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Potbhare AK, Yerpude S, Daddemal-Chaudhary AR, Lambat A, Mondal A, Dadure KM, Rai AR, Abdala A, Chaudhary RG. Catharanthus roseus-mediated CuAl 2O 4 nanocomposites for evaluation of killing kinetics. CHEMOSPHERE 2024; 359:142369. [PMID: 38761825 DOI: 10.1016/j.chemosphere.2024.142369] [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: 08/06/2023] [Revised: 05/06/2024] [Accepted: 05/16/2024] [Indexed: 05/20/2024]
Abstract
The present article portrayed on the killing kinetic of human pathogenic bacteria using bioinspired mesoporous CuAl2O4 nanocomposites (NCs). The NCs was fabricated using leaf extract of medicinal plant Catharanthus roseus (CR) as a green reducer and stabilizer. As bio-fabricated material was calcined at 800 °C and characterized by several analytical techniques like X-ray Diffraction (XRD), Fourier Transform Infrared Spectroscopy (FT-IR), Ultraviolet-Visible Diffuse Reflectance Spectroscopy (UV-DRS), Energy Dispersive X-Ray Spectroscopy (EDS), X-Ray Photoelectron Spectroscopy (XPS), Raman, Brunauer-Emmett-Teller (BET), Scanning Electron Microscopy (SEM), and Transmission Electron Microscopy (TEM) to authenticate its structure, phase, chemical bonding, chemical state, size and morphology behaviors. XRD and TEM revealed a reduced crystallite and nanoscale sizes of biosynthesized NCs. Moreover, XRD study exposed a cubic-structure of material, while transmission electron microscopy rendered an average particles size in range 10-15 nm. However, BET profile advocates a mesoporous nature of the particles. An effective biological molecular docking modulation assessed by substituting natural inhibitor by bioinspired NCs, while the protein PDB ID 4Z8D FabH as a receptor site for the present investigation. After assessment of molecular docking examination, the antibacterial activity of bioinspired NCs were performed against Staphylococcus aureus, Bacillus subtillis, Klebsiella pneumoniae and Escherichia coli using agar-well method. The broth culture method was employed on different pathogenic strains by kinetic growth assays and colony forming unit.
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Affiliation(s)
- Ajay K Potbhare
- Department of Chemistry, S. K. Porwal College of Arts and Science and Commerce, Kamptee, 441001, India
| | - Sachin Yerpude
- Department of Microbiology, S. K. Porwal College of Arts and Science and Commerce, Kamptee, 441001, India
| | - Ankita R Daddemal-Chaudhary
- Lady Amritabai Daga College for Women of Arts, Commerce and Science, Nagpur, 440010, India; Post Graduate Teaching Department of Botany, RTM Nagpur University, Nagpur, 440033, India
| | - Ashish Lambat
- Department of Biology, Sevadal Mahila Mahavidyalaya, Nagpur, India
| | - Aniruddha Mondal
- Department of Chemistry, S. K. Porwal College of Arts and Science and Commerce, Kamptee, 441001, India; Division of Materials Science, Lulea University of Technology, Lulea, 97187, Sweden
| | | | - Alok R Rai
- Department of Microbiology, S. K. Porwal College of Arts and Science and Commerce, Kamptee, 441001, India.
| | - Ahmed Abdala
- Chemical Engineering Program, Texas A&M University at Qatar, Doha, Qatar
| | - Ratiram G Chaudhary
- Department of Chemistry, S. K. Porwal College of Arts and Science and Commerce, Kamptee, 441001, India.
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2
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Beytür S, Essiz S, Özuğur Uysal B. Investigation of Structural and Antibacterial Properties of WS 2-Doped ZnO Nanoparticles. ACS OMEGA 2024; 9:4037-4049. [PMID: 38284036 PMCID: PMC10809239 DOI: 10.1021/acsomega.3c09041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 11/28/2023] [Accepted: 12/21/2023] [Indexed: 01/30/2024]
Abstract
ZnO nanoparticles, well-known for their structural, optical, and antibacterial properties, are widely applied in diverse fields. The doping of different materials to ZnO, such as metals or metal oxides, is known to ameliorate its properties. Here, nanofilms composed of ZnO doped with WS2 at 5, 15, and 25% ratios are synthesized, and their properties are investigated. Supported by molecular docking analyses, the enhancement of the bactericidal properties after the addition of WS2 at different ratios is highlighted and supported by the inhibitory interaction of residues playing a crucial role in the bacterial survival through the targeting of proteins of interest.
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Affiliation(s)
- Sercan Beytür
- Faculty of Engineering and
Natural Sciences, Kadir Has University, Cibali, Fatih, Istanbul 34083, Turkey
| | - Sebnem Essiz
- Faculty of Engineering and
Natural Sciences, Kadir Has University, Cibali, Fatih, Istanbul 34083, Turkey
| | - Bengü Özuğur Uysal
- Faculty of Engineering and
Natural Sciences, Kadir Has University, Cibali, Fatih, Istanbul 34083, Turkey
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3
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Taysi MR, Kirici M, Kirici M, Tuzun B, Poustforoosh A. Antioxidant enzyme activities, molecular docking studies, MM-GBSA, and molecular dynamic of chlorpyrifos in freshwater fish Capoeta umbla. J Biomol Struct Dyn 2024; 42:163-176. [PMID: 36974945 DOI: 10.1080/07391102.2023.2192807] [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: 10/15/2022] [Accepted: 03/10/2023] [Indexed: 03/29/2023]
Abstract
Chlorpyrifos (CPF), which was started to be used in 1965, is a broad spectrum organophosphate insecticide that is used more and more day by day. Commonly used to control pests in farmland and homes, CPF is more toxic to fish than organochlorine compounds. CPF poses a serious threat to the health of humans and aquatic organisms. This paper studies the relationship between CPF exposure and antioxidant enzyme activities in gill, kidney and liver tissues of Capoeta umbla. Different time intervals (12, 24, 48, 72, and 96 h) and CPF doses (55 and 110 µg L-1) were used in the study. Spectrophotometrical measures were taken in all tissues for antioxidant enzyme activities and malondialdehyde (MDA) levels, as indices of the lipid peroxidation (LPO). A positive relationship between CPF and MDA levels was found in the study at a statistically significant level (p < 0.05). The study also found a negative relationship between CPF levels and catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx), and glutathione reductase (GR) activity. Independent variables in the study can act as biomarkers of CPF exposure. The study recommends employing proper ecotoxicological risk evaluations in cases of CPF usage as a pesticide. The activities of the studied molecules against various proteins that are crystal structure of human peroxiredoxin 5 (PDB ID: 1HD2) has docking score value is -2.67, crystal structure of Bovine Xanthine Oxidase (PDB ID: 3NRZ) has docking score value is -3.76, and crystal structure of antibacterial FabH (PDB ID: 4Z8D) has docking score value is -3.16, were compared. Molecular dynamic (MD) calculations were made in 100 ns. MM/GBSA methods are calculated binding free energy. Afterwards, ADME/T analysis was performed to examine the some properties of the molecules.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mehmet Reşit Taysi
- Department of Fisheries, Faculty of Agriculture, Bingol University, Bingöl, Turkey
| | - Muammer Kirici
- Department of Veterinary Health, Food Agriculture and Livestock Vocational School, Bingöl University, Bingöl, Turkey
| | - Mahinur Kirici
- Department of Chemistry, Faculty of Arts and Science, Bingöl University, Bingöl, Turkey
| | - Burak Tuzun
- Plant and Animal Production Department, Technical Sciences Vocational School of Sivas, Sivas Cumhuriyet University, Sivas, Turkey
| | - Alireza Poustforoosh
- Chemical Engineering Department, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
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4
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Ikram M, Shujah T, Shahzadi A, Haider A, Rafique A, Ul-Hamid A, Nabgan W, Haider SK, Alshahrani T, Algaradah MM, Yousaf SA, Haider J. Multiple phases of yttrium-doped molybdenum trioxide nanorods as efficient dye degrader and bactericidal agents with molecular docking analysis. CHEMOSPHERE 2023; 340:139855. [PMID: 37611764 DOI: 10.1016/j.chemosphere.2023.139855] [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: 03/13/2023] [Revised: 06/15/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023]
Abstract
Contaminants removal is usually becoming an exciting subject of research from water considering their environmental and ecological effects. This work provides pathways to remove organic pollutants from water via nanomaterials and is used as an antibiotic against bacteria like Escherichia coli (E. coli). In this study, molybdenum trioxide (MoO3) and yttrium (Y) doped (2 and 4%) MoO3 nanorods were synthesized by co-precipitation method. Advanced characterization techniques have been introduced to study textural structures, morphological developments, and optical characteristics of produced products. X-ray diffraction studied multiple crystalline structures of prepared samples as hexagonal, orthorhombic, and monoclinic of pure MoO3 with decrease in crystallinity and crystallite size upon Y doping. UV-visible spectroscopy unveiled a redshift (bathochromic effect) in absorption pattern attributed to band gap energy (Eg) decreases. Photoluminescence spectra examined the recombination rate of electrons (e-) and holes (h+) as charge carriers. A sufficient catalytic activity (CA) was observed against methylene blue (MB) dye in an acidic medium (99.74%) and efficient bactericidal action was studied against (E. coli) with zone of inhibition (5.20 mm) for 4% Y-doped MoO3. In addition, in silico docking demonstrated potential inhibitory effect of produced nanomaterials on FabH and FabI enzymes of fatty acid biosynthesis.
