s Hospital of Tibet Autonomous Region, Lhasa, Tibet Autonomous Region, P.R. China
| | - Xudong Cao
- Department of Neurosurgery, People’s Hospital of Tibet Autonomous Region, Lhasa, Tibet Autonomous Region, P.R. China
| | - Ruen Liu
- Department of Neurosurgery, Peking University People’s Hospital, Beijing, P.R. China
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Ou L, Liu HR, Shi XY, Peng C, Zou YJ, Jia JW, Li H, Zhu ZX, Wang YH, Su BM, Lai YQ, Chen MY, Zhu WX, Feng Z, Zhang GM, Yao MC. Terminalia chebula Retz. aqueous extract inhibits the Helicobacter pylori-induced inflammatory response by regulating the inflammasome signaling and ER-stress pathway. JOURNAL OF ETHNOPHARMACOLOGY 2024; 320:117428. [PMID: 37981121 DOI: 10.1016/j.jep.2023.117428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/21/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Terminalia chebula Retz., known as the King of Traditional Tibetan Medicine, is widely used for treating various ailments, particularly stomach disorders. It exhibited inhibitory activity against helicobacter pylori. AIM OF THE STUDY The exact mechanism by which T. chebula combats H. pylori infection remains unclear. Therefore, this study aimed to investigate its mechanism of action and the key pathways and targets involved. MATERIAL AND METHODS Minimum inhibitory concentration (MIC) assay, scanning electron microscope, and inhibiting kinetics curves were conducted. The mRNA expressions were measured by RNA-seq analysis and RT-QPCR. ELISA and Western blot were used to detect the changes in proteins. The main compounds were analyzed by High-performance Liquid Chromatography. The interaction between the compound and target was predicted by Molecular Docking. RESULTS The study revealed that T. chebula disrupted the structure of H. pylori bacteria and inhibited Cag A protein expression. Additionally, T. chebula can reduce the expression of flaA, flaB, babA, alpA, alpB, ureE, and ureF genes. Furthermore, T. chebula demonstrated its effectiveness in inhibiting the H. pylori-induced inflammatory response by regulating the inflammasome signaling and ER-stress pathway. Moreover, the study discovered that chebulagic acid has anti-HP activity and inhibits the expression of Cag A protein. CONCLUSIONS T. chebula acts as a natural remedy for combating H. pylori infection. Its ability to disrupt the bacterial structure, inhibit key proteins, regulate inflammatory pathways, and the presence of chebulagic acid contribute to its anti-H. pylori activity.
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Affiliation(s)
- Ling Ou
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, Guangdong, China.
| | - Heng-Rui Liu
- Regenerative Medicine Research Center, Future Homo Sapiens Institute of Regenerative Medicine Co., Ltd, Guangzhou, China.
| | - Xiao-Yan Shi
- International Pharmaceutical Engineering Lab of Shandong Province, Feixian, 273400, Shandong, China.
| | - Chang Peng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, Guangdong, China.
| | - Yuan-Jing Zou
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, Guangdong, China.
| | - Jun-Wei Jia
- International Pharmaceutical Engineering Lab of Shandong Province, Feixian, 273400, Shandong, China.
| | - Hui Li
- International Pharmaceutical Engineering Lab of Shandong Province, Feixian, 273400, Shandong, China.
| | - Zhi-Xiang Zhu
- International Pharmaceutical Engineering Lab of Shandong Province, Feixian, 273400, Shandong, China.
| | - Yan-Hua Wang
- International Pharmaceutical Engineering Lab of Shandong Province, Feixian, 273400, Shandong, China.
| | - Bing-Mei Su
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, Guangdong, China.
| | - Yu-Qian Lai
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, Guangdong, China.
| | - Mei-Yun Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, Guangdong, China.
| | - Wei-Xing Zhu
- Qingyuan Hospital' of Traditional Chinese Medicine, Qingyuan, 511500, Guangdong, China.
| | - Zhong Feng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, Guangdong, China; Lunan Pharmaceutical Group Co., Ltd, Linyi, 276000, Shandong, China.
| | - Gui-Min Zhang
- Lunan Pharmaceutical Group Co., Ltd, Linyi, 276000, Shandong, China.
| | - Mei-Cun Yao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, Guangdong, China.
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Jiao H, Fan Y, Gong A, Li T, Fu X, Yan Z. Xiaoyaosan ameliorates CUMS-induced depressive-like and anorexia behaviors in mice via necroptosis related cellular senescence in hypothalamus. JOURNAL OF ETHNOPHARMACOLOGY 2024; 318:116938. [PMID: 37495029 DOI: 10.1016/j.jep.2023.116938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Depression and anorexia often co-occur and share symptoms such as low mood, lack of energy, and weight loss. Xiaoyaosan is a classic formula comprising of a combination of eight herbs, possessing definitive therapeutic effects, minimal side effects, and economical benefits. It has been extensively employed in clinical treatment of ailments and symptoms such as depression, anxiety, and appetite problems. Nonetheless, its exact pharmacological mechanism with necroptosis remains incompletely explicit. AIM OF THE STUDY The aim of this study is to explore the potential mechanisms of anti-depressive and appetite-regulating effects of the active ingredients in Xiaoyaosan, and to investigate whether there is a correlation with necroptosis. MATERIALS AND METHODS The network pharmacology method was conducted to identify active ingredients, which were used to predict the possible targets of Xiaoyaosan and explore the potential targets in treating depression and anorexia by overlapping with differentially expressed genes (DEGs) screened from GEO datasets (GSE125441, GSE198597, and GSE69151). Afterwards, the protein-protein interaction (PPI) network, enrichment analyses, hub gene identification, co-expression study and molecular docking were used to study the potential mechanism of Xiaoyaosan. Then, a mice model of depression was established by chronic unpredictable mild stress (CUMS) and the incidence of necroptosis in the hypothalamus of CUMS mice was investigated, while verifying the key therapeutic target of Xiaoyaosan. RESULTS Through network pharmacology research, it had been discovered that the 145 active ingredients of the 8 herbs in the Xiaoyaosan could regulate 198 disease targets. Through PPI network analysis and functional enrichment analysis, it had been found that the pharmacological mechanism of Xiaoyaosan mainly involved biological processes such as oxidative stress, kinase activity, and DNA metabolism. It is related to various pathways such as cellular senescence, immune inflammation, and the cell cycle, and 9 hub targets had been identified. Further analysis of the 9 hub targets and the key PPI network clusters clarified the key mechanisms by which Xiaoyaosan exerts anti-depressant and appetite regulating effects, possibly related to necroptosis-mediated cellular senescence. Molecular docking of the key indicators of cellular senescence screened by bioinformatics, SIRT1, ABL1, and MYC, revealed that the key component regulating SIRT1 is 2-[3,4-dihydroxyphenyl]-5,7-dihydroxy-6-[3-methylbut-2-enyl]chromone in licorice root, Glabridin in licorice root regulates ABL1, and β-sitosterol found in Chinese angelica, debark peony root, and fresh ginger regulates MYC. Finally, through in vivo experiments, the expression of necroptosis in the hypothalamus of CUMS mice was verified. The regulatory effects of Xiaoyaosan on key substances RIPK1, RIPK3, MLKL, and p-MLKL were determined, while regulating effects on SIRT1, ABL1, and MYC were also observed. CONCLUSION The present study have revealed the common mechanism of Xiaoyaosan in treating depression and anorexia, indicating that the active ingredients of Xiaoyaosan may alleviate the symptoms of depression and anorexia by intervening in the pathways related to necroptosis and cellular senescence. The hub genes and common pathways identified by the study also provide new insights into the therapeutic targets of depression and anorexia, as well as the exploration of pharmacological mechanism of Xiaoyaosan.
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Affiliation(s)
- Haiyan Jiao
- School of Traditional Chinese Medicine, Hainan Medical University, Haikou 571199, China.
| | - Yingli Fan
- School of Traditional Chinese Medicine, Hainan Medical University, Haikou 571199, China.
| | - Aimin Gong
- School of Traditional Chinese Medicine, Hainan Medical University, Haikou 571199, China.
| | - Tian Li
- School of Traditional Chinese Medicine, Hainan Medical University, Haikou 571199, China.
| | - Xing Fu
- School of Traditional Chinese Medicine, Hainan Medical University, Haikou 571199, China.
| | - Zhiyi Yan
- School of Traditional Chinese Medicine, Hainan Medical University, Haikou 571199, China; Dongfang Hospital Affiliated to Beijing University of Chinese Medicine, Beijing 100078, China.
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18
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Liu Y, Cao Y. Protein-Ligand Blind Docking Using CB-Dock2. Methods Mol Biol 2024; 2714:113-125. [PMID: 37676595 DOI: 10.1007/978-1-0716-3441-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Protein-ligand blind docking is a widely used method for studying the binding sites and poses of ligands and receptors in pharmaceutical and biological research. Recently, our new blind docking server named CB-Dock2 has been released and is currently being utilized by researchers worldwide. CB-Dock2 outperforms state-of-the-art methods due to its accuracy in binding site identification and binding pose prediction, which are enabled by its knowledge-based docking engine. This highly automated server offers interactive and intuitive input and output web interfaces, making it an efficient and user-friendly tool for the bioinformatics and cheminformatics communities. This chapter provides a brief overview of the methods, followed by a detailed guide on using the CB-Dock2 server. Additionally, we present a case study that evaluates the performance of protein-ligand blind docking using this tool.
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Affiliation(s)
- Yang Liu
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
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19
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Yao F, Chen W, Gu W, Xu H, Hou W, Liang G, Zhang Zhu R, Jiang G, Zhang L. Osteoblast Biospecific Extraction Conjugated with HPLC Analysis for Screening Bone Regeneration Active Components from Moutan Cortex. Comb Chem High Throughput Screen 2024; 27:834-844. [PMID: 37287301 DOI: 10.2174/1386207326666230607155913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/26/2023] [Accepted: 04/10/2023] [Indexed: 06/09/2023]
Abstract
INTRODUCTION The function of promoting bone regeneration of Moutan Cortex (MC), a traditional Chinese medicine, has been widely known but, the effective components of MC in promoting osteoblast-mediated bone regeneration were still unclear. OBJECTIVE The method of osteoblast membrane bio-specific extraction conjugated with HPLC analysis was established to screen bone regeneration active components from MC. METHODS The fingerprints, washing eluate and desorption eluate of MC extract were analyzed by the established HPLC-DAD method. The established MC3T3-E1 cells membrane chromatography method was used for the bio-specific extraction of MC. The isolated compounds were identified by MS spectrometry. The effects and possible mechanisms of the isolated compounds were evaluated by molecular docking, ALP activity, cell viability by MTT Assay and proteins expression by Western Blot Analysis. RESULTS The active compound responsible for bone regeneration from MC was isolated using the established method of osteoblast membrane bio-specific extraction conjugated with HPLC analysis, and it was identified as 1,2,3,4,6-penta-O-β-galloyl-D-glucose (PGG) by MS spectrometry. It was further demonstrated through molecular docking that PGG could fit well into the functional ALP, BMP2, and Samd1 binding pocket. The proliferation of osteoblasts was promoted, the level of ALP was increased, and the protein expression of BMP2 and Smad1 was increased as shown by further pharmacological verification. CONCLUSION It was concluded that PGG, the bone regeneration active compound from MC, could stimulate the proliferation of osteoblasts to promote osteoblast differentiation, and its mechanism might be related to the BMP/Smad1 pathway.
