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Basharat Z, Ahmed I, Alnasser SM, Meshal A, Waheed Y. Exploring Lead-Like Molecules of Traditional Chinese Medicine for Treatment Quest against Aliarcobacter butzleri: In Silico Toxicity Assessment, Dynamics Simulation, and Pharmacokinetic Profiling. BIOMED RESEARCH INTERNATIONAL 2024; 2024:9377016. [PMID: 39282570 PMCID: PMC11401669 DOI: 10.1155/2024/9377016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 01/21/2024] [Accepted: 02/07/2024] [Indexed: 09/19/2024]
Abstract
Background Aliarcobacter butzleri is a Gram-negative, curved or spiral-shaped, microaerophilic bacterium and causes human infections, specifically diarrhea, fever, and sepsis. The research objective of this study was to employ computer-aided drug design techniques to identify potential natural product inhibitors of a vital enzyme in this bacterium. The pyrimidine biosynthesis pathway in its core genome fraction is crucial for its survival and presents a potential target for novel therapeutics. Hence, novel small molecule inhibitors were identified (from traditional Chinese medicinal (TCM) compound library) against it, which may be used for possible curbing of infection by A. butzleri. Methods. A comprehensive subtractive genomics approach was utilized to identify a key enzyme (orotidine-5'-phosphate decarboxylase) cluster conserved in the core genome fraction of A. butzleri. It was selected for inhibitor screening due to its vital role in pyrimidine biosynthesis. TCM library (n > 36,000 compounds) was screened against it using pharmacophore model based on orotidylic acid (control), and the obtained lead-like molecules were subjected to structural docking using AutoDock Vina. The top-scoring compounds, ZINC70454134, ZINC85632684, and ZINC85632721, underwent further scrutiny via a combination of physiological-based pharmacokinetics, toxicity assessment, and atomic-scale dynamics simulations (100 ns). Results Among the screened compounds, ZINC70454134 displayed the most favorable characteristics in terms of binding, stability, absorption, and safety parameters. Overall, traditional Chinese medicine (TCM) compounds exhibited high bioavailability, but in diseased states (cirrhosis, renal impairment, and steatosis), there was a significant decrease in absorption, Cmax, and AUC of the compounds compared to the healthy state. Furthermore, MD simulation demonstrated that the ODCase-ZINC70454134 complex had a superior overall binding affinity, supported by PCA proportion of variance and eigenvalue rank analysis. These favorable characteristics underscore its potential as a promising drug candidate. Conclusion The computer-aided drug design approach employed for this study helped expedite the discovery of antibacterial compounds against A. butzleri, offering a cost-effective and efficient approach to address infection by it. It is recommended that ZINC70454134 should be considered for further experimental analysis due to its indication as a potential therapeutic agent for combating A. butzleri infections. This study provides valuable insights into the molecular basis of biophysical inhibition of A. butzleri through TCM compounds.
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Affiliation(s)
| | - Ibrar Ahmed
- Alpha Genomics (Private) Limited, Islamabad 45710, Pakistan
- Group of Biometrology, The Korea Research Institute of Standards and Science (KRISS), Yuseong District, Daejeon 34113, Republic of Korea
| | - Sulaiman Mohammed Alnasser
- Department of Pharmacology and Toxicology, Unaizah College of Pharmacy, Qassim University, Buraydah 52571, Saudi Arabia
| | - Alotaibi Meshal
- Department of Pharmacy Practice, College of Pharmacy, University of Hafr Al Batin, Hafar Al Batin, Saudi Arabia
| | - Yasir Waheed
- Office of Research, Innovation and Commercialization (ORIC), Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad 44000, Pakistan
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos 1401, Lebanon
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Jin X, Xiao J, Lu C, Ma W, Fan Y, Xue X, Xia Y, Chen N, Liu J, Pei X. Breastmilk microbiome changes associated with lactational mastitis and treatment with dandelion extract. Front Microbiol 2023; 14:1247868. [PMID: 38029215 PMCID: PMC10679338 DOI: 10.3389/fmicb.2023.1247868] [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: 06/26/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Dandelion (Pugongying) is one of the most frequently used Chinese herbs for treating lactational mastitis (LM). Pugongying granules, a patented medication primarily comprised of dandelion extract, have been approved by CFDA for LM treatment in China. The aims of this study were to investigate the etiology of LM and the mechanism by which Pugongying granules decrease LM symptoms, with a particular focus on the microbial communities found in breastmilk. Methods