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Affiliation(s)
- Muhammad Ikram
- Solar Cell Applications Research Lab, Department of Physics, Government College, University Lahore, Lahore, 54000, Punjab, Pakistan.
| | - Tahira Shujah
- Department of Physics, University of Central Punjab, Lahore, 54000, Punjab, Pakistan
| | - Anum Shahzadi
- Facutly of Pharmacy, The University of Lahore, Lahore, Pakistan
| | - Ali Haider
- Department of Clinical Medicine, Faculty of Veterinary and Animal Sciences, Muhammad Nawaz Shareef, University of Agriculture, 66000, Multan, Punjab, Pakistan
| | - Aqsa Rafique
- Solar Cell Applications Research Lab, Department of Physics, Government College, University Lahore, Lahore, 54000, Punjab, Pakistan
| | - Anwar Ul-Hamid
- Core Research Facilities, King Fahd University of Petroleum & Minerals, Dhahran, 31261, Saudi Arabia
| | - Walid Nabgan
- Departament d'Enginyeria Química, Universitat Rovira I Virgili, 43007, Tarragona, Spain.
| | - Syed Karrar Haider
- Department of Physics, University of Central Punjab, Lahore, 54000, Punjab, Pakistan
| | - Thamraa Alshahrani
- Department of Physics, College of Sciences, Princess Nourah bint Abdulrahman University (PNU), P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | | | - S Amber Yousaf
- Department of Physics, University of Central Punjab, Lahore, 54000, Punjab, Pakistan
| | - Junaid Haider
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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5
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Ikram M, Karim R, Haider A, Shahzadi A, Algaradah MM, Ul-Hamid A, Nabgan W, Fouda AM, Ali S. Anomalous catalytic and antibacterial activity confirmed by molecular docking analysis of silver and polyacrylic acid doped CeO 2 nanostructures. RSC Adv 2023; 13:26149-26159. [PMID: 37664196 PMCID: PMC10472217 DOI: 10.1039/d3ra04760a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 08/26/2023] [Indexed: 09/05/2023] Open
Abstract
This research presents the novel synthesis of CeO2 nanostructures (NSs) doped with a fixed amount of capping agent (polyacrylic acid-PAA) and different concentrations (0.01 and 0.03) of silver (Ag). This work aimed to examine the catalytic and antibacterial efficacy with evidential molecular docking analysis of Ag/PAA doped CeO2. Systematic characterization was used to analyze the effect of Ag and a capping agent on crystal structure, morphology, absorbance wavelength, and the exciton recombination rate of CeO2. The silver metal and capping agent (PAA) were added into CeO2 to reduce the size of NSs, enhancing the catalytic efficacy. These binary dopants (Ag-PAA) based CeO2 revealed remarkable results for catalytic de-colorization of rhodamine B dye and antimicrobial potential as the dopants provide more active sites. Notably, (0.03) Ag/PAA doped CeO2 NSs exhibited a substantial catalytic reduction (98.9%) of rhodamine B dye in an acidic medium. The higher doped CeO2 revealed a significant inhibition zone (3.75 mm) against Escherichia coli at maximal concentration. Furthermore, in silico docking showed the possible inhibitory impact of produced nanomaterials on the fatty acid biosynthesis enzymes FabI and FabH.
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Affiliation(s)
- Muhammad Ikram
- Solar Cell Applications Research Lab, Department of Physics, Government College University Lahore Lahore 54000 Punjab Pakistan
| | - Rizwan Karim
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University 14 Ali Road Lahore Pakistan
| | - Ali Haider
- Department of Clinical Sciences, Faculty of Veterinary and Animal Sciences, Muhammad Nawaz Shareef University of Agriculture Multan 66000 Pakistan
| | - Anum Shahzadi
- Faculty of Pharmacy, The University of Lahore 54000 Pakistan
| | | | - Anwar Ul-Hamid
- Core Research Facilities, Research Institute, King Fahd University of Petroleum & Minerals Dhahran 31261 Saudi Arabia
| | - Walid Nabgan
- Departament d'Enginyeria Química, Universitat Rovira i Virgili Av Països Catalans 26 43007 Tarragona Spain
| | - Ahmed M Fouda
- Chemistry Department, Faculty of Science, King Khalid University Abha 61413 Saudi Arabia
| | - Salamat Ali
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University 14 Ali Road Lahore Pakistan
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6
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Liu SS, Zeng D, Zhang TH, Hu JH, Yang BX, Yang J, Zhou X, Wang PY, Liu LW, Wu ZB, Yang S. Novel spiro[chromanone-2,4'-piperidine]-4-one derivatives as potential inhibitors of fatty acid synthesis in pathogens: Design, synthesis, and biological evaluation. Eur J Med Chem 2023; 250:115215. [PMID: 36812655 DOI: 10.1016/j.ejmech.2023.115215] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/21/2023]
Abstract
Bacterial survival depends on membrane lipid homeostasis that enables to regulate lipid composition to adapt and optimize their growth in diverse environments. Therefore, the development of inhibitors that interfere with the bacterial fatty acid synthesis process is considered to be a promising tactic. In this study, 58 novel spirochromanone derivatives were prepared and their structure-activity relationship (SAR) was investigated. The bioassay results showed that all most of the compounds showed excellent biological activities, exampled by compounds B14, C1, B15, and B13, which had outstanding inhibitory activities toward various pathogenic bacteria with EC50 values of 0.78 μg/mL ∼3.48 μg/mL. Preliminary antibacterial behavior was studied by a series of biochemical assays including, but not limited to, fluorescence imaging patterns, GC-MS analysis, TEM images, and fluorescence titration experiments. Notably, compound B14 decreased the lipid content of the cell membrane, and increased cell membrane permeability, thereby destroying the integrity of the bacterial cell membrane. Further qRT-PCR results indicated that compound B14 interfered with the mRNA expression levels of fatty acid synthesis process-related genes including ACC, ACP, and Fab family genes. Herein, we highlight the promising bactericidal skeleton based on the spiro[chromanone-2,4'-piperidine]-4-one as a potential inhibitor of fatty acid synthesis.
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Affiliation(s)
- Shuai-Shuai Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Dan Zeng
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Tai-Hong Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Jin-Hong Hu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Bin-Xin Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Jie Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Xiang Zhou
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China.
| | - Pei-Yi Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Li-Wei Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Zhi-Bing Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Song Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China.
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7
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Benjamin AB, Stunkard LM, Ling J, Nice JN, Lohman JR. Structures of chloramphenicol acetyltransferase III and Escherichia coli β-ketoacylsynthase III co-crystallized with partially hydrolysed acetyl-oxa(dethia)CoA. Acta Crystallogr F Struct Biol Commun 2023; 79:61-69. [PMID: 36862094 PMCID: PMC9979976 DOI: 10.1107/s2053230x23001206] [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: 08/25/2022] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
Acetyl coenzyme A (acetyl-CoA) is a reactive metabolite that nonproductively hydrolyzes in a number of enzyme active sites in the crystallization time frame. In order to elucidate the enzyme-acetyl-CoA interactions leading to catalysis, acetyl-CoA substrate analogs are needed. One possible analog for use in structural studies is acetyl-oxa(dethia)CoA (AcOCoA), in which the thioester S atom of CoA is replaced by an O atom. Here, structures of chloramphenicol acetyltransferase III (CATIII) and Escherichia coli ketoacylsynthase III (FabH) from crystals grown in the presence of partially hydrolyzed AcOCoA and the respective nucleophile are presented. Based on the structures, the behavior of AcOCoA differs between the enzymes, with FabH reacting with AcOCoA and CATIII being unreactive. The structure of CATIII reveals insight into the catalytic mechanism, with one active site of the trimer having relatively clear electron density for AcOCoA and chloramphenicol and the other active sites having weaker density for AcOCoA. One FabH structure contains a hydrolyzed AcOCoA product oxa(dethia)CoA (OCoA), while the other FabH structure contains an acyl-enzyme intermediate with OCoA. Together, these structures provide preliminary insight into the use of AcOCoA for enzyme structure-function studies with different nucleophiles.
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Affiliation(s)
- Aaron B. Benjamin
- Purdue University, 175 South University Street, West Lafayette, IN 47907, USA
| | - Lee M. Stunkard
- Purdue University, 175 South University Street, West Lafayette, IN 47907, USA
| | - Jianheng Ling
- Purdue University, 175 South University Street, West Lafayette, IN 47907, USA
| | - Jaelen N. Nice
- Purdue University, 175 South University Street, West Lafayette, IN 47907, USA
| | - Jeremy R. Lohman
- Purdue University, 175 South University Street, West Lafayette, IN 47907, USA,Correspondence e-mail:
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8
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Sun J, Zhang CP, Chen CH, Guo XM, Liu CS, Zhou Y, Hu FL. Design, Synthesis and Molecular Docking of 1,3,4-Oxadiazole-2(3H)-thione Derivatives Containing 1,4-Benzodioxane Skeleton as Potential FabH Inhibitors. Chem Biodivers 2023; 20:e202201060. [PMID: 36579401 DOI: 10.1002/cbdv.202201060] [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: 11/10/2022] [Revised: 12/24/2022] [Accepted: 12/27/2022] [Indexed: 12/30/2022]
Abstract
Fatty acid biosynthesis is essential for bacterial survival. Of these promising targets, β-ketoacyl-acyl carrier protein (ACP) synthase III (FabH) is the most attractive target. A series of novel 1,3,4-oxadiazole-2(3H)-thione derivatives containing 1,4-benzodioxane skeleton targeting FabH were designed and synthesized. These compounds were determined by 1 H-NMR, 13 C-NMR, MS and further confirmed by crystallographic diffraction study for compound 7m and 7n. Most of the compounds exhibited good inhibitory activity against bacteria by computer-assisted screening, antibacterial activity test and E. coli FabH inhibitory activity test, wherein compounds 7e and 7q exhibited the most significant inhibitory activities. Besides, compound 7q showed the best E. coli FabH inhibitory activity (IC50 =2.45 μΜ). Computational docking studies also showed that compound 7q interacts with FabH critical residues in the active site.
