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Brkić N, Švagelj D, Omazić J. Pathohistological Changes in the Gastric Mucosa in Correlation with the Immunohistochemically Detected Spiral and Coccoid Forms of Helicobacter pylori. Microorganisms 2024; 12:1060. [PMID: 38930442 DOI: 10.3390/microorganisms12061060] [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: 04/19/2024] [Revised: 05/19/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND The coccoid form of Helicobacter pylori (H. pylori) is resistant to antibiotics. There are only a few studies that have analyzed the frequency of coccoid H. pylori in patients with gastritis. The aim of this work was to examine the correlation between the H. pylori form and the pathohistological characteristics of the stomach in patients with gastritis. MATERIALS AND METHODS This research was cross-sectional and focused on the gastric mucosa samples of 397 patients from one general hospital in Croatia. Two independent pathologists analyzed the samples regarding the pathohistological characteristics and the form of H. pylori. RESULTS There was a statistically significant difference in the gender of patients with H. pylori gastritis. Only the coccoid form of H. pylori was present in 9.6% of patients. There was a statistically significant difference in the frequency of a certain form of the bacterium depending on its localization in the stomach. The intensity of the bacterium was low in the samples where only the coccoid or spiral form was described. In cases of infection in the antrum, premalignant lesions and the coccoid form of H. pylori were more often present. CONCLUSION In the diagnosis of H. pylori infection, the determination of the form of the bacterium via immunohistochemistry should be included to increase the rate of eradication therapy and reduce the incidence of gastric malignancy.
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Affiliation(s)
- Nikolina Brkić
- Faculty of Medicine, J.J. Strossmayer University of Osijek, 31000 Osijek, Croatia
- Department of Transfusion Medicine, General County Hospital Vinkovci, 32100 Vinkovci, Croatia
| | - Dražen Švagelj
- Department of Pathology and Cytology, General County Hospital Vinkovci, 32100 Vinkovci, Croatia
| | - Jelena Omazić
- Faculty of Medicine, J.J. Strossmayer University of Osijek, 31000 Osijek, Croatia
- Department of Laboratory and Transfusion Medicine, National Memorial Hospital "Dr. Jurjaj Njavro" Vukovar, 32000 Vukovar, Croatia
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, J.J. Strossmayer University of Osijek, 31000 Osijek, Croatia
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Gurnani M, Chauhan A, Ranjan A, Gopi P, Ghosh A, Tuli HS, Haque S, Pandya P, Lal R, Jindal T. Cyanobacterial compound Tolyporphine K as an inhibitor of Apo-PBP (penicillin-binding protein) in A. baumannii and its ADME assessment. J Biomol Struct Dyn 2024; 42:4133-4144. [PMID: 37261797 DOI: 10.1080/07391102.2023.2218930] [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: 02/28/2023] [Accepted: 05/22/2023] [Indexed: 06/02/2023]
Abstract
Antibiotic-resistant Acinetobacter baumannii, is a common pathogen found in hospital settings and has become nosocomial due to its high infection-causing tendency amongst ICU patients. The present study explores the cyanocompoundswhich were capable to inhibit the Penicillin Binding Protein of A. baumannii through molecular docking, ADMET, and molecular dynamicssimulation strategy. A database having structural and origin details was generated for 85 bioactive compounds in MS Excel. The 3-D structures weredownloaded from the PubChem database and minimized. The receptor protein was minimized and validated for structure correctness. The database was screened against the penicillin-binding protein of A. baumannii through PyRx software. The top 5 compounds including the control molecule werefurther redocked to the receptor molecule through Autodock Vina software. The molecule pose having the highest affinity was further subjected to 100ns MD- simulation and simultaneously the in-vitro activity of the methanol extract and hexane extract was checked through agar well diffusion assay.Docking studies indicate Tolyporphine K to be a lead molecule which was further assessed through Molecular dynamics and MM/PBSA. The in-silicoresults suggested that the protein-ligand complex was found to be stable over the 100 ns trajectory with a binding free energy of -8.56 Kcalmol-1. Theligand did not induce any major structural conformation in the protein moiety and was largely stabilized by hydrophobic interactions. The bioactivityscore and ADME properties of the compounds were also calculated. The in-vitro agar well diffusion assay showed a moderate zone of inhibition of12.33mm. The results indicate that the compound Tolyporphin- K could be a potential inhibitor of penicillin-binding protein in A. baumannii. Yet furtherwork needs to be done to have a more concrete basis for the pathway of inhibition.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manisha Gurnani
- Amity Institute of Environmental Sciences, Amity University, Noida, India
| | - Abhishek Chauhan
- Amity Institute of Environment Toxicology and Safety Management, Amity University, Noida, India
| | - Anuj Ranjan
- Amity Institute of Environment Toxicology and Safety Management, Amity University, Noida, India
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Priyanka Gopi