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Affiliation(s)
- Fei Yao
- Central Laboratory, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, Jiangsu, 215000, China
- Clinical Pharmaceutical Laboratory of Traditional Chinese Medicine, Suzhou Academy of Wumen Chinese Medicine, Suzhou, Jiangsu, 215000, China
| | - Wei Chen
- Central Laboratory, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, Jiangsu, 215000, China
- Clinical Pharmaceutical Laboratory of Traditional Chinese Medicine, Suzhou Academy of Wumen Chinese Medicine, Suzhou, Jiangsu, 215000, China
| | - Weiwei Gu
- Central Laboratory, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, Jiangsu, 215000, China
- Department of Pharmacy, Yancheng City Dafeng People's Hospital, Yancheng, Jiangsu, 224000, China
| | - Heng Xu
- Central Laboratory, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, Jiangsu, 215000, China
- Clinical Pharmaceutical Laboratory of Traditional Chinese Medicine, Suzhou Academy of Wumen Chinese Medicine, Suzhou, Jiangsu, 215000, China
| | - Wenyue Hou
- Central Laboratory, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, Jiangsu, 215000, China
| | - Guoqiang Liang
- Central Laboratory, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, Jiangsu, 215000, China
- Clinical Pharmaceutical Laboratory of Traditional Chinese Medicine, Suzhou Academy of Wumen Chinese Medicine, Suzhou, Jiangsu, 215000, China
| | - Ruixian Zhang Zhu
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China
| | - Guorong Jiang
- Central Laboratory, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, Jiangsu, 215000, China
- Clinical Pharmaceutical Laboratory of Traditional Chinese Medicine, Suzhou Academy of Wumen Chinese Medicine, Suzhou, Jiangsu, 215000, China
| | - Lurong Zhang
- Central Laboratory, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, Jiangsu, 215000, China
- Clinical Pharmaceutical Laboratory of Traditional Chinese Medicine, Suzhou Academy of Wumen Chinese Medicine, Suzhou, Jiangsu, 215000, China
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20
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Ibitoye O, Ibrahim MAA, Soliman MES. Exploring the composition of protein-ligand binding sites for cancerous inhibitor of PP2A (CIP2A) by inhibitor guided binding analysis: paving a new way for the Discovery of drug candidates against triple negative breast cancer (TNBC). J Recept Signal Transduct Res 2023; 43:133-143. [PMID: 38166612 DOI: 10.1080/10799893.2023.2298903] [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: 10/31/2023] [Accepted: 12/16/2023] [Indexed: 01/05/2024]
Abstract
Triple-negative breast cancer (TNBC) is associated with high-grade invasive carcinoma leading to a 10% to 15% death rate in younger premenopausal women. Targeting cancerous inhibitors of protein phosphatase (CIP2A) has been a highly effective approach for exploring therapeutic drug candidates. Lapatinib, a dual tyrosine kinase inhibitor, has shown promising inhibition properties by inducing apoptosis in TNBC carcinogenesis in vivo. Despite knowledge of the 3D structure of CIP2A, no reports provide insight into CIP2A ligand binding sites. To this effect, we conducted in silico site identification guided by lapatinib binding. Four of the five sites identified were cross-validated, and the stem domain revealed more excellent ligand binding affinity. The binding affinity of lapatinib in these sites was further computed using the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) approach. According to MM/PBSA//200 ns MD simulations, lapatinib exhibited a higher binding affinity against CIP2A in site 2 with ΔG critical values of -37.1 kcal/mol. The steadiness and tightness of lapatinib with CIP2A inside the stem domain disclosed glutamic acid-318 as the culprit amino acid with the highest electrostatic energy. These results provide clear information on the CIP2A domain capable of ligand binding and validate lapatinib as a promising CIP2A inhibitor in TNBC carcinogenesis.
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Affiliation(s)
- Oluwayimika Ibitoye
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Center for Bioinformatics and Drug Design, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Mahmoud A A Ibrahim
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia,Egypt
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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21
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Shuyuan L, Haoyu C. Mechanism of Nardostachyos Radix et Rhizoma-Salidroside in the treatment of premature ventricular beats based on network pharmacology and molecular docking. Sci Rep 2023; 13:20741. [PMID: 38007574 PMCID: PMC10676380 DOI: 10.1038/s41598-023-48277-0] [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: 09/12/2023] [Accepted: 11/24/2023] [Indexed: 11/27/2023] Open
Abstract
To analyse the mechanism of Nardostachyos Radix et Rhizoma-Salidroside in the treatment of Premature Ventricular Brats by using network pharmacology and molecular docking and to provide the basis for developing the use of experimental and clinical traditional Chinese medicine. The chemical compositions of Nardostachyos Radix et Rhizoma and Salidroside were determined, and their related targets were predicted. The disease-related targets were obtained by searching the common disease databases Genecards, OMIM, Drugbank and DisGeNET, and the intersection between the predicted targets and the disease targets was determined. Then using the STRING database to set up the protein‒protein interactions (PPIs) network between Nardostachyos Radix et Rhizoma-Salidroside and the common targets of PVB. An "herb-ingredient-target" network was constructed and analyzed by Cytoscape3.7.2 software. Using the metascape database to analysis the predicted therapeutic targets based on the GO and KEGG. Finally, molecular docking technology was used toconfirm the capacity of the primary active ingredients of the 2 herbs to bind to central targets using the online CB-Dock2 database. 41 active components of Nardostachyos Radix et Rhizoma-Salidroside were detected, with 420 potential targets of action, with a total of 1688 PVB targets, and the top 10 core targets of herb-disease degree values were AKT1, TNF, GAPDH, SRC, PPARG, EGFR, PTGS2, ESR1, MMP9, and STAT3. KEGG analysis indicated that its mechanism may be related to the calcium signalling pathway, cancer signalling pathway, AGE-RAGE signalling pathway and other pathways. Molecular docking suggested that main of the active ingredients of the Nardostachyos Radix et Rhizoma-Salidroside pairs were well bound to the core targets. Based on novel network pharmacology and molecular docking validation research methods, we revealed for the first time the potential mechanism of Nardostachyos Radix et Rhizoma-Salidroside in PVB therapy.
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Affiliation(s)
- Liu Shuyuan
- The First Clinical Medical School, Shandong University of Traditional Chinese Medicine, Jinan, ShanDong, People's Republic of China, 250013
| | - Chen Haoyu
- Cardiology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, ShanDong, People's Republic of China, 250011.
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22
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Padilla-Vaca F, de la Mora J, García-Contreras R, Ramírez-Prado JH, Vicente-Gómez M, Vargas-Gasca F, Anaya-Velázquez F, Páramo-Pérez I, Rangel-Serrano Á, Cuéllar-Mata P, Vargas-Maya NI, Franco B. Theoretical study of ArcB and its dimerization, interaction with anaerobic metabolites, and activation of ArcA. PeerJ 2023; 11:e16309. [PMID: 37849831 PMCID: PMC10578306 DOI: 10.7717/peerj.16309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/27/2023] [Indexed: 10/19/2023] Open
Abstract
The complex metabolism of Escherichia coli has been extensively studied, including its response to oxygen availability. The ArcA/B two-component system (TCS) is the key regulator for the transition between these two environmental conditions and has been thoroughly characterized using genetic and biochemical approaches. Still, to date, limited structural data is available. The breakthrough provided by AlphaFold2 in 2021 has brought a reliable tool to the scientific community for assessing the structural features of complex proteins. In this report, we analyzed the structural aspects of the ArcA/B TCS using AlphaFold2 models. The models are consistent with the experimentally determined structures of ArcB kinase. The predicted structure of the dimeric form of ArcB is consistent with the extensive genetic and biochemical data available regarding mechanistic signal perception and regulation. The predicted interaction of the dimeric form of ArcB with its cognate response regulator (ArcA) is also consistent with both the forward and reverse phosphotransfer mechanisms. The ArcB model was used to detect putative binding cavities to anaerobic metabolites, encouraging testing of these predictions experimentally. Finally, the highly accurate models of other ArcB homologs suggest that different experimental approaches are needed to determine signal perception in kinases lacking the PAS domain. Overall, ArcB is a kinase with features that need further testing, especially in determining its crystal structure under different conditions.
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Affiliation(s)
| | - Javier de la Mora
- Genética Molecular, Instituto de Fisiología Celular, Mexico City, Mexico City, México
| | | | | | | | | | | | | | | | | | | | - Bernardo Franco
- Biology, Universidad de Guanajuato, Guanajuato, Guanajuato, México
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23
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Wu J, Chen H, Cheng M, Xiong H. CurvAGN: Curvature-based Adaptive Graph Neural Networks for Predicting Protein-Ligand Binding Affinity. BMC Bioinformatics 2023; 24:378. [PMID: 37798653 PMCID: PMC10557336 DOI: 10.1186/s12859-023-05503-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/28/2023] [Indexed: 10/07/2023] Open
Abstract
Accurately predicting the binding affinity between proteins and ligands is crucial for drug discovery. Recent advances in graph neural networks (GNNs) have made significant progress in learning representations of protein-ligand complexes to estimate binding affinities. To improve the performance of GNNs, there frequently needs to look into protein-ligand complexes from geometric perspectives. While the "off-the-shelf" GNNs could incorporate some basic geometric structures of molecules, such as distances and angles, through modeling the complexes as homophilic graphs, these solutions seldom take into account the higher-level geometric attributes like curvatures and homology, and also heterophilic interactions.To address these limitations, we introduce the Curvature-based Adaptive Graph Neural Network (CurvAGN). This GNN comprises two components: a curvature block and an adaptive attention guided neural block (AGN). The curvature block encodes multiscale curvature informaton, then the AGN, based on an adaptive graph attention mechanism, incorporates geometry structure including angle, distance, and multiscale curvature, long-range molecular interactions, and heterophily of the graph into the protein-ligand complex representation. We demonstrate the superiority of our proposed model through experiments conducted on the PDBbind-V2016 core dataset.
