1
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Al Neyadi S, Adem A, Amir N, Ghattas MA, Abdou IM, Salem AA. Novel Thiazolidinedione and Rhodanine Derivatives Regulate Glucose Metabolism, Improve Insulin Sensitivity, and Activate the Peroxisome Proliferator-Activated γ Receptor. ACS OMEGA 2024; 9:5463-5484. [PMID: 38343951 PMCID: PMC10851269 DOI: 10.1021/acsomega.3c07149] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 07/08/2024]
Abstract
Sixteen novel thiazolidinedione (TZD) and rhodanine (RD) derivatives were designed and synthesized by introducing a pyrimidine moiety at different sites of pioglitazone's structure. The effects of synthesized compounds on regulating glucose metabolism, improving insulin sensitivity, and activating the peroxisome proliferator-activated γ receptor (PPAR-γ) were evaluated in βTC6 cells. Compounds TZDs # 7a, 7b, 7c, and 29 reduced the basal insulin secretion by ∼20.0-67.0% and increased insulin secretion stimulated by glucose by ∼25.0-50.0% compared to control. Compounds TZDs # 14 and 21 and RDs # 33a-b and 33d-f increased basal insulin secretion by ∼20.0-100.0%, while its glucose-stimulated secretion remained unchanged. These findings suggested that the former compounds can act as antihypoglycemic during fasting and antihyperglycemic during postprandial conditions. The latter compounds should be administered before meals to avoid their hypoglycemic effect. Additionally, both TZDs and RDs improved insulin sensitivity by increasing glucose uptake by 17.0-155.0% relative to control. In silico molecular docking of synthesized drugs onto the PPAR-γ structure revealed exothermic binding modes through hydrogen bonding, van der Waals forces, and π-π stacking with binding affinities of -6.02 to -9.70 kcal/mol. Insights into the structure-activity relationship revealed that the introduction of pyrimidine linked to sulfonyl or peptide groups accounted for increased antidiabetic activity. These results demonstrated novel TZDs and RDs with high potency in stimulating insulin secretion, enhancing insulin sensitivity, and activating PPAR-γ relative to pioglitazone. They are recommended for further development as potential antidiabetic agents.
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Affiliation(s)
- Shaikha
S. Al Neyadi
- Department
of Chemistry, College of Science, United
Arab Emirates University, Al-Ain 15551, United Arab
Emirates
| | - Abdu Adem
- Department
of Pharmacology and Therapeutics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain 17666, United Arab Emirates
| | - Naheed Amir
- Department
of Pharmacology and Therapeutics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain 17666, United Arab Emirates
| | - Mohammad A. Ghattas
- College
of Pharmacy, Al Ain University, Abu Dhabi 112612, United Arab Emirates
| | - Ibrahim M. Abdou
- Department
of Chemistry, College of Science, United
Arab Emirates University, Al-Ain 15551, United Arab
Emirates
| | - Alaa A. Salem
- Department
of Chemistry, College of Science, United
Arab Emirates University, Al-Ain 15551, United Arab
Emirates
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2
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Chaurasyia A, Chawla P, Monga V, Singh G. Rhodanine derivatives: An insight into the synthetic and medicinal perspectives as antimicrobial and antiviral agents. Chem Biol Drug Des 2023; 101:500-549. [PMID: 36447391 DOI: 10.1111/cbdd.14163] [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: 07/20/2022] [Revised: 10/18/2022] [Accepted: 10/22/2022] [Indexed: 12/02/2022]
Abstract
Rhodanine or 2-Thioxothiazolidin-4-one is a privileged heterocyclic compound offering a wide opportunity for structural modification, lead development, and modification. It is one of the highly decorated scaffolds in the drug discovery process. Rhodanine derivatives possess a plethora of biological activities due to their ability to interact with a diverse range of protein targets, which provide tremendous opportunities to discover new drugs with different modes of action. The most common strategy for developing novel rhodanine derivatives is the introduction of structurally diverse substituents at the C-5 or N-3, or both positions. Since the inception of Epralestat into the market in 1992, the exploration of rhodanine-3-acetic acids has led to the development of novel leads against different biological targets such as MRSA, HHV-6, Mycobacterial tuberculosis, dengue, etc. In the current pandemic era, some rhodanine compounds have been explored against SARS-CoV-2. In recent years, rhodanine and its derivatives have witnessed significant progress in developing new drug leads as potential antimicrobial and antiviral agents. Different synthetic methodologies and recent developments in the medicinal chemistry of rhodanine derivatives, including biological activities, their mechanistic aspects, structure-activity relationships, and in silico findings, have been compiled in the present review. This article will benefit the scientific community and offer perspectives on how these scaffolds as privileged structures might be exploited in the future for rational design and discovery of rhodanine-based bio-active molecules.