Participants were recruited from a previously performed randomized controlled trial (Identifier: NCT03756324, ClinicalTrials.gov). Between 2019 and 2020, women diagnosed with unilateral LM at the Beijing University of Chinese Medicine Third Affiliated Hospital were enrolled. In total, 42 paired breastmilk samples from the healthy and affected breasts of the participants were collected. Additionally, 37 paired pre- and post-treatment breastmilk samples from the affected breast were collected from women who received a 3-day course of either Pugongying granules (20 women) or cefdinir (17 women). Clinical outcomes [e.g., body temperature, visual analogue scale (VAS) score for breast pain, the percentage of neutrophils (NE%)] were analyzed pre- and post-treatment, and the breastmilk samples were subjected to 16S rRNA gene sequencing to analyze the alpha and beta diversities and identify significant bacteria. Finally, the relationship between microorganisms and clinical outcomes was analyzed. Results There was no significant difference in fever and pain between the Pugongying group and cefdinir group. The most prevalent bacterial genera in breastmilk were Streptococcus and Staphylococcus. Compared to healthy breastmilk, microbial diversity was reduced in affected breastmilk, and there was a higher relative abundance of Streptococcus. After Pugongying treatment, there was an increase in microbial diversity with significantly higher abundance of Corynebacterium. A negative correlation was found between Corynebacterium, VAS score, and NE%. Treatment with cefdinir did not affect microbial diversity. Taken together, our results show a correlation between LM and reduced microbial diversity, as well as an increased abundance of Streptococcus in affected breastmilk. Conclusion Pugongying granules enhanced microbial diversity in breastmilk samples. Given the substantial variation in individual microbiomes, identifying specific species of Streptococcus and Corynebacterium associated with LM may provide additional insight into LM pathogenesis and treatment.
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Affiliation(s)
- Xinyan Jin
- Centre for Evidence-based Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- Beijing University of Chinese Medicine Affiliated Xiamen Hospital, Xiamen, China
| | - Jinhe Xiao
- Department of Prevention and Treatment of Breast Disease, Haidian District Maternal and Child Health Care Hospital, Beijing, China
| | - Chunli Lu
- Guangdong Provincial Research Center of Integration of Traditional Chinese Medicine and Western Medicine in Metabolic Diseases (Institute of Chinese Medicine), Guangdong Pharmaceutical University, Guangzhou, China
| | - Wenxin Ma
- Centre for Evidence-based Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Yingyi Fan
- Department of Breast Surgery, Beijing University of Chinese Medicine Third Affiliated Hospital, Beijing, China
| | - Xue Xue
- The First Clinical Medical School, Hubei University of Chinese Medicine, Wuhan, China
| | - Yaru Xia
- Department of Breast Surgery, Beijing University of Chinese Medicine Third Affiliated Hospital, Beijing, China
| | - Nana Chen
- Department of Breast Surgery, Beijing University of Chinese Medicine Third Affiliated Hospital, Beijing, China
| | - Jianping Liu
- Centre for Evidence-based Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaohua Pei
- Beijing University of Chinese Medicine Affiliated Xiamen Hospital, Xiamen, China
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Chanaj-Kaczmarek J, Rosiak N, Szymanowska D, Rajewski M, Wender-Ozegowska E, Cielecka-Piontek J. The Chitosan-Based System with Scutellariae baicalensis radix Extract for the Local Treatment of Vaginal Infections. Pharmaceutics 2022; 14:740. [PMID: 35456574 PMCID: PMC9028937 DOI: 10.3390/pharmaceutics14040740] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 02/01/2023] Open
Abstract
Scutellarie baicalensis radix, as a flavone-rich source, exhibits antibacterial, antifungal, antioxidant, and anti-inflammatory activity. It may be used as a therapeutic agent to treat various diseases, including vaginal infections. In this study, six binary mixtures of chitosan with stable S. baicalensis radix lyophilized extract were obtained and identified by spectral (ATR-FTIR, XRPD) and thermal (TG and DSC) methods. The changes in dissolution rates of active compounds and the significant increase in the biological properties towards metal chelating activity were observed, as well as the inhibition of hyaluronic acid degradation after mixing plant extract with chitosan. Moreover, the combination of S. baicalensis radix lyophilized extract with a carrier allowed us to obtain the binary systems with a higher antifungal activity than the pure extract, which may be effective in developing new strategies in the vaginal infections treatment, particularly vulvovaginal candidiasis.