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Affiliation(s)
- Jianqiu Wu
- Research Center for Graph Computing, Zhejiang Lab, Yuhang, Hangzhou, 311121, Zhejiang, China
| | - Hongyang Chen
- Research Center for Graph Computing, Zhejiang Lab, Yuhang, Hangzhou, 311121, Zhejiang, China.
| | - Minhao Cheng
- Department of Computer Science and Engineering, Hong Kong University of Science and Technology, Jiulongwan, Hongkong, 999077, China
| | - Haoyi Xiong
- Big Data Lab, Baidu Inc., Haidian, Beijing, 100080, China
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24
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Zhang X, Shen C, Wang T, Deng Y, Kang Y, Li D, Hou T, Pan P. ML-PLIC: a web platform for characterizing protein-ligand interactions and developing machine learning-based scoring functions. Brief Bioinform 2023; 24:bbad295. [PMID: 37738401 DOI: 10.1093/bib/bbad295] [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: 06/21/2023] [Revised: 07/17/2023] [Accepted: 07/31/2023] [Indexed: 09/24/2023] Open
Abstract
Cracking the entangling code of protein-ligand interaction (PLI) is of great importance to structure-based drug design and discovery. Different physical and biochemical representations can be used to describe PLI such as energy terms and interaction fingerprints, which can be analyzed by machine learning (ML) algorithms to create ML-based scoring functions (MLSFs). Here, we propose the ML-based PLI capturer (ML-PLIC), a web platform that automatically characterizes PLI and generates MLSFs to identify the potential binders of a specific protein target through virtual screening (VS). ML-PLIC comprises five modules, including Docking for ligand docking, Descriptors for PLI generation, Modeling for MLSF training, Screening for VS and Pipeline for the integration of the aforementioned functions. We validated the MLSFs constructed by ML-PLIC in three benchmark datasets (Directory of Useful Decoys-Enhanced, Active as Decoys and TocoDecoy), demonstrating accuracy outperforming traditional docking tools and competitive performance to the deep learning-based SF, and provided a case study of the Serine/threonine-protein kinase WEE1 in which MLSFs were developed by using the ML-based VS pipeline in ML-PLIC. Underpinning the latest version of ML-PLIC is a powerful platform that incorporates physical and biological knowledge about PLI, leveraging PLI characterization and MLSF generation into the design of structure-based VS pipeline. The ML-PLIC web platform is now freely available at http://cadd.zju.edu.cn/plic/.
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Affiliation(s)
- Xujun Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Chao Shen
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- Hangzhou Carbonsilicon AI Technology Co., Ltd, Hangzhou 310018, Zhejiang, China
| | - Tianyue Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yafeng Deng
- Hangzhou Carbonsilicon AI Technology Co., Ltd, Hangzhou 310018, Zhejiang, China
| | - Yu Kang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Dan Li
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Peichen Pan
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
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25
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Azzam SM, Abdel Khalek MR, Abdel Rahman AAS, Osman AA, Selim HMRM, Sharif AF, El-Khattib YA, Rabea S, Ali SK, Darwish A. Revealing how phenytoin triggers liver damage and the potential protective effects of Balanites Aegyptiaca fruit extracts: Exploring Nrf2/MAPK/ Beclin-1 signaling pathways. Biomed Pharmacother 2023; 165:115265. [PMID: 37541174 DOI: 10.1016/j.biopha.2023.115265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/06/2023] Open
Abstract
Phenytoin-induced liver injury (PHT ILII) is a serious condition that may necessitate discontinuation of the drug. This study investigates the mechanisms of PHT ILII and evaluates the protective effects of Balanites Aegyptiaca (BA) fruit extracts on the liver. We focus on the Nrf2/MAPK/NF-κB/Beclin-1 signaling pathways involved in oxidative stress and inflammation from drug-induced liver injury. Phytochemical analyses of BA fruit extracts (Bu-F and EA-F) are conducted. Molecular docking techniques explore the interaction between phenytoin (PHT) and the Nrf2/MAPK/NF-κB/Beclin-1 pathways. Thirty-six male rats are divided into Control, Bu-F, EA-F, PHT, Bu-F/PHT, and EA-F/PHT groups, and they are observed for 45 days. EA-F extract is rich in phenolics/flavonoids, while Bu-F extract mainly contains saponins.PHT ILII causes histological damage in liver tissues and affects Nrf-2, MAPK, TNF-α, IL-1β, Mcp-1, Beclin-1, iNOS expression, and liver function markers (ALT, AST, ALP). However, EA-F/Bu-F extracts effectively improve the histological structure and significantly reduce biochemical/immunohistochemical parameters, restoring them to near-normal levels. EA-F extract is particularly effective.In conclusion, the Nrf2/MAPK /Beclin-1 pathways play a critical role in the development of PHT ILII. BA fruit extracts show promise as hepato-protective agents, with the EA-F extract demonstrating superior efficacy. These results lay the groundwork for new treatments for PHT ILII and drug-induced liver injuries.
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Affiliation(s)
- Shaimaa M Azzam
- Department of Biochemistry, Egyptian Drug Authority (EDA), Formerly National Organization for Drug Control and Research (NODCAR), Giza, Egypt.
| | - Marwa Refaat Abdel Khalek
- Phytochemistry department, Egyptian Drug Authority (EDA), Formerly National Organization for Drug Control and Research (NODCAR), Giza 11221, Egypt.
| | - Amina A S Abdel Rahman
- Department of Zoology, Faculty of Women for Arts, Science, and Education, Ain Shams University, Asmaa Fahmy Street, Heliopolis, Cairo, Egypt.
| | - Amany Abdelhameid Osman
- Department of Zoology, Faculty of Women for Arts, Science, and Education, Ain Shams University, Asmaa Fahmy Street, Heliopolis, Cairo, Egypt.
| | - Heba Mohammed Refat M Selim
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, AlMaarefa University, Diriyah 3713, Riyadh, Saudi Arabia; Microbiology and Immunology Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt.
| | - Asmaa Fady Sharif
- Forensic Medicine and Clinical Toxicology Department, Faculty of Medicine, Tanta University, Tanta 31527, Egypt; Clinical Medical Sciences Department, College of Medicine, Dar Al Uloom University, Riyadh 13314, Saudi Arabia.
| | | | - Sameh Rabea
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, AlMaarefa University, Diriyah 3713, Riyadh, Saudi Arabia.
| | - Sahar K Ali
- Department of Clinical Pharmacology, Faculty of Medicine, Zagazig University, Zagazig 44519, Egypt.
| | - Alshaymaa Darwish
- Department of Biochemistry, Faculty of Pharmacy, Sohag University, Sohag, Egypt.
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26
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Rana MM, Nguyen DD. Geometric graph learning with extended atom-types features for protein-ligand binding affinity prediction. Comput Biol Med 2023; 164:107250. [PMID: 37515872 DOI: 10.1016/j.compbiomed.2023.107250] [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: 04/12/2023] [Revised: 06/12/2023] [Accepted: 07/07/2023] [Indexed: 07/31/2023]
Abstract
Understanding and accurately predicting protein-ligand binding affinity are essential in the drug design and discovery process. At present, machine learning-based methodologies are gaining popularity as a means of predicting binding affinity due to their efficiency and accuracy, as well as the increasing availability of structural and binding affinity data for protein-ligand complexes. In biomolecular studies, graph theory has been widely applied since graphs can be used to model molecules or molecular complexes in a natural manner. In the present work, we upgrade the graph-based learners for the study of protein-ligand interactions by integrating extensive atom types such as SYBYL and extended connectivity interactive features (ECIF) into multiscale weighted colored graphs (MWCG). By pairing with the gradient boosting decision tree (GBDT) machine learning algorithm, our approach results in two different methods, namely sybylGGL-Score and ecifGGL-Score. Both of our models are extensively validated in their scoring power using three commonly used benchmark datasets in the drug design area, namely CASF-2007, CASF-2013, and CASF-2016. The performance of our best model sybylGGL-Score is compared with other state-of-the-art models in the binding affinity prediction for each benchmark. While both of our models achieve state-of-the-art results, the SYBYL atom-type model sybylGGL-Score outperforms other methods by a wide margin in all benchmarks. Finally, the best-performing SYBYL atom-type model is evaluated on two test sets that are independent of CASF benchmarks.
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Affiliation(s)
- Md Masud Rana
- Department of Mathematics, University of Kentucky, Lexington, 40506, KY, USA.
| | - Duc Duy Nguyen
- Department of Mathematics, University of Kentucky, Lexington, 40506, KY, USA.
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27
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Sabarathinam S, Satheesh S, Ganamurali N, Dhanasekaran D, Raja A. Drug designing and toxicity screening of halogen and nitrogen-augmented catechin in sarcopenic obesity. Nat Prod Res 2023:1-6. [PMID: 37571993 DOI: 10.1080/14786419.2023.2245536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/16/2023] [Accepted: 07/29/2023] [Indexed: 08/14/2023]
Abstract
In this study, the catechin structure was modified with Halogen and Nitrogen base at C-6 and C-8 Positions in Ring A. Pharmacokinetic parameters affirm the drug-likeness property of the designed compounds. Molecular Docking was performed for all the compounds towards the myostatin inhibition target (PDB: 3HH2). Such desirable quality of modified Catechin will create a spark in the novel drug discovery using acting as a bioenhancer. As a result, the present research is aimed to offer an overview of the structural simulation of Cl, F, I, NH2, NO2, and Br at C-6 and C-8 positions in A Ring A of Catechin. This preliminary evidence creates an impact on the novelsemi0synthetic drug discovery for the therapeutic management of sarcopenia.
