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Lv L, Shi Y, Deng Z, Xu J, Ye Z, He J, Chen G, Yu X, Wu J, Huang X, Li G. A polymeric nanocarrier that eradicates breast cancer stem cells and delivers chemotherapeutic drugs. Biomater Res 2023; 27:133. [PMID: 38102651 PMCID: PMC10722842 DOI: 10.1186/s40824-023-00465-9] [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: 09/19/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Drug nanocarriers can markedly reduce the toxicities and side effects of encapsulated chemotherapeutic drugs in the clinic. However, these drug nanocarriers have little effect on eradicating breast cancer stem cells (BCSCs). Although compounds that can inhibit BCSCs have been reported, these compounds are difficult to use as carriers for the widespread delivery of conventional chemotherapeutic drugs. METHODS Herein, we synthesize a polymeric nanocarrier, hyaluronic acid-block-poly (curcumin-dithiodipropionic acid) (HA-b-PCDA), and explore the use of HA-b-PCDA to simultaneously deliver chemotherapeutic drugs and eradicate BCSCs. RESULTS Based on molecular docking and molecular dynamics studies, HA-b-PCDA delivers 35 clinical chemotherapeutic drugs. To further verify the drug deliver ability of HA-b-PCDA, doxorubicin, paclitaxel, docetaxel, gemcitabine and camptothecin are employed as model drugs to prepare nanoparticles. These drug-loaded HA-b-PCDA nanoparticles significantly inhibit the proliferation and stemness of BCSC-enriched 4T1 mammospheres. Moreover, doxorubicin-loaded HA-b-PCDA nanoparticles efficiently inhibit tumor growth and eradicate approximately 95% of BCSCs fraction in vivo. Finally, HA-b-PCDA eradicates BCSCs by activating Hippo and inhibiting the JAK2/STAT3 pathway. CONCLUSION HA-b-PCDA is a polymeric nanocarrier that eradicates BCSCs and potentially delivers numerous clinical chemotherapeutic drugs.
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Affiliation(s)
- Li Lv
- Department of Pharmacy, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510120, China
| | - Yonghui Shi
- Department of Pharmacy, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510120, China
| | - Zhicheng Deng
- Shenshan Medical Center, Memorial Hospital of Sun Yat-Sen University, Shanwei, Guangdong, 516600, China
| | - Jiajia Xu
- School of Pharmacy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Zicong Ye
- Department of Pharmacy, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510120, China
| | - Jianxiong He
- Department of Pharmacy, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510120, China
| | - Guanghui Chen
- Department of Pharmacy, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510120, China
| | - Xiaoxia Yu
- Department of Pharmacy, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510120, China
| | - Junyan Wu
- Department of Pharmacy, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510120, China.
| | - Xingzhen Huang
- School of Pharmacy, Guangxi Medical University, Nanning, Guangxi, 530021, China.
| | - Guocheng Li
- Department of Pharmacy, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510120, China.
- Shenshan Medical Center, Memorial Hospital of Sun Yat-Sen University, Shanwei, Guangdong, 516600, China.
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Liu W, Ou P, Tian F, Liao J, Ma Y, Wang J, Jin X. Anti- Vibrio parahaemolyticus compounds from Streptomyces parvus based on Pan-genome and subtractive proteomics. Front Microbiol 2023; 14:1218176. [PMID: 37485508 PMCID: PMC10361664 DOI: 10.3389/fmicb.2023.1218176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction Vibrio parahaemolyticus is a foodborne pathogen commonly found in seafood, and drug resistance poses significant challenges to its control. This study aimed to identify novel drug targets for antibacterial drug discovery. Methods To identify drug targets, we performed a pan-genome analysis on 58 strains of V. parahaemolyticus genomes to obtain core genes. Subsequently, subtractive proteomics and physiochemical checks were conducted on the core proteins to identify potential therapeutic targets. Molecular docking was then employed to screen for anti-V. parahaemolyticus compounds using a in-house compound library of Streptomyces parvus, chosen based on binding energy. The anti-V. parahaemolyticus efficacy of the identified compounds was further validated through a series of experimental tests. Results and Discussion Pangenome analysis of 58 V. parahaemolyticus genomes revealed that there were 1,392 core genes. After Subtractive proteomics and physiochemical checks, Flagellar motor switch protein FliN was selected as a therapeutic target against V. parahaemolyticus. FliN was modeled and docked with Streptomyces parvus source compounds, and Actinomycin D was identified as a potential anti-V. parahaemolyticus agent with a strong binding energy. Experimental verification confirmed its effectiveness in killing V. parahaemolyticus and significantly inhibiting biofilm formation and motility. This study is the first to use pan-genome and subtractive proteomics to identify new antimicrobial targets for V. parahaemolyticus and to identify the anti-V. parahaemolyticus effect of Actinomycin D. These findings suggest potential avenues for the development of new antibacterial drugs to control V. parahaemolyticus infections.