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Affiliation(s)
- Abhishek Chaurasyia
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, Punjab, India
| | - Pooja Chawla
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, Punjab, India
| | - Vikramdeep Monga
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, India
| | - Gurpreet Singh
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, Punjab, India.,Research Scholar, IK Gujral Punjab Technical University, Kapurthala, Punjab, India
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3
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Green hemi-synthesis of novel thiazole derivatives from Ammodaucus leucotrichus Coss. & Dur. and Cuminum cyminum L. essential oils: stereochemistry, molecular fluorescence spectroscopy, in vitro biologicial activity, and molecular docking study. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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4
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Rhodanine scaffold: A review of antidiabetic potential and structure-activity relationships (SAR). MEDICINE IN DRUG DISCOVERY 2022. [DOI: 10.1016/j.medidd.2022.100131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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5
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Synthesis and Characterization of Novel Thiazolidinones and Thioxothiazolidinones Derived from Substituted Indole. MOLBANK 2021. [DOI: 10.3390/m1284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Based on recent discoveries concerning the numerous biological properties of thiazolidinones and thiosemicarbazones, new N-substituted heterocyclic derivatives have been designed by combining the indole ring with thioxothiazolidinone, thiazolidinone or thiosemicarbazone. Thus, a series of new thioxothiazolidinone, thiazolidinone, or thiosemicarbazone derivatives bearing indole-based moiety have been designed, synthesized, and developed in good yields.
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6
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Lee YW, Yeop J, Lim H, Park WW, Joung JF, Park S, Kwon OH, Kim JY, Woo HY. Fullerene-Based Triads with Controlled Alkyl Spacer Length as Photoactive Materials for Single-Component Organic Solar Cells. ACS APPLIED MATERIALS & INTERFACES 2021; 13:43174-43185. [PMID: 34460240 DOI: 10.1021/acsami.1c14901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Two kinds of dumbbell-shaped acceptor-donor-acceptor (A-D-A)-type triad single-component (SC) photovoltaic molecules based on a benzodithiophene-rhodanine (BDTRh) core and [6,6]-phenyl-C61 butyric acid (PC61BA) termini, BDTRh-C2-PC61BA and BDTRh-C10-PC61BA, were synthesized by modulating the alkyl (C2 and C10) spacer lengths. Both SC photovoltaic structures had similar UV-vis spectra in solution, but BDTRh-C10-PC61BA showed a significantly higher absorption coefficient as a thin film. In films, a more facile intermolecular photo-induced charge transfer was observed for BDTRh-C10-PC61BA in the broad-band transient absorption measurements. BDTRh-C10-PC61BA also exhibited a higher hole mobility (by 25 times) and less bimolecular recombination than BDTRh-C2-PC61BA. By plotting the normalized external quantum efficiency data, a higher charge-transfer state was measured for BDTRh-C10-PC61BA, reducing its voltage loss. A higher power conversion efficiency of ∼2% was obtained for BDTRh-C10-PC61BA, showing higher open-circuit voltage, short-circuit current density, and fill factor than those of BDTRh-C2-PC61BA devices. The different carrier dynamics, voltage loss, and optical and photoelectrical characteristics depending on the spacer length were interpreted in terms of the film morphology. The longer decyl spacer in BDTRh-C10-PC61BA afforded a significantly enhanced intermolecular ordering of the p-type core compared to BDTRh-C2-PC61BA, suggesting that the alkyl spacer length plays a critical role in controlling the intermolecular packing interaction.