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Affiliation(s)
- Sarvesh Sabarathinam
- Drug Testing Laboratory, Interdisciplinary Institute of Indian System of Medicine (IIISM), SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu, India
- Clinical Trial Unit, Metabolic Ward, Interdisciplinary Institute of Indian System of Medicine (IIISM), SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu, India
- Certificate Programme-Analytical Techniques in Herbal Drug Industry, Interdisciplinary Institute of Indian System of Medicine (IIISM), SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu, India
| | - Sanjana Satheesh
- Department of Biotechnology, Birla Institute of Technology and Science, Dubai Campus, Dubai International Academic City, Dubai, United Arab Emirates
| | - Nila Ganamurali
- Certificate Programme-Analytical Techniques in Herbal Drug Industry, Interdisciplinary Institute of Indian System of Medicine (IIISM), SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu, India
| | - Dhivya Dhanasekaran
- Certificate Programme-Analytical Techniques in Herbal Drug Industry, Interdisciplinary Institute of Indian System of Medicine (IIISM), SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu, India
| | - Arun Raja
- Department of Community Medicine, Sree Balaji Medical College and Hospital, Chennai, India
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28
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Yu Q, Liu M, Zhao T, Su M, Wang S, Xu W, He S, Li K, Mu X, Wu J, Sun P, Zheng F, Weng N. Mechanism of baixiangdan capsules on anti-neuroinflammation: combining dry and wet experiments. Aging (Albany NY) 2023; 15:7689-7708. [PMID: 37556347 PMCID: PMC10457058 DOI: 10.18632/aging.204934] [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: 04/03/2023] [Accepted: 07/17/2023] [Indexed: 08/11/2023]
Abstract
Neuroinflammation plays an important role in the pathogenesis of neurological disorders, and despite intensive research, treatment of neuroinflammation remains limited. BaiXiangDan capsule (BXD) is widely used in clinical practice. However, systematic studies on the direct role and mechanisms of BXD in neuroinflammation are still lacking. We systematically evaluated the potential pharmacological mechanisms of BXD on neuroinflammation using network pharmacological analysis combined with experimental validation. Multiple databases are used to mine potential targets for bioactive ingredients, drug targets and neuroinflammation. GO and KEGG pathway analysis was also performed. Interactions between active ingredients and pivotal targets were confirmed by molecular docking. An experimental model of neuroinflammation was used to evaluate possible therapeutic mechanisms for BXD. Network pharmacological analysis revealed that Chrysoeriol, Kaempferol and Luteolin in BXD exerted their anti-neuroinflammatory effects mainly by acting on targets such as NCOA2, PIK3CA and PTGS2. Molecular docking results showed that their average affinity was less than -5 kcal/mol, with an average affinity of -8.286 kcal/mol. Pathways in cancer was found to be a potentially important pathway, with involvement of PI3K/AKT signaling pathways. In addition, in vivo experiments showed that BXD treatment ameliorated neural damage and reduced neuronal cell death. Western blotting, RT-qPCR and ELISA analysis showed that BXD inhibited not only the expression of IL-1β, TNF-α and NO, but also NF-κB, MMP9 and PI3K/AKT signaling pathways. This study applied network pharmacology and in vivo experiments to explore the possible mechanisms of BXD against neuroinflammation, providing insight into the treatment of neuroinflammation.
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Affiliation(s)
- Qingying Yu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250000, China
| | - Molin Liu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250000, China
| | - Tingting Zhao
- College of Foreign Languages, Shandong University of Traditional Chinese Medicine, Jinan 250000, China
| | - Mengyue Su
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250000, China
| | - Shukun Wang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250000, China
| | - Wenhua Xu
- Preventive Treatment Center, Shenzhen Integrated Traditional Chinese and Western Medicine Hospital, Shenzhen 518000, China
| | - Shuhua He
- Department of Psychiatry, Boai Hospitai of Zhongshan, Zhongshan 528400, China
| | - Kejie Li
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan 250000, China
| | - Xiangyu Mu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250000, China
| | - Jibiao Wu
- Innovation Research Institute of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250000, China
| | - Peng Sun
- Innovation Research Institute of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250000, China
| | - Feng Zheng
- Department of Neurosurgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362000, China
| | - Ning Weng
- Department of Traditional Chinese Medicine, Shandong Mental Health Center, Shandong University, Jinan 250000, China
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Hamdi M, Elkashlan AM, Hammad MA, Ali IH. SARS-CoV-2 Papain-like Protease Responsive ZnO/Daclatasvir-Loaded Chitosan/Gelatin Nanofibers as Smart Antimicrobial Medical Textiles: In Silico, In Vitro and Cell Studies. Pharmaceutics 2023; 15:2074. [PMID: 37631287 PMCID: PMC10457880 DOI: 10.3390/pharmaceutics15082074] [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: 06/28/2023] [Revised: 07/23/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
A significant number of deaths are reported annually worldwide due to microbial and viral infections. The development of protective medical textiles for patients and healthcare professionals has attracted many researchers' attention. Therefore, this study aims to develop smart drug-eluting nanofibrous matrices to be used as a basic material for medical textile fabrication. First, chitosan/gelatin nanofibers were selected as the basic material owing to the wide antimicrobial activity of chitosan and the capability of gelatin to be hydrolyzed in the abundance of the papain-like protease (PLpro) enzyme secreted by SARS-CoV-2. Daclatasvir (DAC), an NS5A inhibitor, was selected as the model drug based on in silico studies where it showed high anti-SARS-CoV-2 potential compared to FDA-approved references. Due to their reported antimicrobial and antiviral activities, ZnO NPs were successfully prepared and incorporated with daclatasvir in chitosan/gelatin nanofibrous matrices through electrospinning. Afterward, an in vitro release study in a simulated buffer revealed the controlled release of DAC over 21 days from the nanofibers compared to only 6 h for free DAC. On the other hand, the abundance of PLpro induced the complete release of DAC from the nanofibers in only 4-8 h. Finally, the nanofibers demonstrated a wide antimicrobial activity against S. aureus, E. coli, and C. albicans.
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Affiliation(s)
- Mohamed Hamdi
- Department of Pharmaceutics, Faculty of Pharmacy, University of Sadat City, Sadat City P.O. Box 32897, Egypt;
| | - Akram M. Elkashlan
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat City P.O. Box 32897, Egypt;
| | - Mohamed A. Hammad
- Department of Analytical Chemistry, Faculty of Pharmacy, University of Sadat City, Sadat City P.O. Box 32897, Egypt;
| | - Isra H. Ali
- Department of Pharmaceutics, Faculty of Pharmacy, University of Sadat City, Sadat City P.O. Box 32897, Egypt;
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Younis MK, Elakkad YE, Fakhr Eldeen RR, Ali IH, Khalil IA. Propranolol-Loaded Trehalosome as Antiproliferative Agent for Treating Skin Cancer: Optimization, Cytotoxicity, and In Silico Studies. Pharmaceutics 2023; 15:2033. [PMID: 37631247 PMCID: PMC10458383 DOI: 10.3390/pharmaceutics15082033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
This study aims at preparing propranolol-loaded trehalosomes (a trehalose-coated liposome) to be used as an antiproliferative agent for treating skin cancer. A factorial design was used to select the optimum formula, where trehalose, lecithin, and Tween 80 levels were studied. A total of 24 runs were prepared and characterized according to size, charge, entrapment efficiency, and release after 3 h to select the optimum formula. The optimized formula was investigated using TEM, DSC, and FTIR. Cell studies were carried out against the human melanoma cell line to measure cytotoxicity, apoptosis/necrosis, and cell cycle arrest. In silico studies were conducted to understand the interaction between propranolol and the influential receptors in melanoma. The results showed the selected formula consisted of trehalose (175 mg), lecithin (164 mg), and Tween 80 (200 mg) with a size of 245 nm, a charge of -9 mV, an EE% of 68%, and a Q3 of 62%. Moreover, the selected formula has good cytotoxicity compared to the free drug due to the synergistic effect of the drug and the designed carrier. IC50 of free propranolol and the encapsulation of propranolol were 17.48 μg/mL and 7.26 μg/mL, respectively. Also, propranolol and the encapsulation of propranolol were found to significantly increase early and late apoptosis, in addition to inducing G1 phase cell cycle arrest. An in silico virtual study demonstrated that the highest influential receptors in melanoma were the vitamin D receptor, CRH-R1, VEGFR 1, and c-Kit, which matches the results of experimental apoptotic and cell cycle analysis. In conclusion, the selected formula has good cytotoxicity compared to the free drug due to the synergistic effect of the drug and the designed carrier, which make it a good candidate as an antiproliferative agent for treating skin cancer.
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Affiliation(s)
- Mona K. Younis
- Department of Pharmaceutics, College of Pharmacy and Drug Manufacturing, Misr University of Science and Technology, 6th of October City 12566, Egypt; (M.K.Y.); (Y.E.E.)
| | - Yara E. Elakkad
- Department of Pharmaceutics, College of Pharmacy and Drug Manufacturing, Misr University of Science and Technology, 6th of October City 12566, Egypt; (M.K.Y.); (Y.E.E.)
| | - Rasha R. Fakhr Eldeen
- Department of Biochemistry, College of Pharmacy and Drug Manufacturing, Misr University of Science and Technology, 6th of October City 12566, Egypt;
| | - Isra H. Ali
- Department of Pharmaceutics, Faculty of Pharmacy, University of Sadat City, Sadat City 32897, Egypt;
| | - Islam A. Khalil
- Department of Pharmaceutics, College of Pharmacy and Drug Manufacturing, Misr University of Science and Technology, 6th of October City 12566, Egypt; (M.K.Y.); (Y.E.E.)
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Hsiao WC, Niu GH, Lo CF, Wang JY, Chi YH, Huang WC, Tung CW, Sung PJ, Tsou LK, Zhang MM. Marine diterpenoid targets STING palmitoylation in mammalian cells. Commun Chem 2023; 6:153. [PMID: 37463995 DOI: 10.1038/s42004-023-00956-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
Natural products are important sources of therapeutic agents and useful drug discovery tools. The fused macrocycles and multiple stereocenters of briarane-type diterpenoids pose a major challenge to total synthesis and efforts to characterize their biological activities. Harnessing a scalable source of excavatolide B (excB) from cultured soft coral Briareum stechei, we generated analogs by late-stage diversification and performed structure-activity analysis, which was critical for the development of functional excB probes. We further used these probes in a chemoproteomic strategy to identify Stimulator of Interferon Genes (STING) as a direct target of excB in mammalian cells. We showed that the epoxylactone warhead of excB is required to covalently engage STING at its membrane-proximal Cys91, inhibiting STING palmitoylation and signaling. This study reveals a possible mechanism-of-action of excB, and expands the repertoire of covalent STING inhibitors.
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Affiliation(s)
- Wan-Chi Hsiao
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, 35053, Taiwan
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Guang-Hao Niu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Chen-Fu Lo
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Jing-Ya Wang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Ya-Hui Chi
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Wei-Cheng Huang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Chun-Wei Tung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Ping-Jyun Sung
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804201, Taiwan.
- National Museum of Marine Biology and Aquarium, Pingtung, 944401, Taiwan.
- Chinese Medicine Research and Development Center, China Medical University Hospital, Taichung, 404394, Taiwan.