- Amity Institute of Forensic Sciences, Amity University, Noida, India
| | - Arabinda Ghosh
- Department of Botany, Microbiology Division, Guwahati University, Guwahati, India
| | - Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Ambala, India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Prateek Pandya
- Amity Institute of Forensic Sciences, Amity University, Noida, India
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, India
| | - Tanu Jindal
- Amity Institute of Environmental Sciences, Amity University, Noida, India
- Amity Institute of Environment Toxicology and Safety Management, Amity University, Noida, India
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Hanafiah A, Abd Aziz SNA, Md Nesran ZN, Wezen XC, Ahmad MF. Molecular investigation of antimicrobial peptides against Helicobacter pylori proteins using a peptide-protein docking approach. Heliyon 2024; 10:e28128. [PMID: 38533069 PMCID: PMC10963377 DOI: 10.1016/j.heliyon.2024.e28128] [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: 08/14/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024] Open
Abstract
The impact of H. pylori resistance on patient's treatment failure is a major concern. Therefore, the development of novel or alternative therapies for H. pylori is urgently needed. The purpose of this study was to investigate the molecular interactions of various antimicrobial peptides (AMPs) to H. pylori proteins. We performed the peptide-protein molecular docking using HADDOCK 2.4 webserver. Fourteen AMPs were tested for their binding efficacy against four H. pylori proteins. Simulation of the peptide-protein complex was performed using molecular dynamic software package AMBER20. From molecular docking analysis, five peptides (LL-37, Tilapia piscidin 4, napin, snakin-1 and EcAMP1) showed strong binding interactions against H. pylori proteins. The strongest binding affinity was observed in the interactions between Snakin-1 and PBP2, TP4 and type I HopQ and EcAMP1 and type I HopQ with -11.1, -13.6 and -13.8 kcal/mol, respectively. The dynamic simulation was performed for two complexes (snakin1-PBP2 and EcAMP1-HopQ). Results of the dynamics simulation showed that EcAMP1 had stable interaction and binding to type I HopQ protein without significant structural changes. In conclusion, both results of docking and simulation showed that EcAMP1 might be useful as a potential therapeutic agent for H. pylori treatment. This molecular approach provides deep understanding of the interaction insights between AMPs and H. pylori proteins. It paves the way for the development of novel anti-H. pylori using antimicrobial peptides.
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Affiliation(s)
- Alfizah Hanafiah
- Dept. of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
- GUT Research Group, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Siti Nur Arifah Abd Aziz
- Dept. of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Zarith Nameyrra Md Nesran
- Dept. of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Xavier Chee Wezen
- School of Engineering and Science, Faculty of Engineering, Computing and Science, Swinburne University of Technology, 93350, Kuching, Sarawak, Malaysia
| | - Mohd Fadzli Ahmad
- Faculty of Engineering and Life Sciences, Universiti Selangor, 45600, Bestari Jaya, Selangor, Malaysia
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Jeon E, Kim MK, Park Y. Efficacy of the bee-venom antimicrobial peptide Osmin against sensitive and carbapenem-resistant Klebsiella pneumoniae strains. Int J Antimicrob Agents 2024; 63:107054. [PMID: 38072166 DOI: 10.1016/j.ijantimicag.2023.107054] [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: 07/20/2023] [Revised: 11/21/2023] [Accepted: 12/04/2023] [Indexed: 01/19/2024]
Abstract
The emergence of multidrug-resistant (MDR) Klebsiella pneumoniae strains causes severe problems in the treatment of bacterial infections owing to limited treatment options. Especially, carbapenem-resistant Klebsiella pneumoniae (CRKP) is rapidly spreading worldwide and is emerging as a new cause of drug-resistant healthcare-associated infections. CRKP also has been announced by the Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) as one of the most pressing antibiotic resistance threats. Antimicrobial peptides (AMPs) are drawing considerable attention as ideal antibiotic alternative candidates to combat MDR bacterial infections. In a previous study, Osmin is composed of 17 amino acids and is isolated from solitary bee (Osmia rufa) venom. Herein, we evaluated the potential of Osmin to be used against drug-resistant K. pneumoniae as an alternative to conventional antibiotics. Osmin exhibited significant antimicrobial and anti-biofilm activity and lower toxicity than melittin, a well-known bee venom peptide. Additionally, we confirmed that it possesses a bactericidal mechanism that rapidly destroys bacterial membranes. Osmin was relatively more stable than melittin under the influence of various environmental factors and unlike conventional antibiotics, it exhibited a low bacterial resistance risk. During in vivo tests, Osmin reduced bacterial growth and the expression of pro-inflammatory cytokines and fibrosis-related genes in mice with CRKP-induced sepsis. Overall, our results indicate a high potential for Osmin to be used as a valuable therapeutic agent against drug-resistant K. pneumoniae infections.
