{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T17:05:30Z","timestamp":1792515930763,"version":"4.5.0"},"reference-count":44,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2023,3,31]],"date-time":"2023-03-31T00:00:00Z","timestamp":1680220800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Princess Nourah bint Abdulrahman University","award":["PNURSP2023R205"],"award-info":[{"award-number":["PNURSP2023R205"]}]},{"name":"Princess Nourah bint Abdulrahman University","award":["RSPD2023R620"],"award-info":[{"award-number":["RSPD2023R620"]}]},{"name":"King Saud University","award":["PNURSP2023R205"],"award-info":[{"award-number":["PNURSP2023R205"]}]},{"name":"King Saud University","award":["RSPD2023R620"],"award-info":[{"award-number":["RSPD2023R620"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>Development in the fields of natural-product-derived and synthetic small molecules is in stark contrast to the ongoing demand for novel antimicrobials to treat life-threatening infections caused by extended-spectrum \u03b2-lactamase producing Escherichia coli (ESBL E. coli). Therefore, there is an interest in the antibacterial activities of synthesized N-(4-methylpyridin-2-yl) thiophene-2-carboxamides (4a\u2013h) against ESBL-producing E. coli ST131 strains. A blood sample was obtained from a suspected septicemia patient and processed in the Bactec Alert system. The isolate\u2019s identification and antibacterial profile were determined using the VITEK 2\u00ae compact system. Multi-locus sequence typing of E. coli was conducted by identifying housekeeping genes, while ESBL phenotype detection was performed according to CLSI guidelines. Additionally, PCR was carried out to detect the blaCTX-M gene molecularly. Moreover, molecular docking studies of synthesized compounds (4a\u2013h) demonstrated the binding pocket residues involved in the active site of the \u03b2-lactamase receptor of E. coli. The result confirmed the detection of E. coli ST131 from septicemia patients. The isolates were identified as ESBL producers carrying the blaCTX-M gene, which provided resistance against cephalosporins and beta-lactam inhibitors but sensitivity to carbapenems. Among the compounds tested, 4a and 4c exhibited high activity and demonstrated the best fit and interactions with the binding pocket of the \u03b2-lactamase enzyme. Interestingly, the maximum of the docking confirmations binds at a similar pocket region, further strengthening the importance of binding residues. Hence, the in vitro and molecular docking studies reflect the promising antibacterial effects of 4a and 4c compounds.<\/jats:p>","DOI":"10.3390\/molecules28073118","type":"journal-article","created":{"date-parts":[[2023,3,31]],"date-time":"2023-03-31T03:02:01Z","timestamp":1680231721000},"page":"3118","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Antibacterial Efficacy of N-(4-methylpyridin-2-yl) Thiophene-2-Carboxamide Analogues against Extended-Spectrum-\u03b2-Lactamase Producing Clinical Strain of Escherichia coli ST 131"],"prefix":"10.3390","volume":"28","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9499-4250","authenticated-orcid":false,"given":"Gulraiz","family":"Ahmad","sequence":"first","affiliation":[{"name":"Department of Chemistry, Government College University Faisalabad, Punjab 38000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aqsa","family":"Khalid","sequence":"additional","affiliation":[{"name":"School of Interdisciplinary Engineering & Science (SINES), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2636-238X","authenticated-orcid":false,"given":"Muhammad Usman","family":"Qamar","sequence":"additional","affiliation":[{"name":"Institute of Microbiology, Faculty of Life Sciences, Government College University Faisalabad, Punjab 38000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nasir","family":"Rasool","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Government College University Faisalabad, Punjab 38000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Malik","family":"Saadullah","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Chemistry, Government College University Faisalabad, Punjab 38000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8787-1399","authenticated-orcid":false,"given":"Muhammad","family":"Bilal","sequence":"additional","affiliation":[{"name":"School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2137-5210","authenticated-orcid":false,"given":"Majed A.","family":"Bajaber","sequence":"additional","affiliation":[{"name":"Chemistry Department, Faculty of Science, King Khalid