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Shtaiwi A, Khan SU, Khedraoui M, Alaraj M, Samadi A, Chtita S. A comprehensive computational study to explore promising natural bioactive compounds targeting glycosyltransferase MurG in Escherichia coli for potential drug development. Sci Rep 2024; 14:7098. [PMID: 38532068 DOI: 10.1038/s41598-024-57702-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/21/2024] [Indexed: 03/28/2024] Open
Abstract
Peptidoglycan is a carbohydrate with a cross-linked structure that protects the cytoplasmic membrane of bacterial cells from damage. The mechanism of peptidoglycan biosynthesis involves the main synthesizing enzyme glycosyltransferase MurG, which is known as a potential target for antibiotic therapy. Many MurG inhibitors have been recognized as MurG targets, but high toxicity and drug-resistant Escherichia coli strains remain the most important problems for further development. In addition, the discovery of selective MurG inhibitors has been limited to the synthesis of peptidoglycan-mimicking compounds. The present study employed drug discovery, such as virtual screening using molecular docking, drug likeness ADMET proprieties predictions, and molecular dynamics (MD) simulation, to identify potential natural products (NPs) for Escherichia coli. We conducted a screening of 30,926 NPs from the NPASS database. Subsequently, 20 of these compounds successfully passed the potency, pharmacokinetic, ADMET screening assays, and their validation was further confirmed through molecular docking. The best three hits and the standard were chosen for further MD simulations up to 400 ns and energy calculations to investigate the stability of the NPs-MurG complexes. The analyses of MD simulations and total binding energies suggested the higher stability of NPC272174. The potential compounds can be further explored in vivo and in vitro for promising novel antibacterial drug discovery.
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Affiliation(s)
- Amneh Shtaiwi
- Faculty of Pharmacy, Middle East University, Queen Alia Airport Street, Amman, P.O. Box No. 11610, Jordan.
| | - Shafi Ullah Khan
- Interdisciplinary Research Unit for Cancer Prevention and Treatment, Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F‑14000 François 3 Avenue Général Harris, BP 45026, 14076, Cedex 05 Caen, France
- Centre François Baclesse, Avenue Général Harris, 14076, Caen Cedex, France
| | - Meriem Khedraoui
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, B. P 7955, Casablanca, Morocco
| | - Mohd Alaraj
- Faculty of Pharmacy, University of Jerash, Jerash, Jordan
| | - Abdelouahid Samadi
- Department of Chemistry, College of Science, UAEU, P.O. Box No. 15551, Al Ain, UAE.
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, B. P 7955, Casablanca, Morocco
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Saber S, Al-Qawasmeh RA, Abu-Qatouseh L, Shtaiwi A, Khanfar MA, Al-Soud YA. Novel hybrid motifs of 4-nitroimidazole-piperazinyl tagged 1,2,3-triazoles: Synthesis, crystal structure, anticancer evaluations, and molecular docking study. Heliyon 2023; 9:e19327. [PMID: 37681149 PMCID: PMC10480608 DOI: 10.1016/j.heliyon.2023.e19327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/08/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023] Open
Abstract
4-((4-(1-benzyl-2-methyl-4-nitro-1H-imidazole-5-yl)piperazine-1-yl)methyl)-1-substituted-1H-1,2,3-triazole motifs are designed and synthesized via click chemistry. The reaction of 1-(N1-benzyl- 2-methyl-4-nitro-1H-imidazole- 5-yl)-4-(prop-2-yn-1-yl) piperazine 5 as new scaffold with diverse primary azides to selectively produce 1,4-disubstituted-1,2,3-triazoles 9a-k, 10a-c and 11a-q. Physicochemical methods: when 1H NMR, 13C NMR, and HRMS are utilized to fully characterize all synthesized compounds. X-ray structural determination and analysis for compound 9a is also performed. The newly designed chromophores are assessed for their anti-proliferative potency against three selected human cancer cell lines (MCF-7, HepG2, and PC3), and one normal cell line (Dermal/Fibroblast). Compounds 9g and 9k have shown potent activities against the MCF-7 cell line with IC50 values of (2.00 ± 0.03 μM) and (5.00 ± 0.01 μM) respectively. ADMET studies and Molecular docking investigations are performed on the most active hybrid nitroimidazole derivatives 9g and 9k with 4-hydroxytamoxifen (4-OHT) at the human estrogen receptor alpha (hER) during binding active sites to study the ligand-protein interactions and free binding energies at atomic levels. The triazole ring in the 9g derivative forms a hydrogen bond with Asp58 with distance 3.2 Å. And it is found that polar contact with His231 amino acid residue. In silico assessment of the compounds showed very good pharmacokinetic properties based on their physicochemical values, also the ADMET criteria of the most active hybrid systems are within the acceptable range.