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Affiliation(s)
- Young Woong Lee
- Department of Chemistry and Research Institute for Natural Science (RINS), Korea University, Anam-ro 145, Seoul 02841, Republic of Korea
| | - Jiwoo Yeop
- Department of Energy Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Hyojin Lim
- Department of Chemistry and Research Institute for Natural Science (RINS), Korea University, Anam-ro 145, Seoul 02841, Republic of Korea
| | - Won-Woo Park
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Joonyoung Francis Joung
- Department of Chemistry and Research Institute for Natural Science (RINS), Korea University, Anam-ro 145, Seoul 02841, Republic of Korea
| | - Sungnam Park
- Department of Chemistry and Research Institute for Natural Science (RINS), Korea University, Anam-ro 145, Seoul 02841, Republic of Korea
| | - Oh-Hoon Kwon
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jin Young Kim
- Department of Energy Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Han Young Woo
- Department of Chemistry and Research Institute for Natural Science (RINS), Korea University, Anam-ro 145, Seoul 02841, Republic of Korea
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Pan Z, An W, Wu L, Fan L, Yang G, Xu C. A New Synthesis Strategy for Rhodanine and Its Derivatives. Synlett 2021. [DOI: 10.1055/a-1485-5925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
AbstractRhodanine and its derivatives have been known as privileged structures in pharmacological research because of their wide spectrum of biological activities, but the synthesis method of rhodanine skeleton is limited. In this paper, not only rhodanine skeleton, but also N-aryl rhodanines can be directly prepared via the reaction of thioureas and thioglycolic acid in one step catalyzed by protic acid, which provides a new approach of the synthesis of rhodanine and its derivatives. The developed strategy is straightforward, efficient, atom economical, and convenient in good yields.
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8
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Kargar Razi M, Javahershenas R, Adelzadeh M, Ghobadi M, Kazemi M. Synthetic routes to rhodanine scaffolds. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1812658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Maryam Kargar Razi
- Faculty of Chemistry, North Branch of Tehran, Islamic Azad University, Tehran, Iran
| | - Ramin Javahershenas
- Department of Organic Chemistry, Chemistry Faculty, Urmia University, Urmia, Iran
| | | | - Massoud Ghobadi
- Central Laboratory, llam Petro Chemical Complex (ILPC), Chavar, Ilam, Iran
| | - Mosstafa Kazemi
- Young Researchers and Elite Club, Ilam Branch, Islamic Azad University, Ilam, Iran
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9
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A Concise Approach to N-Substituted Rhodanines through a Base-Assisted One-Pot Coupling and Cyclization Process. Molecules 2020; 25:molecules25051138. [PMID: 32143323 PMCID: PMC7179173 DOI: 10.3390/molecules25051138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 02/27/2020] [Accepted: 03/02/2020] [Indexed: 12/04/2022] Open
Abstract
An efficient approach to obtain functionalized rhodanines was developed through a base-assisted one-pot coupling and continuous cyclization of a primary amine, carbon disulfide, and methyl (2-chloroacetyl)carbamate. This conversion tolerates a broad range of functional groups and can be used to scale the preparation of N-substituted rhodanines in excellent yields.
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10
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Ali I, Lone MN, Alothman ZA, Badjah AY, Alanazi AG. Spectroscopic and In Silico DNA Binding Studies on the Interaction of Some New N-Substituted Rhodanines with Calf-thymus DNA: In Vitro Anticancer Activities. Anticancer Agents Med Chem 2019; 19:425-433. [PMID: 30277166 DOI: 10.2174/1871520618666181002131125] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 03/25/2018] [Accepted: 08/28/2018] [Indexed: 01/13/2023]
Abstract
BACKGROUND In this era of science, cancer is a black dot on the face of humankind. Consequently, the search of promising anticancer agents continues. AIMS Here we designed and synthesized new N-substituted rhodanines (RD1-7), evaluated their multispectroscopic interaction with calf thymus DNA, in silico and anticancer studies against MDA-MB-231cancer cell line. METHODS By MTT assay rhodanine RD1 was found to be the most potent with IC50 value of 72.61 μM. In addition, DNA binding studies (UV-vis and fluorescence) revealed strong binding affinity of RD1-7 with DNA (Kb in the range of 1.5-7.4 × 105 M-1). Moreover, molecular docking study, experimental DNA binding and anticancer studies are all well agreed to each other. RESULTS It was observed that H-bonding and hydrophobic attractions were responsible for stability of DNAcompound adducts. Besides, the reported rhodanines (RD1-7) were found as minor groove binders of DNA. Concisely, RD1-7 indicated promising pharmacological properties and hence, shows auspicious future for the development of novel anticancer agents. CONCLUSION The reported rhodanines showed excellent anticancer properties. Therefore, the described rhodanines may be used as potential anticancer agents in the future.