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Affiliation(s)
- Justyna Chanaj-Kaczmarek
- Department of Pharmacognosy, Poznan University of Medical Sciences, 3 Rokietnicka Street, 60-806 Poznan, Poland; (J.C.-K.); (N.R.)
| | - Natalia Rosiak
- Department of Pharmacognosy, Poznan University of Medical Sciences, 3 Rokietnicka Street, 60-806 Poznan, Poland; (J.C.-K.); (N.R.)
| | - Daria Szymanowska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 48 Wojska Polskiego Street, 60-627 Poznan, Poland;
| | - Marcin Rajewski
- Department of Reproduction, Poznan University of Medical Sciences, 33 Polna Street, 60-535 Poznan, Poland; (M.R.); (E.W.-O.)
| | - Ewa Wender-Ozegowska
- Department of Reproduction, Poznan University of Medical Sciences, 33 Polna Street, 60-535 Poznan, Poland; (M.R.); (E.W.-O.)
| | - Judyta Cielecka-Piontek
- Department of Pharmacognosy, Poznan University of Medical Sciences, 3 Rokietnicka Street, 60-806 Poznan, Poland; (J.C.-K.); (N.R.)
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Liu X, An L, Ren S, Zhou Y, Peng W. Comparative Proteomic Analysis Reveals Antibacterial Mechanism of Patrinia scabiosaefolia Against Methicillin Resistant Staphylococcus epidermidis. Infect Drug Resist 2022; 15:883-893. [PMID: 35281570 PMCID: PMC8912936 DOI: 10.2147/idr.s350715] [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: 11/22/2021] [Accepted: 01/21/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose As a kind of opportunist pathogen, Staphylococcus epidermidis (MRSE) can cause nosocomial infections and easily evolve into resistant bacteria. Among these, methicillin-resistant Staphylococcus epidermidis (MRSE) exhibit significantly higher rates. Our previous study showed that Patrinia scabiosaefolia (PS) possessed strong antibacterial activity against MRSE. However, the mechanism of PS against MRSE is not clear. Methods Here, a tandem mass tag-based (TMT) proteomic analysis was performed to elucidate the potential mechanism of PS against MRSE. We compared the differential expression proteins of MRSE under PS stress. Results Based on a fold change of >1.2 or < 1/1.2 (with p value set at <0.05), a total of 248 proteins (128 up-regulated proteins, 120 down-regulated proteins) were identified. Bioinformatic analysis showed that proteins including arginine deiminase (arcA), ornithine carbamoyltransferase (arcB) and carbamate kinase (arcC), serine–tRNA ligase (serS), phenylalanine–tRNA ligase beta and subunit (pheT), DltD (dlt), d-alanyl carrier protein (dlt), accumulation-associated protein (SasG), serine-aspartate repeat-containing protein C (SdrC) and hemin transport system permease protein HrtB (VraG) played important roles in mechanism of PS against MRSE. Conclusion In summary, these results indicated that arginine deiminase pathway (ADI) pathway, protein synthesis, cell wall synthesis, biofilm formation and uptake of iron were related to mechanisms of PS against MRSE. Our findings provide an insight into the the mechanism of PS against MRSE, and may be valuable in offering new targets to develop more anti-MRSE drugs.
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Affiliation(s)
- Xin Liu
- College of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, People’s Republic of China
- Correspondence: Xin Liu, College of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, People’s Republic of China, Tel +8618886056643, Email
| | - Lili An
- Dermatology Department, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, People’s Republic of China
| | - Shuaijun Ren
- Dermatology Department, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, People’s Republic of China
| | - Yonghui Zhou
- College of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, People’s Republic of China
| | - Wei Peng
- College of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, People’s Republic of China
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