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Affiliation(s)
- Wenbin Liu
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
| | - Peiyu Ou
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
| | - Fangyuan Tian
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jingyang Liao
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yan Ma
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jie Wang
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xiaobao Jin
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
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Pan-Genomics of Escherichia albertii for Antibiotic Resistance Profiling in Different Genome Fractions and Natural Product Mediated Intervention: In Silico Approach. Life (Basel) 2023; 13:life13020541. [PMID: 36836896 PMCID: PMC9962377 DOI: 10.3390/life13020541] [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: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
Escherichia albertii is an emerging, enteric pathogen of significance. It was first isolated in 2003 from a pediatric diarrheal sample from Bangladesh. In this study, a comprehensive in silico strategy was followed to first list out antibiotic-resistant genes from core, accessory and unique genome fractions of 95 available genomes of E. albertii. Then, 56 drug targets were identified from the core essential genome. Finally, ZipA, an essential cell division protein that stabilizes the FtsZ protofilaments by cross-linking them and serves as a cytoplasmic membrane anchor for the Z ring, was selected for further downstream processing. It was computationally modeled using a threading approach, followed by virtual screening of two phytochemical libraries, Ayurvedic (n = 2103 compounds) and Traditional Chinese Medicine (n = 36,043 compounds). ADMET profiling, followed by PBPK modeling in the central body compartment, in a population of 250 non-diseased, 250 cirrhotic and 250 renally impaired people was attempted. ZINC85624912 from Chinese medicinal library showed the highest bioavailability and plasma retention. This is the first attempt to simulate the fate of natural products in the body through PBPK. Dynamics simulation of 20 ns for the top three compounds from both libraries was also performed to validate the stability of the compounds. The obtained information from the current study could aid wet-lab scientists to work on the scaffold of screened drug-like compounds from natural resources and could be useful in our quest for therapy against antibiotic-resistant E. albertii.
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Khan K, Alhar MSO, Abbas MN, Abbas SQ, Kazi M, Khan SA, Sadiq A, Hassan SSU, Bungau S, Jalal K. Integrated Bioinformatics-Based Subtractive Genomics Approach to Decipher the Therapeutic Drug Target and Its Possible Intervention against Brucellosis. Bioengineering (Basel) 2022; 9:633. [PMID: 36354544 PMCID: PMC9687753 DOI: 10.3390/bioengineering9110633] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/28/2022] [Accepted: 10/29/2022] [Indexed: 11/16/2023] Open
Abstract
Brucella suis, one of the causative agents of brucellosis, is Gram-negative intracellular bacteria that may be found all over the globe and it is a significant facultative zoonotic pathogen found in livestock. It may adapt to a phagocytic environment, reproduce, and develop resistance to harmful environments inside host cells, which is a crucial part of the Brucella life cycle making it a worldwide menace. The molecular underpinnings of Brucella pathogenicity have been substantially elucidated due to comprehensive methods such as proteomics. Therefore, we aim to explore the complete Brucella suis proteome to prioritize the novel proteins as drug targets via subtractive proteo-genomics analysis, an effort to conjecture the existence of distinct pathways in the development of brucellosis. Consequently, 38 unique metabolic pathways having 503 proteins were observed while among these 503 proteins, the non-homologs (n = 421), essential (n = 350), drug-like (n = 114), virulence (n = 45), resistance (n = 42), and unique to pathogen proteins were retrieved from Brucella suis. The applied subsequent hierarchical shortlisting resulted in a protein, i.e., isocitrate lyase, that may act as potential drug target, which was finalized after the extensive literature survey. The interacting partners for these shortlisted drug targets were identified through the STRING database. Moreover, structure-based studies were also performed on isocitrate lyase to further analyze its function. For that purpose, ~18,000 ZINC compounds were screened to identify new potent drug candidates against isocitrate lyase for brucellosis. It resulted in the shortlisting of six compounds, i.e., ZINC95543764, ZINC02688148, ZINC20115475, ZINC04232055, ZINC04231816, and ZINC04259566 that potentially inhibit isocitrate lyase. However, the ADMET profiling showed that all compounds fulfill ADMET properties except for ZINC20115475 showing positive Ames activity; whereas, ZINC02688148, ZINC04259566, ZINC04232055, and ZINC04231816 showed hepatoxicity while all compounds were observed to have no skin sensitization. In light of these parameters, we recommend ZINC95543764 compound for further experimental studies. According to the present research, which uses subtractive genomics, proteins that might serve as therapeutic targets and potential lead options for eradicating brucellosis have been narrowed down.
