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Elkanzi NAA, Hrichi H, Muqbil Alsirhani A, Bakr RB. Antioxidant and Antimicrobial Potential of 1,8-Naphthyridine Based Scaffolds: Design, Synthesis and in Silico Simulation Studies within Topoisomerase II. Chem Biodivers 2024; 21:e202301746. [PMID: 38459958 DOI: 10.1002/cbdv.202301746] [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: 11/08/2023] [Revised: 01/24/2024] [Accepted: 03/09/2024] [Indexed: 03/11/2024]
Abstract
A series of spiro β-Lactams (4 a-c, 7 a-c) and thiazolidinones (5 a-c, 8 a-c) possessing 1,8-naphthyridine moiety were synthesized in this study. The structure of the newly synthesized compounds has been confirmed by IR, 1H-NMR, 13C NMR, mass spectra, and elemental analysis. The synthesized compounds were tested in vitro for their antibacterial and antifungal activity against various strains. The antimicrobial data showed that most of the compounds displayed good efficacy against both bacteria and fungi. The structure-activity relationship (SAR) studies suggested that the presence of electron-withdrawing chloro (3 b, 4 b, and 5 b) and nitro groups (7 b, 8 b) at the para position of the phenyl ring improved the antimicrobial activity of the compounds. The free radical scavenging assay showed that all the synthesized compounds exhibited significant antioxidant activity on DPPH. Compounds 8 b (IC50=17.68±0.76 μg/mL) and 4 c (IC50=18.53±0.52 μg/mL) showed the highest antioxidant activity compared to ascorbic acid (IC50=15.16±0.43 μg/mL). Molecular docking studies were also conducted to support the antimicrobial and SAR results.
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Affiliation(s)
- Nadia A A Elkanzi
- Chemistry Department, college of Science, Jouf University, 2014, Sakaka, Saudi Arabia
| | - Hajer Hrichi
- Chemistry Department, college of Science, Jouf University, 2014, Sakaka, Saudi Arabia
| | - Alaa Muqbil Alsirhani
- Chemistry Department, college of Science, Jouf University, 2014, Sakaka, Saudi Arabia
| | - Rania B Bakr
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Beni-Suef University, 62514, Beni-Suef, Egypt
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Chitre TS, Mandot AM, Bhagwat RD, Londhe ND, Suryawanshi AR, Hirode PV, Bhatambrekar AL, Choudhari SY. 2,4,6-Trimethoxy chalcone derivatives: an integrated study for redesigning novel chemical entities as anticancer agents through QSAR, molecular docking, ADMET prediction, and computational simulation. J Biomol Struct Dyn 2024:1-24. [PMID: 38321946 DOI: 10.1080/07391102.2024.2309644] [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: 08/11/2023] [Accepted: 01/18/2024] [Indexed: 02/08/2024]
Abstract
QSAR, an efficient and successful approach for optimizing lead compounds in drug design, was employed to study a reported series of compounds derived from 2,4,6-trimethoxy chalcone derivatives. The ability of these compounds to inhibit CDK1 was examined, with the help of QSARINS software for model development. The generated QSAR model revealed three significant descriptors, exhibiting strong correlations with impressive statistical values: cross-validation leave-one-out correlation coefficient (Q2LOO) = 0.6663, coefficient of determination (R2) = 0.7863, external validation coefficient (R2ext) = 0.7854, cross-validation leave-many-out correlation coefficient (Q2LMO) = 0.6256, Concordance Correlation Coefficient for cross-validation (CCCcv) = 0.8150, CCCtr = 0.8804, and CCCext = 0.8750. From the key structural findings and the insights gained from the descriptors, ETA_dPsi_A, WTPT-5, and GATS7s, new lead molecules were designed. The designed molecules were then evaluated for their CDK1 inhibitory activity using the three-descriptor model developed in this study. To evaluate their drug likeliness, in-silico ADMET predictions were made using Schrodinger's Software. Molecular docking was carried out to determine the interactions of designed compounds with the target protein. The designed compounds having excellent binding pocket molecular stability and anticancer effectiveness was substantiated by the findings of the molecular dynamics simulation. The results of this work point out important properties and crucial interactions necessary for efficient protein inhibition, suggesting lead candidates for further development as novel anticancer agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Trupti S Chitre
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - Aayush M Mandot
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - Ramali D Bhagwat
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - Nikhil D Londhe
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - Atharva R Suryawanshi
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - Purvaj V Hirode