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Affiliation(s)
- Juan Sun
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- School of Biological & Chemical Engineering, Zhejiang University of Science & Technology, Hangzhou, 310023, P. R. China
| | - Cui-Ping Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Chong-Hao Chen
- School of Biological & Chemical Engineering, Zhejiang University of Science & Technology, Hangzhou, 310023, P. R. China
| | - Xiao-Meng Guo
- School of Biological & Chemical Engineering, Zhejiang University of Science & Technology, Hangzhou, 310023, P. R. China
| | - Cai-Shi Liu
- School of Biological & Chemical Engineering, Zhejiang University of Science & Technology, Hangzhou, 310023, P. R. China
| | - Yang Zhou
- Zhejiang Engineering Research Center for Biomedical Materials, Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Fu-Liang Hu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
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9
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Ikram M, Shahzadi A, Bilal M, Haider A, Ul-Hamid A, Nabgan W, Haider J, Ali S, Imran M. Strontium-doped chromium oxide for RhB reduction and antibacterial activity with evidence of molecular docking analysis. Front Chem 2023; 11:1167701. [PMID: 37123878 PMCID: PMC10133565 DOI: 10.3389/fchem.2023.1167701] [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: 02/22/2023] [Accepted: 04/03/2023] [Indexed: 05/02/2023] Open
Abstract
The emergence of multi-drug resistance (MDR) in aquatic pathogens and the presence of cationic dyes are the leading causes of water contamination on a global scale. In this context, nanotechnology holds immense promise for utilizing various nanomaterials with catalytic and antibacterial properties. This study aimed to evaluate the catalytic and bactericidal potential of undoped and Sr-doped Cr2O3 nanostructures (NSs) synthesized through the co-precipitation method. In addition, the morphological, optical, and structural properties of the resultant NSs were also examined. The optical bandgap energy of Cr2O3 has been substantially reduced by Sr doping, as confirmed through extracted values from absorption spectra recorded by UV-Vis studies. The field-emission scanning electron microscopy (FE-SEM) and transmission electron microscopy (TEM) micrographs illustrate that the composition of Cr2O3 primarily consisted of agglomerated, irregularly shaped NSs with a morphology resembling nanoflakes. Moreover, the presence of Sr in the lattice of Cr2O3 increased the roughness of the resulting NSs. The catalytic activity of synthesized NSs was analyzed by their reduction ability of Rhodamine B (RhB) dye in the dark under different pH conditions. Their antibacterial activity was evaluated against MDR Escherichia coli (E. coli). Sr doping increased antibacterial efficiency against MDR E. coli, as indicated by inhibition zone measurements of 10.15 and 11.75 mm at low and high doses, respectively. Furthermore, a molecular docking analysis was conducted to determine the binding interaction pattern between NSs and active sites in the target cell protein. The findings corroborated antimicrobial test results indicating that Sr-Cr2O3 is the most effective inhibitor of FabH and DHFR enzymes.
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Affiliation(s)
- Muhammad Ikram
- Solar Cell Applications Research Lab, Department of Physics, Government College University Lahore, Lahore, Pakistan
- *Correspondence: Muhammad Ikram, ; Walid Nabgan,
| | - Anum Shahzadi
- Faculty of Pharmacy, The University of Lahore, Lahore, Pakistan
| | - Muhammad Bilal
- Solar Cell Applications Research Lab, Department of Physics, Government College University Lahore, Lahore, Pakistan
| | - Ali Haider
- Department of Clinical Sciences, Faculty of Veterinary and Animal Sciences, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Anwar Ul-Hamid
- Core Research Facilities, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - Walid Nabgan
- Departament d’Enginyeria Química, Universitat Rovira i Virgili, Tarragona, Spain
- *Correspondence: Muhammad Ikram, ; Walid Nabgan,
| | - Junaid Haider
- Chinese Academy of Sciences, Tianjin Institute of Industrial Biotechnology, Tianjin, China
| | - Salamat Ali
- Department of Physics, The University of Lahore, Lahore, Pakistan
| | - Muhammad Imran
- Government College University Faisalabad, Sahiwal, Punjab, Pakistan
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10
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Shujah T, Shahzadi A, Haider A, Mustajab M, Haider AM, Ul-Hamid A, Haider J, Nabgan W, Ikram M. Molybdenum-doped iron oxide nanostructures synthesized via a chemical co-precipitation route for efficient dye degradation and antimicrobial performance: in silico molecular docking studies. RSC Adv 2022; 12:35177-35191. [PMID: 36540207 PMCID: PMC9732929 DOI: 10.1039/d2ra07238f] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 11/24/2022] [Indexed: 07/25/2023] Open
Abstract
In this research, various concentrations of molybdenum (2, 4 and 6 wt%) doped Fe3O4 nanostructures (Mo-Fe3O4 NSs) were prepared via a co-precipitation technique. Various techniques were then used to investigate the optical, morphological and structural properties of the NSs in the presence of the dopant materials. X-ray diffraction (XRD) was used to investigate the crystalline nature of the prepared NSs and confirm the orthorhombic and tetragonal structure of Fe3O4, with a decrease in crystallinity and crystallite sizes of 36.11, 38.45, 25.74 and 24.38 nm with increasing concentration of Mo (2, 4 and 6%). Fourier-transform infrared (FTIR) spectroscopy analysis was carried out to examine the functional groups in the NSs. Structure, surface morphology and topography were examined via field emission scanning electron microscopy (FE-SEM) and transmission electron microscopy (TEM), which confirmed the fabrication of nanoparticles and nanorods and a floccule-like morphology with a higher doping concentration and the interlayer d-spacing was calculated using high-resolution (HR)TEM, the results of which were a good match to the XRD data. The presence of Mo, Fe and O in a lattice of Mo (2, 4 and 6%) doped Fe3O4 was confirmed by energy dispersive X-ray spectroscopy (EDS) analysis. The energy band gap (E g) was measured via the optical analysis of pure and doped samples, showing a decrease from 2.76 to 2.64 eV. The photoluminescence (PL) spectra exhibit a higher charge combination rate of electron-hole pairs with a higher concentration of doping. The NSs exhibited excellent catalytic activity (CA) in degrading methylene blue (MB) dye in a basic medium by around 86.25%. Additionally, the antimicrobial activity was tested against Escherichia coli (E. coli) bacteria. Pairs of electrons and holes are the fundamental basis for generating reactive oxygen species that kill bacteria. The significant inhibition zones were calculated against E. coli bacteria at around 3.45 mm compared to ciprofloxacin. In silico docking investigations of the Mo-Fe3O4 NSs for dihydropteroate synthase (DHPS, binding score: 6.16 kcal mol-1), dihydrofolate reductase (DHFR, binding score: 6.01 kcal mol-1), and β-ketoacyl-acyl carrier protein synthase III (FabH, binding score: 5.75 kcal mol-1) of E. coli show the suppression of the aforementioned enzymes as a potential mechanism besides their microbicidal assay.