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, 807378, Taiwan.
| | - Lun Kelvin Tsou
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, 35053, Taiwan.
| | - Mingzi M Zhang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, 35053, Taiwan.
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32
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Huang X, Liu Y, Wang Q, Rehman HM, Horváth D, Zhou S, Fu R, Zhang L, Szöllősi AG, Li Z. Brief literature review and comprehensive bioinformatics analytics unravel the potential mechanism of curcumin in the treatment of periodontitis. BMC Oral Health 2023; 23:469. [PMID: 37422651 PMCID: PMC10329799 DOI: 10.1186/s12903-023-03181-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 06/28/2023] [Indexed: 07/10/2023] Open
Abstract
OBJECTIVE Periodontitis is a chronic oral disease prevalent worldwide, and natural products are recommended as adjunctive therapy due to their minor side effects. Curcumin, a widely used ancient compound, has been reported to possess therapeutic effects in periodontitis. However, the exact mechanism underlying its activity remains unclear. In this context, the present study aimed to conduct computational simulations to uncover the potential mechanism of action of Curcumin in the treatment of periodontitis. MATERIALS AND METHODS Single-cell analysis was conducted using a dataset (i.e., GSE164241) curated from the Gene Expression Omnibus (GEO) database through an R package "Seurat package." Bulk RNA sequencing data were curated from GSE10334 and GSE16134 and processed by R package "Limma." Then, the marker genes in the single-cell transcriptome and differentially expressed genes (DEGs) in the bulk transcriptome were integrated. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were also carried out to reveal their functionalities. Key targets were mined from their protein-protein interaction (PPI) network topologically. Afterward, molecular docking was performed. The top-ranked pose was subjected to molecular dynamics simulations to investigate the stability of the docking result. RESULTS FOS, CXCL1, CXCL8, and IL1B, were filtered after a series of selected processes. The results of molecular modeling suggested that except for IL1B, the Vena Scores of the rest exceeded -5 kcal/mol. Furthermore, the molecular dynamic simulation indicated that the binding of the CXCL8-Curcumin complex was stable over the entire 100 ns simulation. CONCLUSION The present study unlocked the binding modes of CXCL1, FOS, and CXCL8 with the Curcumin molecule, which were relatively stable, especially for CXCL8, hindering its promising potential to serve as the critical targets of Curcumin in periodontitis treatment.
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Affiliation(s)
- Xufeng Huang
- Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
- Department of Immunology, University of Debrecen, Debrecen, Hungary
| | - Ying Liu
- Department of Cardiology, Sixth Medical Center, PLA General Hospital, Beijing, China
| | - Qi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, LahorePunjab, 54590 Pakistan
- Alnoorians Group of Institutes, 55-Elahi Bukhsh Park, Amir Road, Shad Bagh, Lahore, 54000 Pakistan
| | - Dorottya Horváth
- Department of Immunology, University of Debrecen, Debrecen, Hungary
| | - Shujing Zhou
- Department of Immunology, University of Debrecen, Debrecen, Hungary
| | - Rao Fu
- Department of Oral and Maxillofacial-Head and Neck Oncology, College of Stomatology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology and National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Ling Zhang
- Department of Oral and Maxillofacial-Head and Neck Oncology, College of Stomatology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology and National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | | | - Zhengrui Li
- Department of Oral and Maxillofacial-Head and Neck Oncology, College of Stomatology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology and National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
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Çapan İ, Hawash M, Jaradat N, Sert Y, Servi R, Koca İ. Design, synthesis, molecular docking and biological evaluation of new carbazole derivatives as anticancer, and antioxidant agents. BMC Chem 2023; 17:60. [PMID: 37328860 DOI: 10.1186/s13065-023-00961-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/25/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND The carbazole skeleton is an important structural motif occurring naturally or synthesized chemically and has antihistaminic, antioxidant, antitumor, antimicrobial, and anti-inflammatory activities. OBJECTIVES This study aimed to design and synthesize a novel series of carbazole derivatives and evaluate their antiproliferative and antioxidant activities. METHODS The synthesized compounds were characterized utilizing HRMS, 1H-, and 13CAPT-NMR, and assessed for their anticancer, antifibrotic, and antioxidant effects utilizing reference biomedical procedures. In addition, the AutoDock Vina application was used to perform in-silico docking computations. RESULTS A series of carbazole derivatives were synthesized and characterized in the current study. Compounds 10 and 11 were found to have a stronger antiproliferative effect than compounds 2-5 against HepG2, HeLa, and MCF7 cancer cell lines with IC50 values of 7.68, 10.09, and 6.44 µM, respectively. Moreover, compound 9 showed potent antiproliferative activity against HeLa cancer cell lines with an IC50 value of 7.59 µM. However, except for compound 5, all of the synthesized compounds showed moderate antiproliferative activities against CaCo-2 with IC50 values in the range of 43.7-187.23 µM. All of these values were compared with the positive control anticancer drug 5-Fluorouracil (5-FU). In addition, compound 9 showed the most potent anti-fibrotic compound, and the cellular viability of LX-2 was found 57.96% at 1 µM concentration in comparison with the positive control 5-FU. Moreover, 4 and 9 compounds showed potent antioxidant activities with IC50 values of 1.05 ± 0.77 and 5.15 ± 1.01 µM, respectively. CONCLUSION Most of the synthesized carbazole derivatives showed promising antiproliferative, antioxidant, and antifibrotic biological effects, and further in-vivo investigations are needed to approve or disapprove these results.
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Affiliation(s)
- İrfan Çapan
- Department of Material and Material Processing Technologies, Gazi University, Technical Sciences Vocational College, 06560, Ankara, Turkey.
| | - Mohammed Hawash
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, 00970, Nablus, Palestine.
| | - Nidal Jaradat
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, 00970, Nablus, Palestine
| | - Yusuf Sert
- Yozgat Bozok University, Sorgun Vocational School, Yozgat, Turkey
| | - Refik Servi
- Department of Anatomy, Faculty of Medicine, Firat University, Elazig, Turkey
| | - İrfan Koca
- Department of Chemistry, Faculty of Art & Sciences, Yozgat Bozok University, Yozgat, Turkey
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Zhang A, Hou Y, Wang Y, Wang Q, Shan X, Liu J. Highly efficient low-temperature biodegradation of polyethylene microplastics by using cold-active laccase cell-surface display system. BIORESOURCE TECHNOLOGY 2023; 382:129164. [PMID: 37207695 DOI: 10.1016/j.biortech.2023.129164] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/06/2023] [Accepted: 05/09/2023] [Indexed: 05/21/2023]
Abstract
To eliminate efficiency restriction of polyethylene microplastics low-temperature biodegradation, a novel InaKN-mediated Escherichia coli surface display platform for cold-active degrading laccase PsLAC production was developed. Display efficiency of 88.0% for engineering bacteria BL21/pET-InaKN-PsLAC was verified via subcellular extraction and protease accessibility, exhibiting an activity load of 29.6 U/mg. Cell growth and membrane integrity revealed BL21/pET-InaKN-PsLAC maintained stable growth and intact membrane structure during the display process. The favorable applicability was confirmed, with 50.0% activity remaining in 4 days at 15 °C, and 39.0% activity recovery retention after 15 batches of activity substrate oxidation reactions. Moreover, BL21/pET-InaKN-PsLAC possessed high polyethylene low-temperature depolymerizing capacity. Bioremediation experiments proved that the degradation rate was 48.0% within 48 h at 15 °C, and reached 66.0% after 144 h. Collectively, cold-active PsLAC functional surface display technology and its significant contributions to polyethylene microplastics low-temperature degradation constitute an effective improvement strategy for biomanufacturing and microplastics cold remediation.
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Affiliation(s)
- Ailin Zhang
- School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yanhua Hou
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China
| | - Yatong Wang
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China.
| | - Quanfu Wang
- School of Environment, Harbin Institute of Technology, Harbin 150090, China; School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China.
| | - Xuejing Shan
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China
| | - Jianan Liu
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China
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Tse A, Janilkarn-Urena I, Lin J, Chang X, Efthymiou C, Idrissova A, Zhang M, Williams CK, Magaki S, Vinters HV, Davies DL, Gonen T, Gukasyan HJ, Seidler PM. Improving the solubility of pseudo-hydrophobic Alzheimer's Disease medicinal chemicals through co-crystal formulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538327. [PMID: 37162961 PMCID: PMC10168350 DOI: 10.1101/2023.04.25.538327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Natural products are ligands and potential inhibitors of Alzheimer's disease (AD) tau. Dihydromyricetin (DHM) is a CNS active natural product. Despite having signature polyphenolic character, DHM is ostensibly hydrophobic owing to intermolecular hydrogen bonds that shield hydrophilic phenols. Our research shows DHM becomes ionized at near-neutral pH allowing formulation of salts with transformed solubility. The MicroED co-crystal structure with trolamine reveals DHM salts as metastable solids with unlocked hydrogen bonding and a thermodynamic bent to solubilize in water. All salt formulations show better inhibitory activity against AD tau than the non-salt form, with efficacies correlating to enhanced solubilities. These results underscore the role of structural chemistry in guiding selection of solubilizing agents for chemical formulation. We propose DHM salts are appropriate formulations for research as dietary supplements to promote healthy aging by combating protein misfolding. Additionally, DHM is a suitable lead for medicinal chemistry and possible development of CNS pharmaceuticals.