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - Aniket L Bhatambrekar
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - Somdutta Y Choudhari
- Department of Pharmaceutical Chemistry, Modern College of Pharmacy, Pune, Maharashtra, India
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Chitre TS, Hirode PV, Lokwani DK, Bhatambrekar AL, Hajare SG, Thorat SB, Priya D, Pradhan KB, Asgaonkar KD, Jain SP. In-silico studies of 2-aminothiazole derivatives as anticancer agents by QSAR, molecular docking, MD simulation and MM-GBSA approaches. J Biomol Struct Dyn 2023:1-19. [PMID: 37811574 DOI: 10.1080/07391102.2023.2262594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/17/2023] [Indexed: 10/10/2023]
Abstract
Targeting Hec1/Nek2 is considered as crucial target for cancer treatment due to its significant role in cell proliferation. In pursuit of this, a series of twenty-five 2-aminothiazoles derivatives, along with their Hec1/Nek2 inhibitory activities were subjected to QSAR studies utilizing QSARINS software. The significant three descriptor QSAR model was generated, showing noteworthy statistical parameters: a correlation coefficient of cross validation leave one out (Q2LOO) = 0.7965, coefficient of determination (R2) = 0.8436, (R2ext) = 0.6308, cross validation leave many out (Q2LMO) = 0.7656, Concordance Correlation Coefficient (CCCCV = 0.8875), CCCtr = 0.9151, and CCCext = 0.0.7241. The descriptors integral to generated QSAR model include Moreau-Broto autocorrelation, which represents the spatial autocorrelation of a property along the molecular graph's topological structure (ATSC1i), Moran autocorrelation at lag 8, which is weighted by charges (MATS8c) and RPSA representing the total molecular surface area. It was noted that these descriptors significantly influence Hec1/Nek2 inhibitory activity of 2-aminothiazoles derivatives. New lead molecules were designed and predicted for their Hec1/Nek2 inhibitory activity based on the developed three descriptor model. Further, the ADMET and Molecular docking studies were carried out for these designed molecules. The three molecules were selected based on their docking score and further subjected for MD simulation studies. Post-MD MM-GBSA analysis were also performed to predicted the free binding energies of molecules. The study helped us to understand the key interactions between 2-aminothiazoles derivatives and Hec1/Nek2 protein that may be necessary to develop new lead molecules against cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Trupti S Chitre
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - Purvaj V Hirode
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - Deepak K Lokwani
- Rajarshi Shahu College of Pharmacy, Buldhana, Maharashtra, India
| | - Aniket L Bhatambrekar
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - Sayli G Hajare
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - Shubhangi B Thorat
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - D Priya
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRMIST, Kattankulathur, Tamilnadu, India
| | - Kunal B Pradhan
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - Kalyani D Asgaonkar
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - Shirish P Jain
- Rajarshi Shahu College of Pharmacy, Buldhana, Maharashtra, India
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Raza MA, Farwa U, Ishaque F, Al-Sehemi AG. Designing of thiazolidinones against chicken pox, monkey pox, and hepatitis viruses: A computational approach. Comput Biol Chem 2023; 103:107827. [PMID: 36805155 PMCID: PMC9922439 DOI: 10.1016/j.compbiolchem.2023.107827] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/14/2023]
Abstract
Computational designing of four different series (D-G) of thiazolidinone was done starting from different amines which was further condensed with various aldehydes. These underwent in silico molecular investigations for density functional theory (DFT), molecular docking, and absorption, distribution metabolism, excretion, and toxicity (ADMET) studies. The different electrochemical parameters of the compounds are predicted using quantum mechanical modeling approach with Gaussian. The docking software was used to dock the compounds against choosing PDB file for chickenpox, human immunodeficiency, hepatitis, and monkeypox virus as 1OSN, 1VZV, 6VLK, 1RTD, 3I7H, 3TYV, 4JU3, and 4QWO, respectively. The molecular interactions were visualized with discovery studio and maximum binding affinity was observed with D8 compounds against 4QWO (-13.383 kcal/mol) while for compound D5 against 1VZV which was -12.713 kcal/mol. Swiss ADME web tool was used to assess the drug-likeness of the designed compounds under consideration, and it is concluded that these molecules had a drug-like structure with almost zero violations.
