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Kumar H, Sharma A, Kumar D, Marwaha MG, Dhanawat M, Aggarwal N, Marwaha RK. Synthesis, biological evaluation and in silico studies of some new analogues of 3,5-vdisubstituted thiazolidin-2,4-dione. Future Med Chem 2023; 15:2257-2268. [PMID: 37982252 DOI: 10.4155/fmc-2023-0237] [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: 08/12/2023] [Accepted: 10/30/2023] [Indexed: 11/21/2023] Open
Abstract
Background: A new series of 3,5-disubstituted thiazolidin-2,4-dione molecules were derived and characterized using various spectral techniques (1H NMR, IR, carbon, hydrogen, nitrogen, etc.) and physicochemical parameters. Materials & methods: The molecules were derived using Knoevenagel condensation followed by Mannich reaction and further synthesized analogues were screened for their antioxidant and antimicrobial potential using 2,2-diphenyl-1-picrylhydrazyl free radical scavenging method and serial tube dilution method, respectively, along with in silico studies (docking and absorption, distribution, metabolism and excretion parameters) to explore the drug-receptor interaction and druglikeness. Results & conclusion: In antimicrobial screening, the analogs MP2, MM6, MM7 and MM8 displayed promising activity while molecule MM4 exhibited better antioxidant potential in the series. In molecular docking analysis, the best-fitted analogs, namely, MM6 and MM7, showed good interactions.
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Affiliation(s)
- Harsh Kumar
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, 124001, India
- Vaish Institute of Pharmaceutical Education and Research, Rohtak, 124001, India
| | - Aastha Sharma
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, 124001, India
| | - Davinder Kumar
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, 124001, India
| | - Minakshi Gupta Marwaha
- Department of Pharmaceutical Sciences, Sat Priya College of Pharmacy, Rohtak, 124001, India
| | - Meenakshi Dhanawat
- Àmity institute of Pharmacy, Amity University Haryana, Gurugram, 122105, India
| | - Navidha Aggarwal
- MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, 133207, India
| | - Rakesh Kumar Marwaha
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, 124001, India
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Joshi RP, Schultz KJ, Wilson JW, Kruel A, Varikoti RA, Kombala CJ, Kneller DW, Galanie S, Phillips G, Zhang Q, Coates L, Parvathareddy J, Surendranathan S, Kong Y, Clyde A, Ramanathan A, Jonsson CB, Brandvold KR, Zhou M, Head MS, Kovalevsky A, Kumar N. AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2. J Chem Inf Model 2023; 63:1438-1453. [PMID: 36808989 PMCID: PMC9969887 DOI: 10.1021/acs.jcim.2c01377] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/23/2023]
Abstract
Direct-acting antivirals for the treatment of the COVID-19 pandemic caused by the SARS-CoV-2 virus are needed to complement vaccination efforts. Given the ongoing emergence of new variants, automated experimentation, and active learning based fast workflows for antiviral lead discovery remain critical to our ability to address the pandemic's evolution in a timely manner. While several such pipelines have been introduced to discover candidates with noncovalent interactions with the main protease (Mpro), here we developed a closed-loop artificial intelligence pipeline to design electrophilic warhead-based covalent candidates. This work introduces a deep learning-assisted automated computational workflow to introduce linkers and an electrophilic "warhead" to design covalent candidates and incorporates cutting-edge experimental techniques for validation. Using this process, promising candidates in the library were screened, and several potential hits were identified and tested experimentally using native mass spectrometry and fluorescence resonance energy transfer (FRET)-based screening assays. We identified four chloroacetamide-based covalent inhibitors of Mpro with micromolar affinities (KI of 5.27 μM) using our pipeline. Experimentally resolved binding modes for each compound were determined using room-temperature X-ray crystallography, which is consistent with the predicted poses. The induced conformational changes based on molecular dynamics simulations further suggest that the dynamics may be an important factor to further improve selectivity, thereby effectively lowering KI and reducing toxicity. These results demonstrate the utility of our modular and data-driven approach for potent and selective covalent inhibitor discovery and provide a platform to apply it to other emerging targets.
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Affiliation(s)
- Rajendra P. Joshi
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Katherine J. Schultz
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Jesse William Wilson
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Agustin Kruel
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Rohith Anand Varikoti
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Chathuri J. Kombala
- Elson S. Floyd College of Medicine, Department of
Nutrition and Exercise Physiology, Washington State University,
Spokane, Washington 99202, United States
| | - Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Stephanie Galanie
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Biosciences Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United
States
- Department of Process Research and Development,
Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New
Jersey 07065, United States
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Leighton Coates
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Second Target Station, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United
States
| | - Jyothi Parvathareddy
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
| | - Surekha Surendranathan
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
| | - Ying Kong
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
| | - Austin Clyde
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
| | - Arvind Ramanathan
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
| | - Colleen B. Jonsson
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
- Institute for the Study of Host-Pathogen Systems,
University of Tennessee Health Science Center, Memphis,
Tennessee 38103, United States
- Department of Microbiology, Immunology and
Biochemistry, University of Tennessee Health Science Center,
Memphis, Tennessee 38103, United States
| | - Kristoffer R. Brandvold
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- Elson S. Floyd College of Medicine, Department of
Nutrition and Exercise Physiology, Washington State University,
Spokane, Washington 99202, United States
| | - Mowei Zhou
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Martha S. Head
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Joint Institute for Biological Sciences,
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,
United States
- Center for Research Acceleration by Digital
Innovation, Amgen Research, Thousand Oaks, California 91320,
United States
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Neeraj Kumar
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
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3
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Kumar H, Kumar D, Kumar P, Thareja S, Marwaha MG, Navik U, Marwaha RK. Synthesis, biological evaluation and in-silico ADME studies of novel series of thiazolidin-2,4-dione derivatives as antimicrobial, antioxidant and anticancer agents. BMC Chem 2022; 16:68. [PMID: 36109764 PMCID: PMC9479363 DOI: 10.1186/s13065-022-00861-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/30/2022] [Indexed: 11/22/2022] Open
Abstract
Background A novel series of thiazolidine-2,4-dione molecules was derived and their chemical structures were established using physiochemical parameters and spectral techniques (1H-NMR, IR, MS etc.). The synthesized molecule were then evaluated for their antioxidant, anticancer and antimicrobial potential. Results and discussion Serial tube dilution method was employed to evaluate the antimicrobial potential against selected fungal and bacterial strains by taking fluconazole and cefadroxil as reference antifungal and antibacterial drugs respectively. 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging activity was used to assess the antioxidant potential of the synthesized analogues. Further, the anticancer potential of the selected molecules was assessed against DU-145 cancer cell lines using MTT assay. The drug-likeness was also evaluated by studying in-silico ADME parameters of the synthesized analogues. Conclusion In antioxidant evaluation studies, the analogue H5 with IC50 = 14.85 μg/mL was found to be the most active molecule. The antimicrobial evaluation outcomes suggested that the molecules H5, H13, H15 and H18 possessed moderate to promising activity against the selected species of microbial strains having MIC range 7.3 µM to 26.3 µM. The results of anticancer evaluation revealed that all the screened derivatives possess mild anticancer potential. The in-silico ADME studies revealed that all the compounds were found to be drug-like.
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