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Affiliation(s)
- Tahira Shujah
- Department of Physics, University of Central Punjab Lahore 54000 Punjab Pakistan
| | - Anum Shahzadi
- Faculty of Pharmacy, The University of Lahore Lahore Pakistan
| | - Ali Haider
- Department of Clinical Medicine, Faculty of Veterinary and Animal Sciences, Muhammad Nawaz Shareef, University of Agriculture Multan Punjab 66000 Pakistan
| | - Muhammad Mustajab
- Department of Physics, University of Central Punjab Lahore 54000 Punjab Pakistan
| | - Afsah Mobeen Haider
- Department of Physics, University of Central Punjab Lahore 54000 Punjab Pakistan
| | - Anwar Ul-Hamid
- Solar Cell Applications Research Lab, Department of Physics, Government College University Lahore Lahore Punjab Pakistan
- Core Research Facilities, King Fahd University of Petroleum & Minerals Dhahran 31261 Saudi Arabia
| | - Junaid Haider
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences Tianjin 300308 China
| | - Walid Nabgan
- Departament d'Enginyeria Química, Universitat Rovira i Virgili 43007 Tarragona Spain
| | - Muhammad Ikram
- Department of Physics, University of Central Punjab Lahore 54000 Punjab Pakistan
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11
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Bilal M, Ikram M, Shujah T, Haider A, Naz S, Ul-Hamid A, Naz M, Haider J, Shahzadi I, Nabgan W. Chitosan-Grafted Polyacrylic Acid-Doped Copper Oxide Nanoflakes Used as a Potential Dye Degrader and Antibacterial Agent: In Silico Molecular Docking Analysis. ACS OMEGA 2022; 7:41614-41626. [PMID: 36406528 PMCID: PMC9670908 DOI: 10.1021/acsomega.2c05625] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
This study examined the catalytic and bactericidal properties of polymer-doped copper oxide (CuO). For this purpose, a facile co-precipitation method was used to synthesize CuO nanostructures doped with CS-g-PAA. Various concentrations (2, 4, and 6%) of dopants were systematically incorporated into a fixed amount of CuO. The prepared samples were analyzed by different optical, structural, and morphological characterizations. Field emission scanning electron microscopy and transmission electron microscopy micrographs indicated that doping transformed CuO's agglomerated rod-like surface morphology to form nanoflakes. UV-vis spectroscopy revealed that the optical spectra of the samples exhibit a redshift after doping, leading to a decrease in band gap energy from 3.3 to 2.5 eV. The purpose of the study was to test the catalytic activity of pristine and CS-g-PAA doped CuO for the degradation of methylene blue in acidic, basic, and neutral conditions using NaBH4 as a reducing agent in an aqueous medium. Furthermore, antibacterial activity was evaluated against Gram-positive and Gram-negative bacteria, namely, Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli). Overall, enhanced bactericidal performance was observed upon doping CS-g-PAA into CuO, i.e., 4.25-6.15 and 4.40-8.15 mm against S. aureus and 1.35-4.20 and 2.25-5.25 mm against E. coli at the lowest and highest doses, respectively. The relevant catalytic and bactericidal action mechanisms of samples are also proposed in the study. Moreover, in silico molecular docking studies illustrated the role of these prepared nanomaterials as possible inhibitors of FabH and FabI enzymes of the fatty acid biosynthetic pathway.
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Affiliation(s)
- Muhammad Bilal
- Solar
Cell Applications Research Lab, Department of Physics, Government College University Lahore, Lahore54000, Punjab, Pakistan
| | - Muhammad Ikram
- Solar
Cell Applications Research Lab, Department of Physics, Government College University Lahore, Lahore54000, Punjab, Pakistan
| | - Tahira Shujah
- Department
of Physics, University of Central Punjab, Lahore54000, Punjab, Pakistan
| | - Ali Haider
- Department
of Clinical Medicine, Faculty of Veterinary and Animal Sciences, Muhammad
Nawaz Shareef, University of Agriculture, 66000Multan, Punjab, Pakistan
| | - Sadia Naz
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, Tianjin300308, China
| | - Anwar Ul-Hamid
- Core
Research Facilities, King Fahd University
of Petroleum & Minerals, Dhahran31261, Saudi Arabia
| | - Misbah Naz
- Department
of Chemistry, University of the Education, 54000Lahore, Pakistan
| | - Junaid Haider
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, Tianjin300308, China
| | - Iram Shahzadi
- Punjab
University College of Pharmacy, Allama Iqbal Campus, University of the Punjab, Lahore54000, Pakistan
| | - Walid Nabgan
- Departament
d’Enginyeria Química, Universitat
Rovira i Virgili, 43007Tarragona, Spain
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12
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Ikram M, Rasheed F, Haider A, Naz S, Ul-Hamid A, Shahzadi A, Haider J, Shahzadi I, Hayat S, Ali S. Photocatalytic and antibacterial activity of graphene oxide/cellulose-doped TiO 2 quantum dots: in silico molecular docking studies. NANOSCALE ADVANCES 2022; 4:3764-3776. [PMID: 36133332 PMCID: PMC9470022 DOI: 10.1039/d2na00383j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/27/2022] [Indexed: 06/16/2023]
Abstract
Graphene oxide (GO) and cellulose nanocrystal (CNC)-doped TiO2 quantum dots (QDs) were effectively synthesized by employing the co-precipitation method for the degradation of dyes and antimicrobial applications. A series of characterizations, i.e., XRD, FTIR, UV-visible spectroscopy, EDS, FE-SEM, and HR-TEM, was used to characterize the prepared samples. A reduction in PL intensity was observed, while the band gap energy (E g) decreased from 3.22 to 2.96 eV upon the incorporation of GO/CNC in TiO2. In the Raman spectra, the D and G bands were detected, indicating the presence of graphene oxide in the composites. Upon doping, the crystallinity of TiO2 increased. HR-TEM was employed to estimate the interlayer d-spacing of the nanocomposites, which matched well with the XRD data. The photocatalytic potential of the prepared samples was tested against methylene blue, methylene violet, and ciprofloxacin (MB:MV:CF) when exposed to visible light for a certain period. The antibacterial activity of GO/CNC/TiO2 QDs against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) bacteria in vitro was tested to determine their potential for medicinal applications. The molecular docking investigations of CNC-TiO2 and GO/CNC-doped TiO2 against DNA gyrase and FabI from E. coli and S. aureus were found to be consistent with the results of the in vitro bactericidal activity test. We believe that the prepared nanocomposites will be highly efficient for wastewater treatment and antimicrobial activities.
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Affiliation(s)
- Muhammad Ikram
- Solar Cell Applications Research Lab, Department of Physics, Government College University Lahore Lahore 54000 Punjab Pakistan
| | - Fahad Rasheed
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University 14 Ali Road Lahore Pakistan
| | - Ali Haider
- Department of Clinical Sciences, Faculty of Veterinary and Animal Sciences, Muhammad Nawaz Shareef University of Agriculture Multan 6000 Pakistan
| | - Sadia Naz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences Tianjin 300308 China
| | - Anwar Ul-Hamid
- Core Research Facilities, King Fahd University of Petroleum & Minerals Dhahran 31261 Saudi Arabia
| | - Anum Shahzadi
- Faculty of Pharmacy, The University of Lahore Lahore Pakistan
| | - Junaid Haider
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences Tianjin 300308 China
| | - Iram Shahzadi
- Punjab University College of Pharmacy, University of the Punjab 54000 Pakistan
| | - Shaukat Hayat
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University 14 Ali Road Lahore Pakistan
| | - Salamat Ali
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University 14 Ali Road Lahore Pakistan
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Abstract
Antibiotic resistance is a serious public health concern, and new drugs are needed to ensure effective treatment of many bacterial infections. Bacterial type II fatty acid synthesis (FASII) is a vital aspect of bacterial physiology, not only for the formation of membranes but also to produce intermediates used in vitamin production. Nature has evolved a repertoire of antibiotics inhibiting different aspects of FASII, validating these enzymes as potential targets for new antibiotic discovery and development. However, significant obstacles have been encountered in the development of FASII antibiotics, and few FASII drugs have advanced beyond the discovery stage. Most bacteria are capable of assimilating exogenous fatty acids. In some cases they can dispense with FASII if fatty acids are present in the environment, making the prospects for identifying broad-spectrum drugs against FASII targets unlikely. Single-target, pathogen-specific FASII drugs appear the best option, but a major drawback to this approach is the rapid acquisition of resistance via target missense mutations. This complication can be mitigated during drug development by optimizing the compound design to reduce the potential impact of on-target missense mutations at an early stage in antibiotic discovery. The lessons learned from the difficulties in FASII drug discovery that have come to light over the last decade suggest that a refocused approach to designing FASII inhibitors has the potential to add to our arsenal of weapons to combat resistance to existing antibiotics.