University, Abha 61413, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7532-6318","authenticated-orcid":false,"given":"Ahmad J.","family":"Obaidullah","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2821-9373","authenticated-orcid":false,"given":"Hadil Faris","family":"Alotaibi","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jawaher M.","family":"Alotaibi","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,3,31]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1759","DOI":"10.2217\/fmb-2020-0069","article-title":"The present danger of New Delhi metallo-\u03b2-lactamase: A threat to public health","volume":"15","author":"Hassan","year":"2020","journal-title":"Future Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Thompson, T. (2022). The staggering death toll of drug-resistant bacteria. Nature.","DOI":"10.1038\/d41586-022-00228-x"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1038\/s41570-021-00313-1","article-title":"Towards the sustainable discovery and development of new antibiotics","volume":"5","author":"Miethke","year":"2021","journal-title":"Nat. Rev. Chem."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"184","DOI":"10.5001\/omj.2019.37","article-title":"WHO global priority pathogens list: A bibliometric analysis of Medline-PubMed for knowledge mobilization to infection prevention and control practices in Bahrain","volume":"34","author":"Asokan","year":"2019","journal-title":"Oman Med. J."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Arshad, M., Rasool, N., Qamar, M.U., Shah, S.A.A., and Zakaria, Z.A. (2022). Facile Synthesis of Functionalized Phenoxy Quinolines: Antibacterial Activities against ESBL Producing Escherichia coli and MRSA, Docking Studies, and Structural Features Determination through Computational Approach. Molecules, 27.","DOI":"10.3390\/molecules27123732"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.joad.2015.07.007","article-title":"Relation between blaTEM, blaSHV and blaCTX-M genes and acute urinary tract infections","volume":"5","author":"Seyedjavadi","year":"2016","journal-title":"J. Acute Dis."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1128\/CMR.00125-13","article-title":"Escherichia coli ST131, an intriguing clonal group","volume":"27","author":"Bertrand","year":"2014","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/jac\/dkq415","article-title":"Escherichia coli O25b-ST131: A pandemic, multiresistant, community-associated strain","volume":"66","author":"Rogers","year":"2011","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"e00511","DOI":"10.1128\/aac.00511-22","article-title":"Escherichia coli ST1193: Following in the Footsteps of E. coli ST131","volume":"66","author":"Pitout","year":"2022","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1024","DOI":"10.1093\/jac\/dkn084","article-title":"The CTX-M-15-producing Escherichia coli diffusing clone belongs to a highly virulent B2 phylogenetic subgroup","volume":"61","author":"Clermont","year":"2008","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"195","DOI":"10.3201\/eid1402.070350","article-title":"Dissemination of clonally related Escherichia coli strains expressing extended-spectrum \u03b2-lactamase CTX-M-15","volume":"14","author":"Coque","year":"2008","journal-title":"Emerg. Infect. Dis."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1256","DOI":"10.1093\/cid\/cit503","article-title":"Escherichia coli sequence type 131 (ST131) subclone H 30 as an emergent multidrug-resistant pathogen among US veterans","volume":"57","author":"Colpan","year":"2013","journal-title":"Clin. Infect. Dis."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1002\/ardp.201100140","article-title":"Design, Synthesis and Evaluation of Anticonvulsant Activity of Pyridinyl-Pyrrolidones: A Pharmacophore Hybrid Approach","volume":"345","author":"Siddiqui","year":"2012","journal-title":"Arch. Pharm."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"30649","DOI":"10.1021\/acsami.8b09872","article-title":"Rationally developed metallogelators derived from pyridyl derivatives of NSAIDs displaying anti-inflammatory and anticancer activities","volume":"10","author":"Sarkar","year":"2018","journal-title":"ACS Appl. Mater. Interfaces."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"8430","DOI":"10.1021\/acs.inorgchem.7b01101","article-title":"Coordination-driven self-assembly using ditopic pyridyl\u2013pyrazolyl donor and p-cymene Ru (II) Acceptors: [2]Catenane synthesis and anticancer activities","volume":"56","author":"Jo","year":"2017","journal-title":"Inorg. Chem."