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Affiliation(s)
- SadeekahO.W. Saber
- Department of chemistry, School of Science, The University of Jordan, 11942, Amman, Jordan
- Faculty of Pharmacy, Jerash University, Amman-Irbid international highway, Jerash, 26150, Jordan
| | - Raed A. Al-Qawasmeh
- Department of chemistry, School of Science, The University of Jordan, 11942, Amman, Jordan
- Pure and Applied Chemistry Group, Department of Chemistry, College of Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | | | - Amneh Shtaiwi
- Faculty of Pharmacy, Middle East University, Queen Alia Airport Street, 11610, Amman, Jordan
| | - Monther A. Khanfar
- Department of chemistry, School of Science, The University of Jordan, 11942, Amman, Jordan
- Pure and Applied Chemistry Group, Department of Chemistry, College of Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Yaseen A. Al-Soud
- Chemistry Department, Faculty of Science, University of Al al-Bayt, Al-Mafraq, Jordan
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Abbasi BA, Dharan A, Mishra A, Saraf D, Ahamad I, Suravajhala P, Valadi J. In Silico Characterization of Uncharacterized Proteins From Multiple Strains of Clostridium Difficile. Front Genet 2022; 13:878012. [PMID: 36035185 PMCID: PMC9403866 DOI: 10.3389/fgene.2022.878012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
Clostridium difficile (C. difficile) is a multi-strain, spore-forming, Gram-positive, opportunistic enteropathogen bacteria, majorly associated with nosocomial infections, resulting in severe diarrhoea and colon inflammation. Several antibiotics including penicillin, tetracycline, and clindamycin have been employed to control C. difficile infection, but studies have suggested that injudicious use of antibiotics has led to the development of resistance in C. difficile strains. However, many proteins from its genome are still considered uncharacterized proteins that might serve crucial functions and assist in the biological understanding of the organism. In this study, we aimed to annotate and characterise the 6 C. difficile strains using in silico approaches. We first analysed the complete genome of 6 C. difficile strains using standardised approaches and analysed hypothetical proteins (HPs) employing various bioinformatics approaches coalescing, including identifying contigs, coding sequences, phage sequences, CRISPR-Cas9 systems, antimicrobial resistance determination, membrane helices, instability index, secretory nature, conserved domain, and vaccine target properties like comparative homology analysis, allergenicity, antigenicity determination along with structure prediction and binding-site analysis. This study provides crucial supporting information about the functional characterization of the HPs involved in the pathophysiology of the disease. Moreover, this information also aims to assist in mechanisms associated with bacterial pathogenesis and further design candidate inhibitors and bona fide pharmaceutical targets.
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Affiliation(s)
| | | | | | | | | | - Prashanth Suravajhala
- Bioclues.org, Hyderabad, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, India
- *Correspondence: Prashanth Suravajhala, ; Jayaraman Valadi,
| | - Jayaraman Valadi
- Bioclues.org, Hyderabad, India
- School of Computational and Data Sciences, Vidyashilp University, Bengaluru, India
- Department of Computer Science, FLAME University, Pune, India
- *Correspondence: Prashanth Suravajhala, ; Jayaraman Valadi,
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Sharma D, Sharma A, Singh B, Kumar S, Verma S. Neglected scrub typhus: An updated review with a focus on omics technologies. ASIAN PAC J TROP MED 2022. [DOI: 10.4103/1995-7645.364003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Sharma D, Sharma A, Verma SK, Singh B. Targeting metabolic pathways proteins of Orientia tsutsugamushi using combined hierarchical approach to combat scrub typhus. J Mol Recognit 2018; 32:e2766. [DOI: 10.1002/jmr.2766] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 09/04/2018] [Accepted: 09/15/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Dixit Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences; Central University of Himachal Pradesh; Shahpur, District-Kangra Himachal Pradesh India
| | - Ankita Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences; Central University of Himachal Pradesh; Shahpur, District-Kangra Himachal Pradesh India
| | - Shailender Kumar Verma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences; Central University of Himachal Pradesh; Shahpur, District-Kangra Himachal Pradesh India
| | - Birbal Singh
- ICAR-Indian Veterinary Research Institute, Regional Station; Palampur Himachal Pradesh India
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Novel Insight from Computational Virtual Screening Depict the Binding Potential of Selected Phytotherapeutics Against Probable Drug Targets of Clostridium difficile. Interdiscip Sci 2018; 10:583-604. [PMID: 28217823 DOI: 10.1007/s12539-017-0215-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 12/28/2016] [Accepted: 01/03/2017] [Indexed: 10/20/2022]
Abstract
This study explores computational screening and molecular docking approaches to screen novel herbal therapeutics against probable drug targets of Clostridium difficile. The essential genes were predicted by comparative genome analysis of C. difficile and best homologous organisms using BLAST search at database of essential genes (DEG). The functions of these genes in various metabolic pathways were predicted and some of these genes were considered as potential targets. Three major proteins were selected as putative targets, namely permease IIC component, ABC transporter and histidine kinase. The three-dimensional structures of these targets were predicted by molecular modelling. The herbal bioactive compounds were screened by computer-aided virtual screening and binding potentials against the drug targets were predicted by molecular docking. Quercetin present in Psidium guajava (binding energy of -9.1 kcal/mol), Ellagic acid found in Punica granatum and Psidium guajava (binding energy -9.0 kcal/mol) and Curcumin, present in Curcuma longa (binding energy -7.8 kcal/mol) demonstrated minimum binding energy and more number of interacting residues with the drug targets. Further, comparative study revealed that phytoligands demonstrated better binding affinities to the drug targets in comparison with usual ligands. Thus, this investigation explores the therapeutic probabilities of selected phytoligands against the putative drug targets of C. difficile.
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