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Affiliation(s)
- Christopher D Radka
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; ,
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; ,
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Zhou Y, Liang YQ, Wang XY, Chang HY, Hu SP, Sun J. Design, Synthesis and Antibacterial Activities of Novel Amide Derivatives Bearing Dioxygenated Rings as Potential β-Ketoacyl-acyl Carrier Protein Synthase III (FabH) Inhibitors. Chem Pharm Bull (Tokyo) 2022; 70:544-549. [DOI: 10.1248/cpb.c22-00090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yang Zhou
- School of Biological & Chemical Engineering, Zhejiang University of Science & Technology
| | - Yin-Qiu Liang
- Zhejiang International Scientific and Technological Cooperative Base of Biomedical Materials and Technology, Zhejiang Engineering Research Center for Biomedical Materials, Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences
| | - Xin-Yu Wang
- Zhejiang International Scientific and Technological Cooperative Base of Biomedical Materials and Technology, Zhejiang Engineering Research Center for Biomedical Materials, Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences
| | - Hao-Yun Chang
- Zhejiang International Scientific and Technological Cooperative Base of Biomedical Materials and Technology, Zhejiang Engineering Research Center for Biomedical Materials, Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences
| | - Su-Pei Hu
- Department of Medical Research, Hwa Mei Hospital, University of Chinese Academy of Sciences
| | - Juan Sun
- School of Biological & Chemical Engineering, Zhejiang University of Science & Technology
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15
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Erdogan MK, Gundogdu R, Yapar Y, Gecibesler IH, Kirici M, Behcet L, Tuzun B, Taslimi P. The Evaluation of Anticancer, Antioxidant, Antidiabetic and Anticholinergic Potentials of Endemic
Rhabdosciadium microcalycinum
Supported by Molecular Docking Study. ChemistrySelect 2022. [DOI: 10.1002/slct.202200400] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Mehmet Kadir Erdogan
- Department of Molecular Biology and Genetics Faculty of Arts and Sciences Bingol University 12000 Bingol Turkey
| | - Ramazan Gundogdu
- Department of Pharmacy Services Vocational School of Health Services Bingol University 12000- Bingol Turkey
| | - Yakup Yapar
- Department of Molecular Biology and Genetics Faculty of Arts and Sciences Bingol University 12000 Bingol Turkey
| | - Ibrahim Halil Gecibesler
- Department of Occupational Health and Safety Faculty of Health Science Bingol University 12000- Bingol Turkey
| | - Mahinur Kirici
- Department of Chemistry Faculty of Arts and Sciences Bingol University 12000- Bingol Turkey
| | - Lutfi Behcet
- Department of Molecular Biology and Genetics Faculty of Arts and Sciences Bingol University 12000 Bingol Turkey
| | - Burak Tuzun
- Plant and Animal Production Department Technical Sciences Vocational School of Sivas Sivas Cumhuriyet University Sivas Turkey
| | - Parham Taslimi
- Department of Biotechnology Faculty of Science Bartin University 74100 - Bartin Turkey
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16
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Interrogation of Essentiality in the Reconstructed Haemophilus influenzae Metabolic Network Identifies Lipid Metabolism Antimicrobial Targets: Preclinical Evaluation of a FabH β-Ketoacyl-ACP Synthase Inhibitor. mSystems 2022; 7:e0145921. [PMID: 35293791 PMCID: PMC9040583 DOI: 10.1128/msystems.01459-21] [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] [Indexed: 11/20/2022] Open
Abstract
Expediting drug discovery to fight antibacterial resistance requires holistic approaches at system levels. In this study, we focused on the human-adapted pathogen Haemophilus influenzae, and by constructing a high-quality genome-scale metabolic model, we rationally identified new metabolic drug targets in this organism. Contextualization of available gene essentiality data within in silico predictions identified most genes involved in lipid metabolism as promising targets. We focused on the β-ketoacyl-acyl carrier protein synthase III FabH, responsible for catalyzing the first step in the FASII fatty acid synthesis pathway and feedback inhibition. Docking studies provided a plausible three-dimensional model of FabH in complex with the synthetic inhibitor 1-(5-(2-fluoro-5-(hydroxymethyl)phenyl)pyridin-2-yl)piperidine-4-acetic acid (FabHi). Validating our in silico predictions, FabHi reduced H. influenzae viability in a dose- and strain-dependent manner, and this inhibitory effect was independent of fabH gene expression levels. fabH allelic variation was observed among H. influenzae clinical isolates. Many of these polymorphisms, relevant for stabilization of the dimeric active form of FabH and/or activity, may modulate the inhibitory effect as part of a complex multifactorial process with the overall metabolic context emerging as a key factor tuning FabHi activity. Synergies with antibiotics were not observed and bacteria were not prone to develop resistance. Inhibitor administration during H. influenzae infection on a zebrafish septicemia infection model cleared bacteria without signs of host toxicity. Overall, we highlight the potential of H. influenzae metabolism as a source of drug targets, metabolic models as target-screening tools, and FASII targeting suitability to counteract this bacterial infection. IMPORTANCE Antimicrobial resistance drives the need of synergistically combined powerful computational tools and experimental work to accelerate target identification and drug development. Here, we present a high-quality metabolic model of H. influenzae and show its usefulness both as a computational framework for large experimental data set contextualization and as a tool to discover condition-independent drug targets. We focus on β-ketoacyl-acyl carrier protein synthase III FabH chemical inhibition by using a synthetic molecule with good synthetic and antimicrobial profiles that specifically binds to the active site. The mechanistic complexity of FabH inhibition may go beyond allelic variation, and the strain-dependent effect of the inhibitor tested supports the impact of metabolic context as a key factor driving bacterial cell behavior. Therefore, this study highlights the systematic metabolic evaluation of individual strains through computational frameworks to identify secondary metabolic hubs modulating drug response, which will facilitate establishing synergistic and/or more precise and robust antibacterial treatments.
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17
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Fragment-to-lead tailored in silico design. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 40:44-57. [PMID: 34916022 DOI: 10.1016/j.ddtec.2021.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 06/25/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023]
Abstract
Fragment-based drug discovery (FBDD) emerged as a disruptive technology and became established during the last two decades. Its rationality and low entry costs make it appealing, and the numerous examples of approved drugs discovered through FBDD validate the approach. However, FBDD still faces numerous challenges. Perhaps the most important one is the transformation of the initial fragment hits into viable leads. Fragment-to-lead (F2L) optimization is resource-intensive and is therefore limited in the possibilities that can be actively pursued. In silico strategies play an important role in F2L, as they can perform a deeper exploration of chemical space, prioritize molecules with high probabilities of being active and generate non-obvious ideas. Here we provide a critical overview of current in silico strategies in F2L optimization and highlight their remarkable impact. While very effective, most solutions are target- or fragment- specific. We propose that fully integrated in silico strategies, capable of automatically and systematically exploring the fast-growing available chemical space can have a significant impact on accelerating the release of fragment originated drugs.
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18
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Shaheen S, Iqbal A, Ikram M, Ul-Ain K, Naz S, Ul-Hamid A, Shahzadi A, Haider A, Nabgan W, Haider J. Effective Disposal of Methylene Blue and Bactericidal Benefits of Using GO-Doped MnO 2 Nanorods Synthesized through One-Pot Synthesis. ACS OMEGA 2021; 6:24866-24878. [PMID: 34604668 PMCID: PMC8482489 DOI: 10.1021/acsomega.1c03723] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/09/2021] [Indexed: 05/28/2023]
Abstract
Graphene oxide (GO)-doped MnO2 nanorods loaded with 2, 4, and 6% GO were synthesized via the chemical precipitation route at room temperature. The aim of this work was to determine the catalytic and bactericidal activities of prepared nanocomposites. Structural, optical, and morphological properties as well as elemental composition of samples were investigated with advanced techniques such as X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, UV-visible (vis) spectroscopy, photoluminescence (PL), energy-dispersive spectrometry (EDS), and high-resolution transmission electron microscopy (HR-TEM). XRD measurements confirmed the monoclinic structure of MnO2. Vibrational mode and rotational mode of functional groups (O-H, C=C, C-O, and Mn-O) were evaluated using FTIR results. Band gap energy and blueshift in the absorption spectra of MnO2 and GO-doped MnO2 were identified with UV-vis spectroscopy. Emission spectra were attained using PL spectroscopy, whereas elemental composition of prepared materials was recorded with scanning electron microscopy (SEM)-EDS. Moreover, HR-TEM micrographs of doped and undoped MnO2 revealed elongated nanorod-like structure. Efficient degradation of methylene blue enhanced the catalytic activity in the presence of a reducing agent (NaBH4); this was attributed to the implantation of GO on MnO2 nanorods. Furthermore, substantial inhibition areas were measured for Escherichia coli (EC) ranging 2.10-2.85 mm and 2.50-3.15 mm at decreased and increased levels for doped MnO2 nanorods and 3.05-4.25 mm and 4.20-5.15 mm for both attentions against SA, respectively. In silico molecular docking studies suggested the inhibition of FabH and DNA gyrase of E. coli and Staphylococcus aureus as a possible mechanism behind the bactericidal activity of MnO2 and MnO2-doped GO nanoparticles (NPs).
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Affiliation(s)
- Saira Shaheen
- Department
of Physics, School of Science, University
of Management and Technology, Lahore 54000, Pakistan
| | - Azhar Iqbal
- Department
of Physics, School of Science, University
of Management and Technology, Lahore 54000, Pakistan
| | - Muhammad Ikram
- Solar
Cell Applications Research Lab, Government
College University Lahore, Lahore 54000, Pakistan
| | - Kashaf Ul-Ain
- Department
of Physics, RICAS, Riphah International
University, Lahore Campus, Lahore 54000, Pakistan
| | - Sadia Naz
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Anwar Ul-Hamid
- Core
Research Facilities, Research Institute, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia
| | - Anum Shahzadi
- Punjab University
College of Pharmacy, University of the Punjab, Lahore 54000, Pakistan
| | - Ali Haider
- Department
of Clinical Medicine and Surgery, University
of Veterinary and Animal Sciences, Lahore 54000, Punjab, Pakistan
| | - Walid Nabgan
- School
of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Junaid Haider
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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19
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Ali S, Alam M, Hasan GM, Hassan MI. Potential therapeutic targets of Klebsiella pneumoniae: a multi-omics review perspective. Brief Funct Genomics 2021; 21:63-77. [PMID: 34448478 DOI: 10.1093/bfgp/elab038] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/15/2022] Open
Abstract
The multidrug resistance developed in many organisms due to the prolonged use of antibiotics has been an increasing global health crisis. Klebsiella pneumoniae is a causal organism for various infections, including respiratory, urinary tract and biliary diseases. Initially, immunocompromised individuals are primarily affected by K. pneumoniae. Due to the emergence of hypervirulent strains recently, both healthy and immunocompetent individuals are equally susceptible to K. pneumoniae infections. The infections caused by multidrug-resistant and hypervirulent K. pneumoniae strains are complicated to treat, illustrating an urgent need to develop novel and more practical approaches to combat the pathogen. We focused on the previously performed high-throughput analyses by other groups to discover several novel enzymes that may be considered attractive drug targets of K. pneumoniae. These targets qualify most of the selection criteria for drug targeting, including an absence of its homolog's gene in the host. The capsule, lipopolysaccharide, fimbriae, siderophores and essential virulence factors facilitate the pathogen entry, infection and survival inside the host. This review discusses K. pneumoniae pathophysiology, including its virulence determinants and further the potential drug targets that might facilitate the discovery of novel drugs and effective treatment regimens shortly.