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"3734","DOI":"10.1016\/j.tetlet.2017.08.030","article-title":"Preparation of bis (2-pyridyl) diselenide derivatives: Synthesis of selenazolo [5, 4-b] pyridines and unsymmetrical diorganyl selenides, and evaluation of antioxidant and anticholinesterasic activities","volume":"58","author":"Peglow","year":"2017","journal-title":"Tetrahedron Lett."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1207","DOI":"10.1002\/ps.3672","article-title":"Synthesis and insecticidal activities of novel pyrazole oxime ether derivatives with different substituted pyridyl rings","volume":"70","author":"Fu","year":"2014","journal-title":"Pest Manag. Sci."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1507","DOI":"10.1002\/jccs.201900198","article-title":"Synthesis, antimicrobial, and antioxidant activities of new pyridyl-and thiazolyl-bearing carbohydrazides","volume":"66","author":"Muluk","year":"2019","journal-title":"J. Chin. Chem. Soc."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/j.ejphar.2011.12.008","article-title":"Activation of \u03b17 nicotinic acetylcholine receptors persistently enhances hippocampal synaptic transmission and prevents A\u00df-mediated inhibition of LTP in the rat hippocampus","volume":"677","author":"Ondrejcak","year":"2012","journal-title":"Eur. J. Pharmacol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1042\/BJ20061638","article-title":"The power to reduce: Pyridine nucleotides\u2013small molecules with a multitude of functions","volume":"402","author":"Pollak","year":"2007","journal-title":"Biochem. J."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.molstruc.2005.10.025","article-title":"Synthesis, structural and conformational study of some amides derived from N-methylpiperazine","volume":"787","author":"Iriepa","year":"2006","journal-title":"J. Mol. Struct."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1021\/jo971347w","article-title":"A novel cleavage technique to generate small molecule compounds and libraries via a two-resin system","volume":"63","author":"Ouyang","year":"1998","journal-title":"J. Org. Chem."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1007\/s11243-005-2384-4","article-title":"Ambidentate behavior of pentadentate N, N\u2032-bis (2-hydroxyphenyl)-pyridine-2, 6-dicarboxamide towards transition metal (II) salts","volume":"30","author":"Gudasi","year":"2005","journal-title":"Transit. Met. Chem."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1703","DOI":"10.1039\/a902521i","article-title":"Acid-catalysed N\u2013alkyl heterolysis of tertiary pyridinecarboxamides and benzamides under mild conditions","volume":"2","author":"Auzeil","year":"1999","journal-title":"J. Chem. Soc. Perkin Trans."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"933","DOI":"10.1128\/CMR.14.4.933-951.2001","article-title":"Extended-spectrum \u03b2-lactamases in the 21st century: Characterization, epidemiology, and detection of this important resistance threat","volume":"14","author":"Bradford","year":"2001","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"103662","DOI":"10.1016\/j.arabjc.2021.103662","article-title":"Arylation of halogenated thiophene carboxylate via Suzuki\u2013Miyaura reaction: Anti-bacterial study against clinically isolated extensively drug resistant Escherichia coli sequence type 405 and computational investigation","volume":"15","author":"Mujahid","year":"2022","journal-title":"Arab. J. Chem."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"103270","DOI":"10.1016\/j.arabjc.2021.103270","article-title":"Facile synthesis of 4-aryl-N-(5-methyl-1H-pyrazol-3-yl) benzamides via Suzuki Miyaura reaction: Antibacterial activity against clinically isolated NDM-1-positive bacteria and their Docking Studies","volume":"14","author":"Ahmad","year":"2021","journal-title":"Arab. J. Chem."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"841","DOI":"10.3390\/ph15070841","article-title":"Synthesis of Functionalized N-(4-Bromophenyl) furan-2-carboxamides via Suzuki-Miyaura Cross-Coupling: Anti-Bacterial Activities against Clinically Isolated Drug Resistant A. baumannii, K. pneumoniae, E. cloacae and MRSA and Its Validation via a Computational Approach","volume":"15","author":"Siddiqa","year":"2022","journal-title":"Pharmaceuticals"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"103216","DOI":"10.1016\/j.bioorg.2019.103216","article-title":"Synthesis, in-vitro cholinesterase inhibition, in-vivo anticonvulsant activity and in-silico exploration of N-(4-methylpyridin-2-yl) thiophene-2-carboxamide analogs","volume":"92","author":"Ahmad","year":"2019","journal-title":"Bioorg. Chem."