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Affiliation(s)
- A Tse
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Mann School of Pharmacy and Pharmaceutical Sciences, 1985 Zonal Ave, Los Angeles, CA 90089-9121, USA
- Authors contributed equally to experimental work
| | - I Janilkarn-Urena
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Mann School of Pharmacy and Pharmaceutical Sciences, 1985 Zonal Ave, Los Angeles, CA 90089-9121, USA
- Authors contributed equally to experimental work
| | - J Lin
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, David Geffen School of Medicine at University of California, Los Angeles, California 90095
- Authors contributed equally to experimental work
| | - X Chang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Mann School of Pharmacy and Pharmaceutical Sciences, 1985 Zonal Ave, Los Angeles, CA 90089-9121, USA
| | - C Efthymiou
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Mann School of Pharmacy and Pharmaceutical Sciences, 1985 Zonal Ave, Los Angeles, CA 90089-9121, USA
| | - A Idrissova
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Mann School of Pharmacy and Pharmaceutical Sciences, 1985 Zonal Ave, Los Angeles, CA 90089-9121, USA
| | - M Zhang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Mann School of Pharmacy and Pharmaceutical Sciences, 1985 Zonal Ave, Los Angeles, CA 90089-9121, USA
| | - CK Williams
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles, California 90095
| | - S Magaki
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles, California 90095
| | - HV Vinters
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles, California 90095
- Department of Neurology, David Geffen School of Medicine at University of California, Los Angeles, California 90095
| | - DL Davies
- Titus Family Department of Clinical Pharmacy, University of Southern California School of Pharmacy, Los Angeles, CA 90089, USA
| | - T Gonen
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Physiology, University of California Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - HJ Gukasyan
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Mann School of Pharmacy and Pharmaceutical Sciences, 1985 Zonal Ave, Los Angeles, CA 90089-9121, USA
| | - PM Seidler
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Mann School of Pharmacy and Pharmaceutical Sciences, 1985 Zonal Ave, Los Angeles, CA 90089-9121, USA
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Dodaro A, Pavan M, Moro S. Targeting the I7L Protease: A Rational Design for Anti-Monkeypox Drugs? Int J Mol Sci 2023; 24:ijms24087119. [PMID: 37108279 PMCID: PMC10138331 DOI: 10.3390/ijms24087119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/29/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
The latest monkeypox virus outbreak in 2022 showcased the potential threat of this viral zoonosis to public health. The lack of specific treatments against this infection and the success of viral protease inhibitors-based treatments against HIV, Hepatitis C, and SARS-CoV-2, brought the monkeypox virus I7L protease under the spotlight as a potential target for the development of specific and compelling drugs against this emerging disease. In the present work, the structure of the monkeypox virus I7L protease was modeled and thoroughly characterized through a dedicated computational study. Furthermore, structural information gathered in the first part of the study was exploited to virtually screen the DrugBank database, consisting of drugs approved by the Food and Drug Administration (FDA) and clinical-stage drug candidates, in search for readily repurposable compounds with similar binding features as TTP-6171, the only non-covalent I7L protease inhibitor reported in the literature. The virtual screening resulted in the identification of 14 potential inhibitors of the monkeypox I7L protease. Finally, based on data collected within the present work, some considerations on developing allosteric modulators of the I7L protease are reported.
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Affiliation(s)
- Andrea Dodaro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Matteo Pavan
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
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Luo L, Guan Z, Jin X, Guan Z, Jiang Y. Identification of kukoamine a as an anti-osteoporosis drug target using network pharmacology and experiment verification. Mol Med 2023; 29:36. [PMID: 36941586 PMCID: PMC10029210 DOI: 10.1186/s10020-023-00625-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 02/16/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Osteoporosis (OP) is a major and growing public health problem characterized by decreased bone mineral density and destroyed bone microarchitecture. Previous studies found that Lycium Chinense Mill (LC) has a potent role in inhibiting bone loss. Kukoamine A (KuA), a bioactive compound extract from LC was responsible for the anti-osteoporosis effect. This study aimed to investigate the anti-osteoporosis effect of KuA isolated from LC in treating OP and its potential molecular mechanism. METHOD In this study, network pharmacology and molecular docking were investigated firstly to find the active ingredients of LC such as KuA, and the target genes of OP by the TCMSP platform. The LC-OP-potential Target gene network was constructed by the STRING database and network maps were built by Cytoscape software. And then, the anti-osteoporotic effect of KuA in OVX-induced osteoporosis mice and MC3T3-E1 cell lines were investigated and the potential molecular mechanism including inflammation level, cell apoptosis, and oxidative stress was analyzed by dual-energy X-ray absorptiometry (DXA), micro-CT, ELISA, RT-PCR, and Western Blotting. RESULT A total of 22 active compounds were screened, and we found KuA was identified as the highest active ingredient. Glycogen Phosphorylase (PYGM) was the target gene associated with a maximum number of active ingredients of LC and regulated KuA. In vivo, KuA treatment significantly increased the bone mineral density and improve bone microarchitecture for example increased BV/TV, Tb.N and Tb.Th but reduced Tb.Sp in tibia and lumber 4. Furthermore, KuA increased mRNA expression of osteoblastic differentiation-related genes in OVX mice and protects against OVX-induced cell apoptosis, oxidative stress level and inflammation level. In vitro, KuA significantly improves osteogenic differentiation and mineralization in cells experiment. In addition, KuA also attenuated inflammation levels, cell apoptosis, and oxidative stress level. CONCLUSION The results suggest that KuA could protect against the development of OP in osteoblast cells and ovariectomized OP model mice and these found to provide a better understanding of the pharmacological activities of KuA again bone loss.
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Affiliation(s)
- Liying Luo
- Department of Ophthalmology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Zhiyuan Guan
- Department of Orthopedics, The Shanghai Tenth People's Hospital of Tongji University, Shanghai, China
| | - Xiao Jin
- Department of Rheumatology and Immunology, The First People's Hospital of Xuzhou, Xuzhou, Jiangsu, 221002, People's Republic of China.
| | - Zhiqiang Guan
- Department of Dermatology, Xuzhou Municipal Hospital Affiliated With Xuzhou Medical University, Xuzhou, Jiangsu, 221002, People's Republic of China.
| | - Yanyun Jiang
- Department of Ophthalmology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Shi G, Shi C, Luo Y, Hong H, Zhang J, Li Y, Tan Y. Interaction and phase behavior of whey protein and propylene glycol alginate complex condensates. Food Chem 2023; 404:134556. [PMID: 36444012 DOI: 10.1016/j.foodchem.2022.134556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/12/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
Whey protein (WP) is ubiquitously applied in food products, but its sensitivity to food processing conditions has limited its application. Herein, we chose propylene glycol alginate (PGA) to combine with WP to enhance its stability. The ideal ratio of WP/PGA for coacervation was 3:1, and the soluble complex and insoluble complex were formed at pH 5.2 (pHc) and pH 4.4 (pHφ1) at this ratio, respectively. The UV absorption spectra, fluorescence spectra, and XRD results revealed that the interaction between PGA and WP changed the tertiary conformation of WP. The FTIR and molecular docking results suggested electrostatic interactions, hydrogen bonding and hydrophobic interactions were all involved in the formation of WP-PGA complexes, and the thermal stability of WP was improved based on the DSC results. These findings supported PGA to keep dairy products stable and transparent at the isoelectric point and WP-PGA complexes could be applied in encapsulating bioactive substances.
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Affiliation(s)
- Ge Shi
- Beijing Laboratory for Food Quality and Sfety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China; National Engineering Laboratory for Agri-product Quality Traceability, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China.
| | - Ce Shi
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China; National Engineering Laboratory for Agri-product Quality Traceability, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China.
| | - Yongkang Luo
- Beijing Laboratory for Food Quality and Sfety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Hui Hong
- Beijing Laboratory for Food Quality and Sfety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; Center of Food Colloids and Delivery for Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Jiaran Zhang
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China; National Engineering Laboratory for Agri-product Quality Traceability, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China.
| | - Yan Li
- Beijing Laboratory for Food Quality and Sfety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Yuqing Tan
- Beijing Laboratory for Food Quality and Sfety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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González-Paz L, Lossada C, Hurtado-León ML, Fernández-Materán FV, Paz JL, Parvizi S, Cardenas Castillo RE, Romero F, Alvarado YJ. Intrinsic Dynamics of the ClpXP Proteolytic Machine Using Elastic Network Models. ACS OMEGA 2023; 8:7302-7318. [PMID: 36873006 PMCID: PMC9979342 DOI: 10.1021/acsomega.2c04347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 10/25/2022] [Indexed: 06/18/2023]
Abstract
ClpXP complex is an ATP-dependent mitochondrial matrix protease that binds, unfolds, translocates, and subsequently degrades specific protein substrates. Its mechanisms of operation are still being debated, and several have been proposed, including the sequential translocation of two residues (SC/2R), six residues (SC/6R), and even long-pass probabilistic models. Therefore, it has been suggested to employ biophysical-computational approaches that can determine the kinetics and thermodynamics of the translocation. In this sense, and based on the apparent inconsistency between structural and functional studies, we propose to apply biophysical approaches based on elastic network models (ENM) to study the intrinsic dynamics of the theoretically most probable hydrolysis mechanism. The proposed models ENM suggest that the ClpP region is decisive for the stabilization of the ClpXP complex, contributing to the flexibility of the residues adjacent to the pore, favoring the increase in pore size and, therefore, with the energy of interaction of its residues with a larger portion of the substrate. It is predicted that the complex may undergo a stable configurational change once assembled and that the deformability of the system once assembled is oriented, to increase the rigidity of the domains of each region (ClpP and ClpX) and to gain flexibility of the pore. Our predictions could suggest under the conditions of this study the mechanism of the interaction of the system, of which the substrate passes through the unfolding of the pore in parallel with a folding of the bottleneck. The variations in the distance calculated by molecular dynamics could allow the passage of a substrate with a size equivalent to ∼3 residues. The theoretical behavior of the pore and the stability and energy of binding to the substrate based on ENM models suggest that in this system, there are thermodynamic, structural, and configurational conditions that allow a possible translocation mechanism that is not strictly sequential.