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Affiliation(s)
- Sabeeha Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
| | - Manzar Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
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20
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Pazoki F, Esfandiarpour R, Mohsenzadeh F, Mohammadpanah F, Heydari A. Molecular docking and DFT studies of a series of tetrazole derivatives and computational studies of Fe3O4@Phenyl phosphate creatine. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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21
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Asad M, Khan SA, Arshad MN, Asiri AM, Rehan M. Design and synthesis of novel pyrazoline derivatives for their spectroscopic, single crystal X-ray and biological studies. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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22
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Mureed S, Naz S, Haider A, Raza A, Ul-Hamid A, Haider J, Ikram M, Ghaffar R, Irshad M, Ghaffar A, Saeed A. Development of Multi-concentration Cu:Ag Bimetallic Nanoparticles as a Promising Bactericidal for Antibiotic-Resistant Bacteria as Evaluated with Molecular Docking Study. NANOSCALE RESEARCH LETTERS 2021; 16:91. [PMID: 34021844 PMCID: PMC8141091 DOI: 10.1186/s11671-021-03547-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
The present study is concerned with evaluating the influence of various concentrations of Ag within Cu:Ag bimetallic nanoparticles developed for use as a promising anti-bacterial agent against antibiotic-resistant bacteria. Here, Cu:Ag bimetallic nanoparticles with various concentration ratios (2.5, 5.0, 7.5, and 10 wt%) of Ag in fixed amount of Cu labeled as 1:0.025, 1:0.050, 1:0.075, and 1:0.1 were synthesized using co-precipitation method with ammonium hydroxide and deionized water as solvent, polyvinyl pyrrolidone as a capping agent, and sodium borohydride and ascorbic acid as reducing agents. These formulated products were characterized through a variety of techniques. XRD confirmed phase purity and detected the presence of distinct fcc structures belonging to Cu and Ag phases. FTIR spectroscopy confirmed the presence of vibrational modes corresponding to various functional groups and recorded characteristic peak emanating from the bimetallic. UV-visible spectroscopy revealed reduction in band gap with increasing Ag content. SEM and HR-TEM micrographs revealed spherical morphology of Ag-doped Cu bimetallic with small and large scale agglomerations. The samples exhibited varying dimensions and interlayer spacing. Bactericidal action of synthesized Cu:Ag bimetallic NPs depicted statistically significant (P < 0.05) inhibition zones recorded for various concentrations of Ag dopant against Staphylococcus aureus (S. aureus), Escherichia coli (E. coli), and Acinetobacter baumannii (A. baumannii) ranging from (0.85-2.8 mm), (0.55-1.95 mm) and (0.65-1.85 mm), respectively. Broadly, Cu:Ag bimetallic NPs were found to be more potent against gram-positive compared with gram-negative. Molecular docking study of Ag-Cu bimetallic NPs was performed against β-lactamase which is a key enzyme of cell wall biosynthetic pathway from both S. aureus (Binding score: - 4.981 kcal/mol) and A. bauminnii (Binding score: - 4.013 kcal/mol). Similarly, binding interaction analysis against FabI belonging to fatty acid biosynthetic pathway from A. bauminnii (Binding score: - 3.385 kcal/mol) and S. aureus (Binding score: - 3.012 kcal/mol) along with FabH from E. coli (Binding score: - 4.372 kcal/mol) was undertaken. These theoretical computations indicate Cu-Ag bimetallic NPs as possible inhibitor of selected enzymes. It is suggested that exploring in vitro inhibition potential of these materials may open new avenues for antibiotic discovery.
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Affiliation(s)
- Shumaila Mureed
- Solar Cell Applications Research Lab, Department of Physics, Government College University Lahore, Lahore, 54000, Punjab, Pakistan
- Department of Physics, Government College University Lahore, Lahore, 54000, Punjab, Pakistan
| | - Sadia Naz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Ali Haider
- Department of Clinical Medicine and Surgery, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Ali Raza
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University, 14 Ali Road, Lahore, Pakistan
| | - Anwar Ul-Hamid
- Core Research Facilities, King Fahd University of Petroleum & Minerals, Dhahran, 31261, Saudi Arabia.
| | - Junaid Haider
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Muhammad Ikram
- Solar Cell Applications Research Lab, Department of Physics, Government College University Lahore, Lahore, 54000, Punjab, Pakistan.
| | - Rabia Ghaffar
- Division of Science and Technology, Department of Botany, University of Education, Lahore, 54000, Pakistan
| | - Muneeb Irshad
- Department of Physics, University of Engineering and Technology, Lahore, 54890, Pakistan
| | - Abdul Ghaffar
- Department of Physics, Government College University Lahore, Lahore, 54000, Punjab, Pakistan
| | - Aamer Saeed
- Department of Chemistry, Quaid-I-Azam University, Islamabad, 45320, Pakistan
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Ikram M, Aslam S, Haider A, Naz S, Ul-Hamid A, Shahzadi A, Ikram M, Haider J, Ahmad SOA, Butt AR. Doping of Mg on ZnO Nanorods Demonstrated Improved Photocatalytic Degradation and Antimicrobial Potential with Molecular Docking Analysis. NANOSCALE RESEARCH LETTERS 2021; 16:78. [PMID: 33934207 PMCID: PMC8088420 DOI: 10.1186/s11671-021-03537-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/22/2021] [Indexed: 05/22/2023]
Abstract
Various concentrations of Mg-doped ZnO nanorods (NRs) were prepared using co-precipitation technique. The objective of this study was to improve the photocatalytic properties of ZnO. The effect of Mg doping on the structure, phase constitution, functional groups presence, optical properties, elemental composition, surface morphology and microstructure of ZnO was evaluated with XRD, FTIR, UV-Vis spectrophotometer, EDS, and HR-TEM, respectively. Optical absorption spectra obtained from the prepared samples showed evidence of blueshift upon doping. XRD results revealed hexagonal wurtzite phase of nanocomposite with a gradual decrease in crystallite size with Mg addition. PL spectroscopy showed trapping efficiency and migration of charge carriers with electron-hole recombination behavior, while HR-TEM estimated interlayer d-spacing. The presence of chemical bonding, vibration modes and functional groups at the interface of ZnO was revealed by FTIR and Raman spectra. In this study, photocatalytic, sonocatalytic and sonophotocatalytic performance of prepared NRs was systematically investigated by degrading a mixture of methylene blue and ciprofloxacin (MBCF). Experimental results suggested that improved degradation performance was shown by Mg-doped ZnO NRs. We believe that the product synthesized in this study will prove to be a beneficial and promising photocatalyst for wastewater treatment. Conclusively, Mg-doped ZnO exhibited substantial (p < 0.05) efficacy against gram-negative (G-ve) as compared to gram-positive (G+ve) bacteria. In silico molecular docking studies of Mg-doped ZnO NRs against DHFR (binding score: - 7.518 kcal/mol), DHPS (binding score: - 6.973 kcal/mol) and FabH (- 6.548 kcal/mol) of E. coli predicted inhibition of given enzymes as possible mechanism behind their bactericidal activity.
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Affiliation(s)
- Muhammad Ikram
- Solar Cell Applications Research Lab, Department of Physics, Government College University, Lahore, Punjab, 54000, Pakistan.
| | - Sidra Aslam
- Physics Department, Lahore Garrison University, Lahore, Punjab, 54000, Pakistan
| | - Ali Haider
- Department of Clinical Medicine and Surgery, University of Veterinary and Animal Sciences, Lahore, Punjab, 54000, Pakistan
| | - Sadia Naz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Anwar Ul-Hamid
- Core Research Facilities, King Fahd University of Petroleum & Minerals, Dhahran, 31261, Saudi Arabia.
| | - Anum Shahzadi
- University College of Pharmacy, University of the Punjab, Lahore, 54000, Pakistan
| | - Mujtaba Ikram
- Institute of Chemical Engineering and Technology (ICET), University of the Punjab, Lahore, 54000, Pakistan
| | - Junaid Haider
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Syed Ossama Ali Ahmad
- Solar Cell Applications Research Lab, Department of Physics, Government College University, Lahore, Punjab, 54000, Pakistan
| | - Alvina Rafiq Butt
- Physics Department, Lahore Garrison University, Lahore, Punjab, 54000, Pakistan
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Jebli N, Arfaoui Y, Van Hecke K, Cavalier JF, Touil S. Experimental and computational investigation of Z/E isomerism, X-ray crystal structure and molecular docking study of (2-(hydroxyimino)cyclohexyl)diphenylphosphine sulfide, a potential antibacterial agent. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Li Y, Weng X, Deng Y, Pan J, Zhu S, Wen Z, Yuan Y, Li S, Shen B, Duan Y, Huang Y. Semisynthesis and Biological Evaluation of Platencin Thioether Derivatives: Dual FabF and FabH Inhibitors against MRSA. ACS Med Chem Lett 2021; 12:433-442. [PMID: 33738071 DOI: 10.1021/acsmedchemlett.0c00653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/08/2021] [Indexed: 12/28/2022] Open
Abstract
The discovery and clinical use of multitarget monotherapeutic antibiotics is regarded as a promising approach to reduce the development of antibiotic resistance. Platencin (PTN), a potent natural antibiotic initially isolated from a soil actinomycete, targets both FabH and FabF, the initiation and elongation condensing enzymes for bacterial fatty acid biosynthesis. However, its further clinical development has been hampered by poor pharmacokinetics. Herein we report the semisynthesis and biological evaluation of platencin derivatives 1-15 with potent antibacterial activity against methicillin-resistant Staphylococcus aureus in vitro. Some of these PTN analogues showed similar yet distinct interactions with FabH and FabF, as shown by molecular docking, differential scanning fluorometry, and isothermal titration calorimetry. Compounds 3, 8, 10, and 14 were further evaluated in a mouse peritonitis model, among which 8 showed in vivo antibacterial activity comparable to that of PTN. Our results suggest that semisynthetic modification of PTN is a rapid route to obtain active PTN derivatives that might be further developed as promising antibiotics against drug-resistant major pathogens.