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Affiliation(s)
- Eunyeong Jeon
- Department of Biomedical Sciences, Chosun University, Gwangju, Republic of Korea
| | - Min Kyung Kim
- Department of Biomedical Sciences, Chosun University, Gwangju, Republic of Korea
| | - Yoonkyung Park
- Department of Biomedical Sciences, Chosun University, Gwangju, Republic of Korea; Research Center for Proteineous Materials (RCPM), Chosun University, Gwangju, Republic of Korea.
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Li HL, Chen YN, Cai J, Liao T, Zu XY. Identification, Screening and Antibacterial Mechanism Analysis of Novel Antimicrobial Peptides from Sturgeon ( Acipenser ruthenus) Spermary. Mar Drugs 2023; 21:386. [PMID: 37504917 PMCID: PMC10381568 DOI: 10.3390/md21070386] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/29/2023] Open
Abstract
Fish is an important source of antimicrobial peptides. This study aimed to identify and screen antibacterial peptides with excellent antibacterial activity derived from sturgeon spermary peptides (SSPs) and to analyze their antibacterial activity and mechanism. Liquid chromatography-mass spectrometry/mass spectrometry methods were used to analyze and identify peptide sequences, computational prediction tool and molecular docking methods were used for virtual screening of antimicrobial peptides, and finally, candidate peptides were synthesized by solid-phase synthesis method. The results demonstrate that SSPs have excellent inhibitory activity against Escherichia coli with an inhibitory rate of 76.46%. Most parts of the SSPs were derived from the sturgeon (Acipenser ruthenus) histones, and the coverage of histone H2B was the highest (45%). Two novel peptides (NDEELNKLM and RSSKRRQ) were obtained by in silico prediction tools and molecular docking, which may interact with the DNA gyrase and dihydrofolate reductase of E. coli by forming salt bridges and hydrogen bonds. Compared to the individual peptides, the antibacterial effect was significantly improved by mixing the two peptides in equal proportions. Two novel peptides change the permeability of the E. coli cell membranes and may exert antimicrobial activity by inhibiting the metabolic process of the nucleic acids.
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Affiliation(s)
- Hai-Lan Li
- Key Laboratory of Cold Chain Logistics Technology for Agro-Product (Ministry of Agriculture and Rural Affairs), Institute of Agro-Products Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Ya-Nan Chen
- Key Laboratory of Cold Chain Logistics Technology for Agro-Product (Ministry of Agriculture and Rural Affairs), Institute of Agro-Products Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Jun Cai
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Tao Liao
- Key Laboratory of Cold Chain Logistics Technology for Agro-Product (Ministry of Agriculture and Rural Affairs), Institute of Agro-Products Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Xiao-Yan Zu
- Key Laboratory of Cold Chain Logistics Technology for Agro-Product (Ministry of Agriculture and Rural Affairs), Institute of Agro-Products Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
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Muhammad Rehman H, Rehman HM, Naveed M, Khan MT, Shabbir MA, Aslam S, Bashir H. In Silico Investigation of a Chimeric IL24-LK6 Fusion Protein as a Potent Candidate Against Breast Cancer. Bioinform Biol Insights 2023; 17:11779322231182560. [PMID: 37377793 PMCID: PMC10291407 DOI: 10.1177/11779322231182560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Targeted delivery of therapeutic anticancer chimeric molecules enhances the efficacy of drug by improving cellular uptake and circulation time. Engineering the molecules to facilitate the specific interaction between chimeric protein and its receptor is critical to elucidate biological mechanism as well as accuracy in modeling of complexes. A theoretically designed novel protein-protein interfaces can serve as a bottom-up method for comprehensive understanding of interacting protein residues. This study was aimed for in silico analyses of a chimeric fusion protein against breast cancer. The amino acid sequences of the interleukin 24 (IL-24) and LK-6 peptide were used to design the chimeric fusion protein via a rigid linker. The secondary and tertiary structures along with physicochemical properties by ProtParam and solubility were predicted using online software. The validation and quality of the fusion protein was confirmed by Rampage and ERRAT2. The newly designed fusion construct has a total length of 179 amino acids. The top-ranked structure from alpha fold2 showed 18.1 KD molecular weight by ProtParam, quality factor of 94.152 by ERRAT, and a valid structure by a Ramachandran plot with 88.5% residues in the favored region. Finally, the docking and simulation studies were performed using HADDOCK and Desmond module of Schrodinger. The quality, validity, interaction analysis, and stability of the fusion protein depict a functional molecule. The fusion gene IL24-LK6 after cloning and expression in a suitable prokaryotic cell might be a useful candidate for developing a novel anticancer therapy.