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Affiliation(s)
- Muhammad Asam Raza
- Department of Chemistry, Hafiz Hayat Campus, University of Gujrat, Gujrat, Pakistan.
| | - Umme Farwa
- Department of Chemistry, Hafiz Hayat Campus, University of Gujrat, Gujrat, Pakistan
| | - Fatima Ishaque
- Department of Chemistry, Hafiz Hayat Campus, University of Gujrat, Gujrat, Pakistan
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Patil SM, Asgaonkar KD, Bakhle B, Abhang K, Khater A, Singh M, Chitre TS. In search of HIV entry inhibitors using molecular docking, ADME and toxicity studies of some Thiazolidinone-Pyrazine derivatives against CXCR4 co-receptor. Curr HIV Res 2022; 20:152-162. [PMID: 35156573 DOI: 10.2174/1570162x20666220214123331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 12/07/2021] [Accepted: 01/10/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Entry inhibitors prevent binding of human immunodeficiency virus protein to the chemokine receptor CXCR4 and are used along with conventional anti-HIV therapy. They aid in restoring immunity and can prevent the development of HIV-TB co-infection. AIM In the present study various thiazolidinone-pyrazine derivatives earlier studied for NNRT inhibition activity were gauged for their entry inhibitor potential. OBJECTIVE Objective of the study is to perform molecular docking, ADME, toxicity studies of some Thiazolidinone-Pyrazine Derivatives as entry inhibitors targeting CXCR4 co-receptors. METHODS In-silico docking studies were performed using AutoDock Vina software and compounds were further studied for ADME and toxicity using SwissADME and pkCSM software respectively. RESULTS Taking into consideration the docking results, pharmacokinetic behaviour and toxicity profile four molecules (compound 1, 9, 11 and 16) have shown potential as entry inhibitors. CONCLUSION These compounds have shown potential as both NNRTI and entry inhibitors and hence can be used in management of immune compromised diseases like TB-HIV coinfection.
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Affiliation(s)
- Shital M Patil
- AISSMS College of Pharmacy, Kennedy Road, Pune-01, India
| | | | | | | | - Ayush Khater
- AISSMS College of Pharmacy, Kennedy Road, Pune-01, India
| | - Muskan Singh
- AISSMS College of Pharmacy, Kennedy Road, Pune-01, India
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Sang Y, Pannecouque C, De Clercq E, Zhuang C, Chen F. Pharmacophore-fusing design of pyrimidine sulfonylacetanilides as potent non-nucleoside inhibitors of HIV-1 reverse transcriptase. Bioorg Chem 2020; 96:103595. [PMID: 32006797 DOI: 10.1016/j.bioorg.2020.103595] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 01/14/2020] [Accepted: 01/18/2020] [Indexed: 11/28/2022]
Abstract
Twenty-seven derivatives (40-66) were generated by pharmacophore fusing of sulfonylacetanilide-diarylpyrimidine (1) with rilpivirine or biphenyl-diarylpyrimidines. They displayed up to single-digit nanomolar activity against wild-type (WT) virus and various drug-resistant mutant strains in HIV-1-infected MT-4 cells, thereby targeting the reverse transcriptase (RT) enzyme. Compound 51 displayed exceptionally potent activity against WT virus (EC50 = 6 nM) and several mutant strains (L100I, EC50 = 8 nM, K103N, EC50 = 6 nM, Y181C, EC50 = 26 nM, Y188L, EC50 = 122 nM, E138K, EC50 = 26 nM). The structure-activity relationships of the newly obtained pyrimidine sulfonylacetanilides were also elucidated. Molecular docking analysis explained the activity and provided a structural insight for follow-up research.
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Affiliation(s)
- Yali Sang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, People's Republic of China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, People's Republic of China
| | | | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Chunlin Zhuang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, People's Republic of China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, People's Republic of China.
| | - Fener Chen
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, People's Republic of China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, People's Republic of China; Institute of Pharmaceutical Science and Technology, Zhejiang University of Technology, 18 Chao Wang Road, 310014 Hangzhou, People's Republic of China.
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