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Affiliation(s)
- Yuling Li
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, China
| | - Xiang Weng
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, China
| | - Youchao Deng
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, China
| | - Jian Pan
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, China
| | - Saibin Zhu
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, China
| | - Zhongqing Wen
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, China
| | - Yanqiu Yuan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Shaowen Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Ben Shen
- Departments of Chemistry and Molecular Medicine and Natural Product Discovery Center at Scripps Research, Scripps Research, Jupiter, Florida 33458, United States
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, China
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, Hunan 410011, China
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan 410011, China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, China
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan 410011, China
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Rashid M, Ikram M, Haider A, Naz S, Haider J, Ul-Hamid A, Shahzadi A, Aqeel M. Photocatalytic, dye degradation, and bactericidal behavior of Cu-doped ZnO nanorods and their molecular docking analysis. Dalton Trans 2021; 49:8314-8330. [PMID: 32515772 DOI: 10.1039/d0dt01397h] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanostructures of Cu-doped ZnO (Cu:ZnO) were prepared with the chemical precipitation technique with an aim to enhance the photocatalytic and antibacterial properties of ZnO. Phase constitution, the presence of functional groups, optical properties, elemental composition, surface morphology and microstructure were evaluated using an X-ray diffractometer (XRD), Fourier transform infrared spectroscopy (FTIR), UV-Vis spectrophotometer, energy dispersive X-ray spectroscopy (EDS), field emission scanning electron microscope (FESEM) and high resolution transmission electron microscope (HR-TEM), respectively. Emission spectra were obtained with a photoluminescence (PL) spectroscope whereas interlayer d-spacing was estimated through HR-TEM. ZnO consisted of a hexagonal wurtzite structure. The crystallinity of the sample was observed to increase with increasing doping concentration. The addition of Cu to ZnO served to transform nanoclusters into nanorods as revealed during SEM analysis. Catalytic activity enhanced due to the formation of nanorods, and UV-Vis absorption spectra showed that methylene blue (MB) degraded more efficiently with ZnO nanoclusters compared to the NaBH4 reagent. In addition, the doped NPs showed enhanced bacterial efficiency for G +ve. Finally, a molecular docking study was undertaken to highlight the importance of the binding interactions of the Cu-doped ZnO nanorods with β-lactamase and beta-ketoacyl-acyl carrier protein synthase III (FabH) as possible enzyme targets. This research indicates that Cu-doped Zn nanorods are a highly efficient photocatalyst and can be aptly employed for wastewater treatment and antibacterial applications.
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Affiliation(s)
- Mehak Rashid
- Solar Cell Applications Research Lab, Department of Physics, Government College University Lahore, 54000, Punjab, Pakistan.
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Jebli N, Hamimed S, Van Hecke K, Cavalier J, Touil S. Synthesis, Antimicrobial Activity and Molecular Docking Study of Novelα‐(Diphenylphosphoryl)‐ andα‐(Diphenylphosphorothioyl)cycloalkanone Oximes. Chem Biodivers 2020; 17:e2000217. [DOI: 10.1002/cbdv.202000217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/15/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Nejib Jebli
- University of CarthageFaculty of Sciences of BizerteLaboratory of Hetero-Organic Compounds and Nanostructured Materials (LR18ES11) CP 7021- Jarzouna Tunisia
| | - Selma Hamimed
- University of CarthageFaculty of Sciences of BizerteLaboratory of Biochemistry and Molecular Biology 7021 Jarzouna Tunisia
| | - Kristof Van Hecke
- XStructDepartment of Inorganic and Physical Chemistry Krijgslaan 281-S3 CP 9000-Ghent Belgium
| | | | - Soufiane Touil
- University of CarthageFaculty of Sciences of BizerteLaboratory of Hetero-Organic Compounds and Nanostructured Materials (LR18ES11) CP 7021- Jarzouna Tunisia
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Altaf S, Haider A, Naz S, Ul-Hamid A, Haider J, Imran M, Shahzadi A, Naz M, Ajaz H, Ikram M. Comparative Study of Selenides and Tellurides of Transition Metals (Nb and Ta) with Respect to its Catalytic, Antimicrobial, and Molecular Docking Performance. NANOSCALE RESEARCH LETTERS 2020; 15:144. [PMID: 32643064 PMCID: PMC7343698 DOI: 10.1186/s11671-020-03375-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/23/2020] [Indexed: 05/13/2023]
Abstract
The present research is a comparative study that reports an economical and accessible method to synthesize niobium (Nb) and Tantalum (Ta) selenides and tellurides with useful application in the removal of pollutants in textile, paper, and dyeing industries as well as in medical field. In this study, solid-state process was used to generate nanocomposites and various characterization techniques were employed to compare two groups of materials under investigation. Structure, morphology, elemental constitution, and functional groups of synthesized materials were analyzed with XRD, FESEM coupled with EDS, FTIR, and Raman spectroscopy, respectively. HR-TEM images displayed nanoscale particles with tetragonal and monoclinic crystal structures. The optical properties were evaluated in terms of cut-off wavelength and optical band gap using UV-visible spectroscopy. A comparative behavior of both groups of compounds was assessed with regards to their catalytic and microcidal properties. Extracted nanocomposites when used as catalysts, though isomorphs of each other, showed markedly different behavior in catalytic degradation of MB dye in the presence of NaBH4 that was employed as a reducing agent. This peculiar deviation might be attributed to slight structural differences between them. Escherichia coli and Staphylococcus aureus (G -ve and + ve bacteria, respectively) were designated as model strains for in vitro antibacterial tests of both clusters by employing disk diffusion method. Superior antibacterial efficacy was observed for telluride system (significant inhibition zones of 26-35 mm) compared with selenide system (diameter of inhibition zone ranged from 0.8 mm to 1.9 mm). In addition, molecular docking study was undertaken to ascertain the binding interaction pattern between NPs and active sites in targeted cell protein. The findings were in agreement with antimicrobial test results suggesting NbTe4 to be the best inhibitor against FabH and FabI enzymes.
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Affiliation(s)
- S Altaf
- Department of Chemistry, University of Engineering and Technology, Lahore, 54000, Pakistan
| | - A Haider
- Department of Clinical Medicine and Surgery, University of Veterinary and Animal Sciences, Lahore, Punjab, 54000, Pakistan
| | - S Naz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - A Ul-Hamid
- Center for Engineering Research, Research Institute, King Fahd University of Petroleum & Minerals, Dhahran, 31261, Saudi Arabia
| | - J Haider
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - M Imran
- State key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Centre for Soft Matter Science and Engineering, Beijing Engineering Center for Hierarchical Catalysts, Beijing University of Chemical Technology, Beijing, 100029, China
| | - A Shahzadi
- University College of Pharmacy, University of the Punjab, Lahore, 54000, Pakistan
| | - M Naz
- Biochemistry Lab, Department of Chemistry, Government College University, Lahore, Punjab, 54000, Pakistan
| | - H Ajaz
- Department of Chemistry, University of Engineering and Technology, Lahore, 54000, Pakistan
| | - M Ikram
- Solar Cell Applications Research Lab, Department of Physics, Government College University, Lahore, Punjab, 54000, Pakistan.