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Affiliation(s)
- Lenin González-Paz
- Facultad
Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio
de Genética y Biología Molecular (LGBM), Universidad del Zulia (LUZ), 4001 Maracaibo, Zulia, República Bolivariana
de Venezuela
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Biocomputación
(LB), Instituto Venezolano de Investigaciones
Científicas (IVIC), 4001 Maracaibo, Zulia, República Bolivariana de Venezuela
| | - Carla Lossada
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Biocomputación
(LB), Instituto Venezolano de Investigaciones
Científicas (IVIC), 4001 Maracaibo, Zulia, República Bolivariana de Venezuela
| | - Maria Laura Hurtado-León
- Facultad
Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio
de Genética y Biología Molecular (LGBM), Universidad del Zulia (LUZ), 4001 Maracaibo, Zulia, República Bolivariana
de Venezuela
| | - Francelys V. Fernández-Materán
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Biocomputación
(LB), Instituto Venezolano de Investigaciones
Científicas (IVIC), 4001 Maracaibo, Zulia, República Bolivariana de Venezuela
| | - José Luis Paz
- Departamento
Académico de Química Inorgánica, Facultad de
Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, 15081 Lima, Perú
| | - Shayan Parvizi
- Pulmonary,
Critical Care and Sleep Medicine, Baylor
College of Medicine, Houston, Texas 77030, United States
| | | | - Freddy Romero
- Pulmonary,
Critical Care and Sleep Medicine, Baylor
College of Medicine, Houston, Texas 77030, United States
| | - Ysaias J. Alvarado
- Centro
de Biomedicina Molecular (CBM), Laboratorio de Química Biofísica
Teórica y Experimental (LQBTE), Instituto
Venezolano de Investigaciones Cientificas (IVIC), 4001 Maracaibo, Zulia, República Bolivariana de Venezuela
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Antileishmanial Activity and In Silico Molecular Docking Studies of Malachra alceifolia Jacq. Fractions against Leishmania mexicana Amastigotes. Trop Med Infect Dis 2023; 8:tropicalmed8020115. [PMID: 36828531 PMCID: PMC9960462 DOI: 10.3390/tropicalmed8020115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Malachra alceifolia Jacq. (family Malvaceae), known as "malva," is a medicinal plant used as a traditional therapy in many regions of America, Africa and Asia. Traditionally, this plant is used in the form of extracts, powder and paste by populations for treating fever, stomachache, inflammation, and parasites. However, the ethnopharmacological validation of M. alceifolia has been scarcely researched. This study showed that the chloroform fraction (MA-IC) and subfraction (MA-24F) of the leaves of M. alceifolia exhibited a potential antileishmanial activity against axenic amastigotes of Leishmania mexicana pifanoi (MHOM/VE/60/Ltrod) and had high and moderate cytotoxic effects on the viability and morphology of macrophages RAW 264.7. This study reports, for the first time, possible terpenoid metabolites and derivatives present in M. alceifolia with activity against some biosynthetic pathways in L. mexicana amastigotes. The compounds from the subfractions MA-24F were highly active and were analyzed by gas chromatography-mass spectrometry (GC-MS) and by a molecular docking study in L. mexicana target protein. This study demonstrates the potential modes of interaction and the theoretical affinity energy of the metabolites episwertenol, α-amyrin and methyl commate A, which are present in the active fraction MA-24F, at allosteric sites of the pyruvate kinase, glyceraldehyde-3-phosphate dehydrogenase, triose phosphate isomerase, aldolase, phosphoglucose isomerase, transketolase, arginase and cysteine peptidases A, target proteins in some vital biosynthetic pathways were responsible for the survival of L. mexicana. Some phytoconstituents of M. alceifolia can be used for the search for potential new drugs and molecular targets for treating leishmaniases and infectious diseases. Furthermore, contributions to research and the validation and conservation of traditional knowledge of medicinal plants are needed globally.
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Souza RM, Oliveira DF, Gomes VM, Viana AJS, Silva GH, Machado ART. Meloidogyne enterolobii-induced Changes in Guava Root Exudates Are Associated With Root Rotting Caused by Neocosmospora falciformis. J Nematol 2023; 55:20230055. [PMID: 38264459 PMCID: PMC10805520 DOI: 10.2478/jofnem-2023-0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Indexed: 01/25/2024] Open
Abstract
Despite the worldwide importance of disease complexes involving root-feeding nematodes and soilborne fungi, there have been few in-depth studies on how these organisms interact at the molecular level. Previous studies of guava decline have shown that root exudates from Meloidogyne enterolobii-parasitized guava plants (NP plants), but not from nematode-free plants (NF plants), enable the fungus Neocosmospora falciformis to rot guava roots, leading to plant death. To further characterize this interaction, NP and NF root exudates were lyophilized; extracted with distinct solvents; quantified regarding amino acids, soluble carbohydrates, sucrose, phenols, and alkaloids; and submitted to a bioassay to determine their ability to enable N. falciformis to rot the guava seedlings' roots. NP root exudates were richer than NF root exudates in amino acids, carbohydrates, and sucrose. Only the fractions NP-03 and NP-04 enabled fungal root rotting. NP-03 was then sequentially fractionated through chromatographic silica columns. At each step, the main fractions were reassessed in bioassay. The final fraction that enabled fungal root rotting was submitted to analysis using high performance liquid chromatography, nuclear magnetic resonance, mass spectrometry, energy-dispersive X-ray fluorescence, and computational calculations, leading to the identification of 1,5-dinitrobiuret as the predominant substance. In conclusion, parasitism by M. enterolobii causes an enrichment of guava root exudates that likely favors microorganisms capable of producing 1,5-dinitrobiuret in the rhizosphere. The accumulation of biuret, a known phytotoxic substance, possibly hampers root physiology and the innate immunity of guava to N. falciformis.
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Affiliation(s)
- Ricardo M. Souza
- Departamento de Entomologia e Fitopatologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | | | - Vicente M. Gomes
- Departamento de Entomologia e Fitopatologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | | | - Geraldo H. Silva
- Laboratório de Desenvolvimento de Agroquímicos Naturais, Universidade Federal de Viçosa, Rio Paranaíba, Brazil
| | - Alan R. T. Machado
- Departamento de Ciências Exatas, Universidade do Estado de Minas Gerais, João Monlevade, Brazil
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Carrillo-Tripp M, Reyes Y, Delgado-Coello B, Mas-Oliva J, Gutiérrez-Vidal R. Peptide Helix-Y 12 as Potential Effector for Peroxisome Proliferator-Activated Receptors. PPAR Res 2023; 2023:8047378. [PMID: 37096195 PMCID: PMC10122583 DOI: 10.1155/2023/8047378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/26/2023] Open
Abstract
Peroxisome proliferator-activated receptors (PPARs) are nuclear receptors involved in the regulation of lipids and glucose metabolism, and immune response. Therefore, they have been considered pharmacological targets for treating metabolic diseases, such as dyslipidemia, atherosclerosis, and non-alcoholic fatty liver disease. However, the available synthetic ligands of PPARs have mild to significant side effects, generating the necessity to identify new molecules that are selective PPAR ligands with specific biological responses. This study aimed to evaluate some components of the atheroprotective and hepatoprotective HB-ATV-8 nanoparticles [the amphipathic peptide Helix-Y12, thermozeaxanthin, thermozeaxanthin-13, thermozeaxanthin-15, and a set of glycolipids], as possible ligands of PPARs through blind molecular docking. According to the change in free energy upon protein-ligand binding, ∆G b, thermozeaxanthins show a more favorable interaction with PPARs, followed by Helix-Y12. Moreover, Helix-Y12 interacts with most parts of the Y-shaped ligand-binding domain (LBD), surrounding helix 3 of PPARs, and reaching helix 12 of PPARα and PPARγ. As previously reported for other ligands, Tyr314 and Tyr464 of PPARα interact with Helix-Y12 through hydrogen bonds. Several PPARα's amino acids are involved in the ligand binding by hydrophobic interactions. Furthermore, we identified additional PPARs' amino acids interacting with Helix-Y12 through hydrogen bonds still not reported for known ligands. Our results show that, from the studied ligand set, the Helix-Y12 peptide and Tzeaxs have the most significant probability of binding to the PPARs' LBD, suggesting novel ligands for PPARs.
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Affiliation(s)
- Mauricio Carrillo-Tripp
- Biomolecular Diversity Laboratory, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Monterrey, Vía del Conocimiento 201, PIIT, C.P. 66600, Apodaca, Nuevo León, Mexico
| | - Yair Reyes
- Metabolic Diseases Laboratory, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Monterrey, Vía del Conocimiento 201, PIIT, C.P. 66600, Apodaca, Nuevo León, Mexico
- Universidad Politécnica de Puebla, Tercer Carril del Ejido, Serrano s/n, Cuanalá, C.P. 7264, Puebla, Mexico
| | - Blanca Delgado-Coello
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, C.P. 04510, CDMX, Mexico
| | - Jaime Mas-Oliva
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, C.P. 04510, CDMX, Mexico
| | - Roxana Gutiérrez-Vidal
- Metabolic Diseases Laboratory, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Monterrey, Vía del Conocimiento 201, PIIT, C.P. 66600, Apodaca, Nuevo León, Mexico
- Programa de Investigadoras e Investigadores por México, Conacyt, CDMX, Mexico
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Alavi M, Mozafari MR, Ghaemi S, Ashengroph M, Hasanzadeh Davarani F, Mohammadabadi M. Interaction of Epigallocatechin Gallate and Quercetin with Spike Glycoprotein (S-Glycoprotein) of SARS-CoV-2: In Silico Study. Biomedicines 2022; 10:biomedicines10123074. [PMID: 36551830 PMCID: PMC9775955 DOI: 10.3390/biomedicines10123074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/14/2022] [Accepted: 11/19/2022] [Indexed: 12/03/2022] Open
Abstract
Severe acute respiratory syndrome (SARS)-CoV-2 from the family Coronaviridae is the cause of the outbreak of severe pneumonia, known as coronavirus disease 2019 (COVID-19), which was first recognized in 2019. Various potential antiviral drugs have been presented to hinder SARS-CoV-2 or treat COVID-19 disease. Side effects of these drugs are among the main complicated issues for patients. Natural compounds, specifically primary and secondary herbal metabolites, may be considered as alternative options to provide therapeutic activity and reduce cytotoxicity. Phenolic materials such as epigallocatechin gallate (EGCG, polyphenol) and quercetin have shown antibacterial, antifungal, antiviral, anticancer, and anti-inflammatory effects in vitro and in vivo. Therefore, in this study, molecular docking was applied to measure the docking property of epigallocatechin gallate and quercetin towards the transmembrane spike (S) glycoprotein of SARS-CoV-2. Results of the present study showed Vina scores of -9.9 and -8.3 obtained for EGCG and quercetin by CB-Dock. In the case of EGCG, four hydrogen bonds of OG1, OD2, O3, and O13 atoms interacted with the Threonine (THR778) and Aspartic acid (ASP867) amino acids of the spike glycoprotein (6VSB). According to these results, epigallocatechin gallate and quercetin can be considered potent therapeutic compounds for addressing viral diseases.
