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Singh K, Singh VK, Mishra R, Sharma A, Pandey A, Srivastava SK, Chaurasia H. Design, Synthesis, DFT, docking Studies, and antimicrobial evaluation of novel benzimidazole containing sulphonamide derivatives. Bioorg Chem 2024; 149:107473. [PMID: 38820940 DOI: 10.1016/j.bioorg.2024.107473] [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: 03/26/2024] [Revised: 05/05/2024] [Accepted: 05/16/2024] [Indexed: 06/02/2024]
Abstract
In silico approaches have been employed to design a new series of benzimidazole-containing sulphonamide derivatives and qualified compounds have been synthesized to analyze their potential as antimicrobial agents. Antibacterial screening of all synthesized compounds was done using the broth microdilution method against several human pathogenic bacteria, viz. Gram-positive bacteria [B. cerus (NCIN-2156), B. subtilis (ATCC-6051), S. aureus (NCIM-2079)] and Gram-negative bacteria [P. aeruginosa (NCIM-2036), E. coli (NCIM-2065), and a drug-resistant strain of E. coli (U-621)], and the compounds presented admirable MIC values, ranging between 100-1.56 µg/mL. The combinatorial analysis showed the magnificent inhibitory efficiency of the tested compounds, acquired equipotent to ten-fold more potency compared to original MIC values. An immense synergistic effect was exhibited by the compounds during combination studies with reference drugs chloramphenicol and sulfamethoxazole was presented as fractional inhibitory concentration (∑FIC). Enzyme inhibition studies of all synthesized compounds were done by using peptidyl transferase and dihydropteroate synthase enzymes isolated from E. coli and S. aureus and each of the compound presented the admirable IC50 values, where the lead compound 3 bound to peptidyl transferase (of S. aureus with IC50 363.51 ± 2.54 µM and E. coli IC50 1.04 ± 0.08 µM) & dihydropteroate synthase (of S. aureus IC50 3.51 ± 0.82 µM and E. coli IC50 2.77 ± 0.65 µM), might account for the antimicrobial effect, exhibited excellent inhibition potential. Antifungal screening was also performed employing food poisoning methods against several pathogenic fungal species, viz A. flavus, F. oxysporum, A. niger, and A. brassicae. The obtained result indicated that few compounds can prove to be a potent drug regimen against dreaded MDR strains of microbes. Structural activity relationship (SAR) analysis and docking studies reveal that the presence of electron-withdrawing, polar, and more lipophilic substituents positively favor the antibacterial activity, whereas, electron-withdrawing, more polar, and hydrophilic substituents favor the antifungal activities. A robust coherence has been found in in-silico and in-vitro biological screening results of the compounds.
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Affiliation(s)
- Kajal Singh
- Photophysical and Therapeutic Laboratory, Department of Chemistry, C.M.P. Degree College (A constituent P.G. College of University of Allahabad), Prayagraj 211002, India
| | - Vishal K Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Richa Mishra
- Bio-organic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj 211002, India
| | - Ashwani Sharma
- Photophysical and Therapeutic Laboratory, Department of Chemistry, C.M.P. Degree College (A constituent P.G. College of University of Allahabad), Prayagraj 211002, India
| | - Archana Pandey
- Photophysical and Therapeutic Laboratory, Department of Chemistry, C.M.P. Degree College (A constituent P.G. College of University of Allahabad), Prayagraj 211002, India
| | - Santosh K Srivastava
- Photophysical and Therapeutic Laboratory, Department of Chemistry, C.M.P. Degree College (A constituent P.G. College of University of Allahabad), Prayagraj 211002, India
| | - Himani Chaurasia
- Photophysical and Therapeutic Laboratory, Department of Chemistry, C.M.P. Degree College (A constituent P.G. College of University of Allahabad), Prayagraj 211002, India.
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Srivastava R, Panda SK, Sen Gupta PS, Chaudhary A, Naaz F, Yadav AK, Ram NK, Rana MK, Singh RK, Srivastava R. In silico evaluation of S-adenosyl-L-homocysteine analogs as inhibitors of nsp14-viral cap N7 methyltranferase and PLpro of SARS-CoV-2: synthesis, molecular docking, physicochemical data, ADMET and molecular dynamics simulations studies. J Biomol Struct Dyn 2023:1-18. [PMID: 38147408 DOI: 10.1080/07391102.2023.2297005] [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: 07/18/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023]
Abstract
A series of S-adenosyl-L-homosysteine (SAH) analogs, with modification in the base and sugar moiety, have been designed, synthesized and screened as nsp14 and PLpro inhibitors of severe acute respiratory syndrome corona virus (SARS-CoV-2). The outcomes of ADMET (Adsorption, Distribution, Metabolism, Excretion, and Toxicity) studies demonstrated that the physicochemical properties of all analogs were permissible for development of these SAH analogs as antiviral agents. All molecules were screened against different SARS-CoV-2 targets using molecular docking. The docking results revealed that the SAH analogs interacted well in the active site of nsp14 protein having H-bond interactions with the amino acid residues Arg289, Val290, Asn388, Arg400, Phe401 and π-alkyl interactions with Arg289, Val290 and Phe426 of Nsp14-MTase site. These analogs also formed stable H-bonds with Leu163, Asp165, Arg167, Ser246, Gln270, Tyr274 and Asp303 residues of PLpro proteins and found to be quite stable complexes therefore behaved as probable nsp14 and PLpro inhibitors. Interestingly, analog 3 showed significant in silico activity against the nsp14 N7 methyltransferase of SARS-CoV-2. The molecular dynamics (MD) and post-MD results of analog 3 unambiguously established the higher stability of the nsp14 (N7 MTase):3 complex and also indicated its behavior as probable nsp14 inhibitor like the reference sinefungin. The docking and MD simulations studies also suggested that sinefungin did act as SARS-CoV-2 PLpro inhibitor as well. This study's findings not only underscore the efficacy of the designed SAH analogs as potent inhibitors against crucial SARS-CoV-2 proteins but also pinpoint analog 3 as a particularly promising candidate. All the study provides valuable insights, paving the way for potential advancements in antiviral drug development against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ritika Srivastava
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Odisha, India
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, India
| | - Saroj Kumar Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Odisha, India
| | - Parth Sarthi Sen Gupta
- School of Biosciences and Bioengineering, D Y Patil International University, Akurdi, India
| | - Anvita Chaudhary
- Department of Applied Chemistry, Delhi Technological University, Delhi, India
| | - Farha Naaz
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, India
| | - Aditya K Yadav
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, India
| | - Nand Kumar Ram
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Odisha, India
| | - Ramendra K Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, India
| | - Richa Srivastava
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, India
- Department of Applied Chemistry, Delhi Technological University, Delhi, India
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