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Ikram M, Umar E, Raza A, Haider A, Naz S, Ul-Hamid A, Haider J, Shahzadi I, Hassan J, Ali S. Dye degradation performance, bactericidal behavior and molecular docking analysis of Cu-doped TiO 2 nanoparticles. RSC Adv 2020; 10:24215-24233. [PMID: 35516171 PMCID: PMC9055104 DOI: 10.1039/d0ra04851h] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 06/18/2020] [Indexed: 11/21/2022] Open
Abstract
Copper-doped TiO2 was prepared with a sol-gel chemical method. Various concentrations (3, 6, and 9 wt%) of Cu dopant were employed. Several techniques were implemented to assess the structural, optical, morphological and chemical properties of the synthesized samples. Evaluation of elemental composition using SEM-EDS and XRF techniques showed the presence of dopant element in the prepared samples. XRD analysis confirmed the presence of anatase (TiO2) phase with interstitial doping. Incorporation of dopant was observed to enhance the crystallinity and increase the crystallite size of the synthesized products. SAED profiles revealed a high degree of crystallinity in the prepared specimens, which was also evident in the XRD spectra. Optical properties studied using UV-vis spectroscopy depicted a shift of the maximum absorption to the visible region (redshift) that signified a reduction in the band gap energy of Cu-doped TiO2 samples. Examination of morphological features with scanning and high-resolution transmission electron microscopes revealed the formation of spherical nanoparticles with a tendency to agglomerate with increasing dopant concentration. Molecular vibrations and the formation of Ti-O-Ti bonds were revealed through FTIR spectra. PL spectroscopy recorded the trapping efficiency and migration of charge carriers, which exhibited electron-hole recombination behavior. Doped nanostructures showed enhanced bactericidal performance and synergism against S. aureus and E. coli. In summary, Cu-doped TiO2 nanostructures were observed to impede bacteria effectively, which is deemed beneficial in overcoming ailments caused by pathogens such as microbial etiologies. Furthermore, molecular docking analysis was conducted to study the interaction of Cu-doped TiO2 nanoparticles with multiple proteins namely β-lactamase (binding score: -4.91 kcal mol-1), ddlB (binding score: -5.67 kcal mol-1) and FabI (binding score: -6.13 kcal mol-1) as possible targets with active site residues. Dye degradation/reduction of control and Cu-doped samples were studied through absorption spectroscopy. The obtained outcomes of the performed experiment indicated that the photocatalytic activity of Cu-TiO2 enhanced with increasing dopant concentration, which is thought to be due to a decreased rate of electron-hole pair recombination. Consequently, it is suggested that Cu-TiO2 can be exploited as an effective candidate for antibacterial and dye degradation applications.
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Affiliation(s)
- M Ikram
- Solar Cell Applications Research Lab, Department of Physics, Government College University Lahore Punjab 54000 Pakistan +923005406667
| | - E Umar
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University 14 Ali Road Lahore Pakistan
| | - A Raza
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University 14 Ali Road Lahore Pakistan
| | - A Haider
- Department of Clinical Medicine and Surgery, University of Veterinary and Animal Sciences Lahore 54000 Punjab Pakistan
| | - S Naz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences Tianjin 300308 China
| | - A Ul-Hamid
- Center for Engineering Research, Research Institute, King Fahd University of Petroleum & Minerals Dhahran 31261 Saudi Arabia
| | - J Haider
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences Tianjin 300308 China
| | - I Shahzadi
- College of Pharmacy, University of the Punjab Lahore 54000 Pakistan
| | - J Hassan
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University 14 Ali Road Lahore Pakistan
| | - S Ali
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University 14 Ali Road Lahore Pakistan
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Wang YT, Shi TQ, Fu J, Zhu HL. Discovery of novel bacterial FabH inhibitors (Pyrazol-Benzimidazole amide derivatives): Design, synthesis, bioassay, molecular docking and crystal structure determination. Eur J Med Chem 2019; 171:209-220. [DOI: 10.1016/j.ejmech.2019.03.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/11/2019] [Accepted: 03/11/2019] [Indexed: 10/27/2022]
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31
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Zhang J, Huang H, Zhou X, Xu Y, Chen B, Tang W, Xu K. N-Benzylanilines as Fatty Acid Synthesis Inhibitors against Biofilm-related Methicillin-resistant Staphylococcus aureus. ACS Med Chem Lett 2019; 10:329-333. [PMID: 30891135 DOI: 10.1021/acsmedchemlett.8b00612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/28/2019] [Indexed: 01/07/2023] Open
Abstract
Bacterial fatty acid synthase system is a well validated target for the development of novel antimicrobial agents. This study reports the synthesis of Schiff bases and their reductive N-benzylanilines. Most N-benzylanilines were active against Gram-positive bacteria, among which compound 4k performed best against both S. aureus and MRSA with the MIC value at 0.5 mg/L. Moreover, we identified the strong antibacterial activity for compound 4k against 19 clinical MRSA strains isolated from different specimen, which indicated its potential in clinical application. In vitro biofilm inhibition and microscopy assay revealed compound 4k inhibits biofilm formation and eradicates preformed biofilm effectively. The size-exclusion chromatography and docking study indicated that compound 4k mimics the binding mode of triclosan with saFabI. The efficiency of the protein-inhibitor interaction was evaluated by measuring NADPH reduction using trans-2-octenoyl-CoA as substrate. Overall, our data demonstrate that N-benzylaniline is a promising scaffold for anti-staphylococcal drug development.
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Affiliation(s)
- Jing Zhang
- Prevention and Treatment Center for Occupational Disease, Anhui No. 2 Provincial People’s Hospital, Hefei 230022, China
| | - Hao Huang
- College of Basic Medical, Anhui Medical University, Hefei 230032, China
| | - Xueting Zhou
- College of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Yingying Xu
- College of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Baochun Chen
- Prevention and Treatment Center for Occupational Disease, Anhui No. 2 Provincial People’s Hospital, Hefei 230022, China
| | - Wenjian Tang
- College of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Kehan Xu
- College of Basic Medical, Anhui Medical University, Hefei 230032, China
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Chow J, Danso D, Ferrer M, Streit WR. The Thaumarchaeon N. gargensis carries functional bioABD genes and has a promiscuous E. coli ΔbioH-complementing esterase EstN1. Sci Rep 2018; 8:13823. [PMID: 30218044 PMCID: PMC6138646 DOI: 10.1038/s41598-018-32059-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/28/2018] [Indexed: 12/15/2022] Open
Abstract
Biotin is an essential cofactor required for carboxylation and decarboxylation reactions in all domains of life. While biotin biosynthesis in most Bacteria and Eukarya is well studied, the complete pathway for this vitamer in Archaea is still not known. Detailed genome searches indicated the presence of possible bio gene clusters only in Methanococcales and Thaumarchaeota. Therefore, we analysed the functionality of the predicted genes bioA, bioB, bioD and bioF in the Thaumarchaeon Nitrososphaera gargensis Ga2.9 which are essential for the later steps of biotin synthesis. In complementation tests, the gene cluster-encoded N. gargensis bioABD genes except bioF restored growth of corresponding E. coli Rosetta-gami 2 (DE3) deletion mutants. To find out how biotin biosynthesis is initiated, we searched the genome for a possible bioH analogue encoding a pimeloyl-ACP-methylester carboxylesterase. The respective amino acid sequence of the ORF estN1 showed weak conserved domain similarity to this class of enzymes (e-value 3.70e-42). Remarkably, EstN1 is a promiscuous carboxylesterase that complements E. coli ΔbioH and Mesorhizobium loti ΔbioZ mutants for growth on biotin-free minimal medium. Additional 3D-structural models support the hypothesis that EstN1 is a BioH analogue. Thus, this is the first report providing experimental evidence that Archaea carry functional bio genes.
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Affiliation(s)
- Jennifer Chow
- Microbiology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany
| | - Dominik Danso
- Microbiology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | - Wolfgang R Streit
- Microbiology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany.
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Johnson CN, Erlanson DA, Jahnke W, Mortenson PN, Rees DC. Fragment-to-Lead Medicinal Chemistry Publications in 2016. J Med Chem 2017; 61:1774-1784. [PMID: 29087197 DOI: 10.1021/acs.jmedchem.7b01298] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The popularity of fragment-based drug discovery (FBDD) is demonstrated by the number of recent successful fragment-to-lead (F2L) publications. This Miniperspective provides a tabulated summary of the F2L literature published in the year 2016, along with discussion of general trends. It uses the same format as our summary of the 2015 literature and is intended to be a resource for both FBDD practitioners and medicinal chemists in general.
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Affiliation(s)
- Christopher N Johnson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
| | - Daniel A Erlanson
- Carmot Therapeutics Inc. , 740 Heinz Avenue , Berkeley , California 94710 , United States
| | - Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics , 4002 Basel , Switzerland
| | - Paul N Mortenson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
| | - David C Rees
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
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Bacterial fatty acid metabolism in modern antibiotic discovery. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1300-1309. [PMID: 27668701 DOI: 10.1016/j.bbalip.2016.09.014] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/12/2016] [Accepted: 09/19/2016] [Indexed: 12/28/2022]
Abstract
Bacterial fatty acid synthesis is essential for many pathogens and different from the mammalian counterpart. These features make bacterial fatty acid synthesis a desirable target for antibiotic discovery. The structural divergence of the conserved enzymes and the presence of different isozymes catalyzing the same reactions in the pathway make bacterial fatty acid synthesis a narrow spectrum target rather than the traditional broad spectrum target. Furthermore, bacterial fatty acid synthesis inhibitors are single-targeting, rather than multi-targeting like traditional monotherapeutic, broad-spectrum antibiotics. The single-targeting nature of bacterial fatty acid synthesis inhibitors makes overcoming fast-developing, target-based resistance a necessary consideration for antibiotic development. Target-based resistance can be overcome through multi-targeting inhibitors, a cocktail of single-targeting inhibitors, or by making the single targeting inhibitor sufficiently high affinity through a pathogen selective approach such that target-based mutants are still susceptible to therapeutic concentrations of drug. Many of the pathogens requiring new antibiotic treatment options encode for essential bacterial fatty acid synthesis enzymes. This review will evaluate the most promising targets in bacterial fatty acid metabolism for antibiotic therapeutics development and review the potential and challenges in advancing each of these targets to the clinic and circumventing target-based resistance. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
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