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1775","DOI":"10.5897\/AJMR2015.7895","article-title":"Extended spectrum-\u00ce\u00b2-lactamase producing Escherichia coli and Klebsiella pneumoniae causing urinary tract infection","volume":"10","author":"Batool","year":"2016","journal-title":"Afr. J. Microbiol. Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"805","DOI":"10.2147\/IDR.S296219","article-title":"The Escherichia coli sequence type 131 harboring extended-spectrum beta-lactamases and carbapenemases genes from poultry birds","volume":"14","author":"Ilyas","year":"2021","journal-title":"Infect. Drug Resist."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"417","DOI":"10.3389\/fmicb.2016.00417","article-title":"Escherichia coli \u03b2-lactamases: What really matters","volume":"7","author":"Bajaj","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2007","DOI":"10.3389\/fmicb.2016.02007","article-title":"A mechanism of synergistic effect of streptomycin and cefotaxime on CTX-M-15 type \u03b2-lactamase producing strain of E. cloacae: A first report","volume":"7","author":"Maryam","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1186","DOI":"10.1016\/j.ijbiomac.2018.05.153","article-title":"Combination of aztreonam and cefotaxime against CTX-M-15 type \u03b2-lactamases: A mechanism based effective therapeutic approach","volume":"116","author":"Maryam","year":"2018","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"e01793-21","DOI":"10.1128\/mbio.01793-21","article-title":"Penicillanic Acid Sulfones Inactivate the Extended-Spectrum b-Lactamase CTX-M-15 through Formation of a Serine-Lysine Cross-Link: An Alternative Mechanism of b-Lactamase Inhibition","volume":"13","author":"Hinchliffe","year":"2022","journal-title":"Mbio"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"D297","DOI":"10.1093\/nar\/gkt1208","article-title":"MMDB and VAST+: Tracking structural similarities between macromolecular complexes","volume":"42","author":"Madej","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_37","unstructured":"CcG, C. (2016). Molecular Operating Environment (MOE), Chem Comput Gr Inc."},{"key":"ref_38","unstructured":"Kelly, K. (2013). 3D Bioinformatics and Comparative Protein Modeling in MOE, Chem Comput Group."},{"key":"ref_39","unstructured":"Molecular Operating Environment (MOE) (2019). Chemical Computing Group ULC, 1010 Sherbooke St. West, Suite# 910, MOE."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"9977","DOI":"10.3390\/molecules20069977","article-title":"DockBench: An integrated informatic platform bridging the gap between the robust validation of docking protocols and virtual screening simulations","volume":"20","author":"Cuzzolin","year":"2015","journal-title":"Molecules"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Attique, S.A., Hassan, M., Usman, M., Atif, R.M., Mahboob, S., Al-Ghanim, K.A., Bilal, M., and Nawaz, M.Z. (2019). A molecular docking approach to evaluate the pharmacological properties of natural and synthetic treatment candidates for use against hypertension. Int. J. Environ. Res. Public Health, 16.","DOI":"10.3390\/ijerph16060923"},{"key":"ref_42","unstructured":"Biovia, D.S. (2022, December 10). Discovery Studio Modeling Environment. Release: 2017. Available online: https:\/\/www.3ds.com\/."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1701","DOI":"10.1002\/jcc.20291","article-title":"GROMACS: Fast, flexible, and free","volume":"26","author":"Lindahl","year":"2005","journal-title":"J. Comput. Chem."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"13046","DOI":"10.1002\/jcb.28575","article-title":"Interaction and molecular dynamics simulation study of Osimertinib (AstraZeneca 9291) anticancer drug with the EGFR kinase domain in native protein and mutated L844V and C797S","volume":"120","author":"Assadollahi","year":"2019","journal-title":"J. Cell. Biochem."}],"container-title":["Molecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1420-3049\/28\/7\/3118\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T19:07:58Z","timestamp":1760123278000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1420-3049\/28\/7\/3118"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,3,31]]},"references-count":44,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2023,4]]}},"alternative-id":["molecules28073118"],"URL":"https:\/\/doi.org\/10.3390\/molecules28073118","relation":{},"ISSN":["1420-3049"],"issn-type":[{"value":"1420-3049","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,3,31]]}}}