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Affiliation(s)
- Mehran Alavi
- Department of Biological Science, Faculty of Science, University of Kurdistan, Kurdistan 6617715175, Iran
- Nanobiotechnology Department, Faculty of Innovative Science and Technology, Razi University, Kermanshah 6714414971, Iran
- Correspondence: (M.A.); (M.R.M.)
| | - M. R. Mozafari
- Australasian Nanoscience and Nanotechnology Initiative (ANNI), Monash University LPO, Clayton, VIC 3168, Australia
- Correspondence: (M.A.); (M.R.M.)
| | - Saba Ghaemi
- Research Committee of Medical School, Alborz University of Medical Science, Karaj 3149779453, Iran
| | - Morahem Ashengroph
- Department of Biological Science, Faculty of Science, University of Kurdistan, Kurdistan 6617715175, Iran
| | | | - Mohammadreza Mohammadabadi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman 7616913439, Iran
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Arteannuin-B and (3-Chlorophenyl)-2-Spiroisoxazoline Derivative Exhibit Anti-Inflammatory Effects in LPS-Activated RAW 264.7 Macrophages and BALB/c Mice-Induced Proinflammatory Responses via Downregulation of NF-κB/P38 MAPK Signaling. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27228068. [PMID: 36432169 PMCID: PMC9699497 DOI: 10.3390/molecules27228068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/09/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022]
Abstract
Host inflammatory responses are key to protection against injury; however, persistent inflammation is detrimental and contributes to morbidity and mortality. Herein, we demonstrated the anti-inflammatory role of Arteannuin-B (1) and its new spirocyclic-2-isoxazoline derivative JR-9 and their side effects in acute inflammatory condition in vivo using LPS-induced cytokines assay, carrageenan-induced paw edema, acetic acid-induced writhing and tail immersion. The results show that the spirocyclic-2-isoxazoline derivative is a potent anti-inflammatory agent with minimal cell toxicity as compared to Arteannuin-B. In addition, the efficacies of these compounds were also validated by flow cytometric, computational, and histopathological analysis. Our results show that the anti-inflammatory response of JR-9 significantly reduces the ability of mouse macrophages to produce NO, TNF-α, and IL-6 following LPS stimulation. Therefore, JR-9 is a prospective candidate for the development of anti-inflammatory drugs and its molecular mechanism is likely related to the regulation of NF-κB and MAPK signaling pathway.
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Ochoa R, Cossio P, Fox T. Protocol for iterative optimization of modified peptides bound to protein targets. J Comput Aided Mol Des 2022; 36:825-835. [PMID: 36258137 PMCID: PMC9640467 DOI: 10.1007/s10822-022-00482-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/03/2022] [Indexed: 12/02/2022]
Abstract
Peptides are commonly used as therapeutic agents. However, they suffer from easy degradation and instability. Replacing natural by non-natural amino acids can avoid these problems, and potentially improve the affinity towards the target protein. Here, we present a computational pipeline to optimize peptides based on adding non-natural amino acids while improving their binding affinity. The workflow is an iterative computational evolution algorithm, inspired by the PARCE protocol, that performs single-point mutations on the peptide sequence using modules from the Rosetta framework. The modifications can be guided based on the structural properties or previous knowledge of the biological system. At each mutation step, the affinity to the protein is estimated by sampling the complex conformations and applying a consensus metric using various open protein-ligand scoring functions. The mutations are accepted based on the score differences, allowing for an iterative optimization of the initial peptide. The sampling/scoring scheme was benchmarked with a set of protein-peptide complexes where experimental affinity values have been reported. In addition, a basic application using a known protein-peptide complex is also provided. The structure- and dynamic-based approach allows users to optimize bound peptides, with the option to personalize the code for further applications. The protocol, called mPARCE, is available at: https://github.com/rochoa85/mPARCE/.
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Affiliation(s)
- Rodrigo Ochoa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellín, 050010, Colombia. .,Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach/Riss, Germany.
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellín, 050010, Colombia.,Center for Computational Mathematics, Flatiron Institute, New York, 10010, USA.,Center for Computational Biology, Flatiron Institute, New York, 10010, USA
| | - Thomas Fox
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach/Riss, Germany
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Rana MM, Nguyen DD. EISA-Score: Element Interactive Surface Area Score for Protein–Ligand Binding Affinity Prediction. J Chem Inf Model 2022; 62:4329-4341. [DOI: 10.1021/acs.jcim.2c00697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Md Masud Rana
- Department of Mathematics, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Duc Duy Nguyen
- Department of Mathematics, University of Kentucky, Lexington, Kentucky 40506, United States
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Pathomorphogenesis of Glycogen-Ground Glass Hepatocytic Inclusions (Polyglucosan Bodies) in Children after Liver Transplantation. Int J Mol Sci 2022; 23:ijms23179996. [PMID: 36077394 PMCID: PMC9456521 DOI: 10.3390/ijms23179996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/27/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
Seventeen out of 764 liver biopsies from transplanted (Tx) livers in children showed glycogen-ground glass (GGG) hepatocytic inclusions. The inclusions were not present in pre-Tx or in the explanted or donor’s liver. Under the electron microscope (EM), the stored material within the cytosol appeared as non-membrane-bound aggregates of electron-lucent globoid or fibrillar granules, previously described as abnormally structured glycogen and identified as Polyglucosan bodies (PB). The appearance of GGG in our children was analogous to that of PB-GGG occurring in a number of congenital diseases due to gene mutations such as Lafora’s d., Andersen’s d., Adult Polyglucosan Body Disease and glycogenin deficiency. The same type of GGG was previously reported in the liver of patients undergoing transplants, immunosuppressive or antiblastic treatment. To explore the potential mechanism of GGG formation, we examined whether the drugs after whose treatment this phenomenon was observed could have a role. By carrying out molecular docking, we found that such drugs somehow present a high binding affinity for the active region of glycogenin, implicating that they can inactivate the protein, thus preventing its interaction with glycogen synthase (GS), as well as the maturation of the nascent glycogen towards gamma, beta or alfa glycogen granules. We could also demonstrate that PG inclusions consist of a complex of PAS positive material (glycogen) and glycogen-associated proteins, i.e., glicogenin-1 and -2 and ubiquitin. These features appear to be analogous to congenital GGG, suggesting that, in both cases, they result from the simultaneous dysregulation of glycogen synthesis and degradation. Drug-induced GGG appear to be toxic to the cell, despite their reversibility.
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Network Pharmacology and Molecular Docking Study of Yupingfeng Powder in the Treatment of Allergic Diseases. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:1323744. [PMID: 35855823 PMCID: PMC9288288 DOI: 10.1155/2022/1323744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022]
Abstract
Objective To explore the potential mechanisms of Yupingfeng Powder (YPFP) in the treatment of allergic diseases by using network pharmacology and molecular docking technology. Methods The active components and targets of YPFP were screened by the TCMSP database. The targets associated with atopic dermatitis, asthma, allergic rhinitis, and food allergy were obtained from GeneCards and OMIM databases, respectively. The intersection of the above disease-related targets was identified as allergy-related targets. Then, allergy-related targets and YPFP-related targets were crossed to obtain the potential targets of YPFP for allergy treatment. A protein-protein-interaction (PPI) network and a drug-target-disease topology network were constructed to screen hub targets and key ingredients. Next, GO and KEGG pathway enrichment analyses were performed separately on the potential targets and hub targets to identify the biological processes and signaling pathways involved. Finally, molecular docking was conducted to verify the binding affinity between key ingredients and hub targets. Results In this study, 45 active ingredients were identified from YPFP, and 48 allergy-related targets were predicted by network pharmacology. IL6, TNF, IL1B, PTGS2, CXCL8, JUN, CCL2, IL10, IFNG, and IL4 were screened as hub targets by the PPI network. However, quercetin, kaempferol, wogonin, formononetin, and 7-O-methylisomucronulatol were identified as key ingredients by the drug-target-disease topological network. GO and KEGG pathway enrichment analysis indicated that the therapeutic effect of YPFP on allergy involved multiple biological processes and signaling pathways, including positive regulation of fever generation, positive regulation of neuroinflammatory response, vascular endothelial growth factor production, negative regulation of cytokine production involved in immune response, positive regulation of mononuclear cell migration, type 2 immune response, and negative regulation of lipid storage. Molecular docking verified that all the key ingredients had good binding affinity with hub targets. Conclusion This study revealed the key ingredients, hub targets, and potential mechanisms of YPFP antiallergy, and these data can provide some theoretical basis for subsequent allergy treatment and drug development.
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Structural and biochemical analysis reveals how ferulic acid improves catalytic efficiency of Humicola grisea xylanase. Sci Rep 2022; 12:11409. [PMID: 35794132 PMCID: PMC9259647 DOI: 10.1038/s41598-022-15175-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Humicolagrisea var. thermoidea is an aerobic and thermophilic fungus that secretes the GH11 xylanase HXYN2 in the presence of sugarcane bagasse. In this study, HXYN2 was expressed in Pichiapastoris and characterized biochemically and structurally in the presence of beechwood xylan substrate and ferulic acid (FA). HXYN2 is a thermally stable protein, as indicated by circular dichroism, with greater activity in the range of 40–50 °C and pH 5.0–9.0, with optimal temperature and pH of 50 °C and 6.0, respectively. FA resulted in a 75% increase in enzyme activity and a 2.5-fold increase in catalytic velocity, catalytic efficiency, and catalytic rate constant (kcat), with no alteration in enzyme affinity for the substrate. Fluorescence quenching indicated that FA forms a complex with HXYN2 interacting with solvent-exposed tryptophan residues. The binding constants ranged from moderate (pH 7.0 and 9.0) to strong (pH 4.0) affinity. Isothermal titration calorimetry, structural models and molecular docking suggested that hydrogen bonds and hydrophobic interactions occur in the aglycone region inducing conformational changes in the active site driven by initial and final enthalpy- and entropy processes, respectively. These results indicate a potential for biotechnological application for HXYN2, such as in the bioconversion of plant residues rich in ferulic acid.
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Liu Y, Yang X, Gan J, Chen S, Xiao ZX, Cao Y. CB-Dock2: improved protein-ligand blind docking by integrating cavity detection, docking and homologous template fitting. Nucleic Acids Res 2022; 50:W159-W164. [PMID: 35609983 PMCID: PMC9252749 DOI: 10.1093/nar/gkac394] [Citation(s) in RCA: 231] [Impact Index Per Article: 115.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/24/2022] [Accepted: 05/05/2022] [Indexed: 11/14/2022] Open
Abstract
Protein-ligand blind docking is a powerful method for exploring the binding sites of receptors and the corresponding binding poses of ligands. It has seen wide applications in pharmaceutical and biological researches. Previously, we proposed a blind docking server, CB-Dock, which has been under heavy use (over 200 submissions per day) by researchers worldwide since 2019. Here, we substantially improved the docking method by combining CB-Dock with our template-based docking engine to enhance the accuracy in binding site identification and binding pose prediction. In the benchmark tests, it yielded the success rate of ∼85% for binding pose prediction (RMSD < 2.0 Å), which outperformed original CB-Dock and most popular blind docking tools. This updated docking server, named CB-Dock2, reconfigured the input and output web interfaces, together with a highly automatic docking pipeline, making it a particularly efficient and easy-to-use tool for the bioinformatics and cheminformatics communities. The web server is freely available at https://cadd.labshare.cn/cb-dock2/.
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Affiliation(s)
- Yang Liu
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaocong Yang
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jianhong Gan
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Shuang Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhi-Xiong Xiao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China
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