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Affiliation(s)
- Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi City 75270, Pakistan
| | | | - Muhammad Naseer Abbas
- Department of Pharmacy, Kohat University of Science and Technology, Kohat 26000, Pakistan
| | - Syed Qamar Abbas
- Department of Pharmacy, Sarhad University of Science and Technology, Peshawar 25000, Pakistan
| | - Mohsin Kazi
- Department of Pharmaceutics, College of Pharmacy, P.O. Box-2457, King Saud University, Riyadh 11451, Saudi Arabia
| | - Saeed Ahmad Khan
- Department of Pharmacy, Kohat University of Science and Technology, Kohat 26000, Pakistan
- Division of Molecular Pharmaceutics and Drug Delivery, The University of Texas at Austin, 2409 University Ave., Austin, TX 78712, USA
| | - Abdul Sadiq
- Department of Pharmacy, Faculty of Biological Sciences, University of Malakand, Chakdara 18000, Pakistan
| | - Syed Shams ul Hassan
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Natural Product Chemistry, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania
| | - Khurshid Jalal
- HEJ Research Institute of Chemistry International Center for Chemical and Biological Sciences, University of Karachi, Karachi City 75270, Pakistan
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Inferring Therapeutic Targets in Candida albicans and Possible Inhibition through Natural Products: A Binding and Physiological Based Pharmacokinetics Snapshot. Life (Basel) 2022; 12:life12111743. [DOI: 10.3390/life12111743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/12/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022] Open
Abstract
Despite being responsible for invasive infections, fungal pathogens have been underrepresented in computer aided therapeutic target mining and drug design. Excess of Candida albicans causes candidiasis, causative of thrush and vaginal infection due to off-balance. In this study, we attempted to mine drug targets (n = 46) using a subtractive proteomic approach in this pathogenic yeast and screen natural products with inhibition potential against fructose-bisphosphate aldolase (FBA) of the C. albicans. The top compound selected on the basis of best docking score from traditional Indian medicine/Ayurvedic library was (4-Hydroxybenzyl)thiocarbamic acid, from the ZINC FBA inhibitor library was ZINC13507461 (IUPAC name: [(2R)-2-hydroxy-3-phosphonooxypropyl] (9E,12E)-octadeca-9,12-dienoate), and from traditional Tibetan medicine/Sowa rigpa was Chelerythrine (IUPAC name: 1,2-Dimethoxy-12-methyl-9H-[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium), compared to the control (2E)-1-(4-nitrophenyl)-2-[(4-nitrophenyl)methylidene]hydrazine. No Ames toxicity was predicted for prioritized compounds while control depicted this toxicity. (4-Hydroxybenzyl)thiocarbamic acid showed hepatotoxicity, while Chelerythrine depicted hERG inhibition, which can lead to QT syndrome, so we recommend ZINC13507461 for further testing in lab. Pharmacological based pharmacokinetic modeling revealed that it has low bioavailability and hence, absorption in healthy state. In cirrhosis and renal impairment, absorption and plasma accumulation increased so we recommend further investigation into this occurrence and recommend high dosage in further tests to increase bioavailability.
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