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Affiliation(s)
- Hafiz Muhammad Rehman
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
- University Institute of Medical Lab Technology, Faculty of Allied Health Sciences, The University of Lahore, Pakistan
| | - Hafiz Muzzammel Rehman
- School of Biochemistry & Biotechnology, University of the Punjab, Lahore, Pakistan
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore, Pakistan
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Science & Technology, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Tahir Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Aqib Shabbir
- Department of Biotechnology, Faculty of Science & Technology, University of Central Punjab, Lahore, Pakistan
| | - Shakira Aslam
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
| | - Hamid Bashir
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
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Polinário G, Primo LMDG, Rosa MABC, Dett FHM, Barbugli PA, Roque-Borda CA, Pavan FR. Antimicrobial peptides as drugs with double response against Mycobacterium tuberculosis coinfections in lung cancer. Front Microbiol 2023; 14:1183247. [PMID: 37342560 PMCID: PMC10277934 DOI: 10.3389/fmicb.2023.1183247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023] Open
Abstract
Tuberculosis and lung cancer are, in many cases, correlated diseases that can be confused because they have similar symptoms. Many meta-analyses have proven that there is a greater chance of developing lung cancer in patients who have active pulmonary tuberculosis. It is, therefore, important to monitor the patient for a long time after recovery and search for combined therapies that can treat both diseases, as well as face the great problem of drug resistance. Peptides are molecules derived from the breakdown of proteins, and the membranolytic class is already being studied. It has been proposed that these molecules destabilize cellular homeostasis, performing a dual antimicrobial and anticancer function and offering several possibilities of adaptation for adequate delivery and action. In this review, we focus on two important reason for the use of multifunctional peptides or peptides, namely the double activity and no harmful effects on humans. We review some of the main antimicrobial and anti-inflammatory bioactive peptides and highlight four that have anti-tuberculosis and anti-cancer activity, which may contribute to obtaining drugs with this dual functionality.
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Affiliation(s)
- Giulia Polinário
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | | | | | | | - Paula Aboud Barbugli
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | | | - Fernando Rogério Pavan
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
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Tabassum R, Kousar S, Mustafa G, Jamil A, Attique SA. In Silico Method for the Screening of Phytochemicals against Methicillin-Resistant Staphylococcus Aureus. BIOMED RESEARCH INTERNATIONAL 2023; 2023:5100400. [PMID: 37250750 PMCID: PMC10212682 DOI: 10.1155/2023/5100400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 05/31/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has evolved resistance even against the last resort β-lactam antibiotics. This is because of the acquisition of an additional penicillin-binding protein 2a (PBP2a) which is a resistance determinant in MRSA. Currently, available PBP2a inhibitors are ineffective against life-threatening and fatal infections caused by microorganisms. Therefore, there is an urgent need to screen natural compounds that could overpass the resistance issue alone or in combination with antibacterial drugs. We studied the interactions of different phytochemicals with PBP2a so that crosslinking of peptidoglycans could be inhibited. In structure-based drug designing, in silico approach plays a key role in determining phytochemical interactions with PBP2a. In this study, a total of 284 antimicrobial phytochemicals were screened using the molecular docking approach. The binding affinity of methicillin, -11.241 kcal/mol, was used as the threshold value. The phytochemicals having binding affinities with PBP2a stronger than methicillin were identified, and the drug-likeness properties and toxicities of the screened phytochemicals were calculated. Out of the multiple phytochemicals screened, nine were found as good inhibitors to be PBP2a, among which cyanidin, tetrandrine, cyclomorusin, lipomycin, and morusin showed strong binding potential with the receptor protein. These best-selected phytochemicals were also docked to the allosteric site of PBP2a, and most of the compounds revealed strong interactions with the allosteric site. These compounds were safe to be used as drugs because they did not show any toxicity and had good bioactivity scores. Cyanidin had the highest binding affinity (S-score of -16.061 kcal/mol) with PBP2a and with high gastrointestinal (GI) absorption. Our findings suggest that cyanidin can be used as a drug against MRSA infection either in purified form or that its structure can lead to the development of more potent anti-MRSA medicines. However, experimental studies are required to evaluate the inhibitory potential of these phytochemicals against MRSA.
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Affiliation(s)
- Riaz Tabassum
- Department of Biochemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Sumaira Kousar
- Department of Biochemistry, Government College Women University, Faisalabad, Pakistan
| | - Ghulam Mustafa
- Department of Biochemistry, Government College University, Faisalabad 38000, Pakistan
| | - Amer Jamil
- Department of Biochemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Syed Awais Attique
- School of Interdisciplinary Engineering & Science (SINES), National University of Sciences & Technology (NUST), Islamabad, Pakistan
- Agency for Science, Technology and Research (ASTAR), Bioinformatics Institute, 30 Biopolis Street, Matrix, Singapore 138671, Singapore
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