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Affiliation(s)
- Imran Ali
- Department of Chemistry, College of Sciences, Taibah University, Al-Medina Al-Munawara-41477, Saudi Arabia.,Department of Chemistry, Jamia Millia Islamia (Central University), New Delhi-110025, India
| | - Mohammad N Lone
- Department of Chemistry, College of Sciences, Taibah University, Al-Medina Al-Munawara-41477, Saudi Arabia
| | - Zeid A Alothman
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmad Y Badjah
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah G Alanazi
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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11
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Mermer A, Demirbas N, Cakmak U, Colak A, Demirbas A, Alagumuthu M, Arumugam S. Discovery of Novel Sulfonamide‐Based 5‐Arylidenerhodanines as Effective Carbonic Anhydrase (II) Inhibitors: Microwave‐Assisted and Ultrasound‐Assisted One‐Pot Four‐Component Synthesis, Molecular Docking, and Anti‐CA II Screening Studies. J Heterocycl Chem 2019. [DOI: 10.1002/jhet.3635] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Arif Mermer
- Department of ChemistryKaradeniz Technical University Trabzon Turkey
| | - Neslihan Demirbas
- Department of ChemistryKaradeniz Technical University Trabzon Turkey
| | - Ummuhan Cakmak
- Department of ChemistryKaradeniz Technical University Trabzon Turkey
| | - Ahmet Colak
- Department of ChemistryKaradeniz Technical University Trabzon Turkey
| | - Ahmet Demirbas
- Department of ChemistryKaradeniz Technical University Trabzon Turkey
| | | | - Sivakumar Arumugam
- Department of Biotechnology, School of Bio‐Science and TechnologyVIT Vellore India
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12
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Mermer A, Demirbas N, Colak A, Demir EA, Kulabas N, Demirbas A. One‐pot, Four‐Component Green Synthesis, Carbonic Anhydrase II Inhibition and Docking Studies of 5‐Arylidenerhodanines. ChemistrySelect 2018. [DOI: 10.1002/slct.201802677] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Arif Mermer
- Karadeniz Technical UniversityDepartment of Chemistry 61080 Trabzon TURKEY
| | - Neslihan Demirbas
- Karadeniz Technical UniversityDepartment of Chemistry 61080 Trabzon TURKEY
| | - Ahmet Colak
- Karadeniz Technical UniversityDepartment of Chemistry 61080 Trabzon TURKEY
| | | | - Necla Kulabas
- Department of Pharmaceutical ChemistryFaculty of PharmacyMarmara University Haydarpaşa 34668 İstanbul TURKEY
| | - Ahmet Demirbas
- Karadeniz Technical UniversityDepartment of Chemistry 61080 Trabzon TURKEY
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13
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Molnar M, Brahmbhatt H, Rastija V, Pavić V, Komar M, Karnaš M, Babić J. Environmentally Friendly Approach to Knoevenagel Condensation of Rhodanine in Choline Chloride: Urea Deep Eutectic Solvent and QSAR Studies on Their Antioxidant Activity. Molecules 2018; 23:E1897. [PMID: 30060629 PMCID: PMC6222480 DOI: 10.3390/molecules23081897] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/16/2018] [Accepted: 07/27/2018] [Indexed: 12/22/2022] Open
Abstract
A series of rhodanine derivatives was synthesized in the Knoevenagel condensation of rhodanine and different aldehydes using choline chloride:urea (1:2) deep eutectic solvent. This environmentally friendly and catalyst free approach was very effective in the condensation of rhodanine with commercially available aldehydes, as well as the ones synthesized in our laboratory. All rhodanine derivatives were subjected to 1,1-diphenyl-2-picrylhydrazyl radical (DPPH) scavenging activity investigation and quantitative structure-activity relationship (QSAR) studies were performed to elucidate their structure-activity relationship. The best multiple linear QSAR model demonstrate a stability in the internal validation and Y-randomization (R² = 0.81; F = 24.225; Q²loo = 0.72; R²Yscr = 0.148). Sphericity of the molecule, ratio of symmetric atoms enhanced atomic mass along the principle axes in regard to total number of atoms in molecule, and 3D distribution of the atoms higher electronegativity (O, N, and S) in molecules are important characteristic for antioxidant ability of rhodanine derivatives. Molecular docking studies were carried out in order to explain in silico antioxidant studies, a specific protein tyrosine kinase (2HCK). The binding interactions of the most active compound have shown strong hydrogen bonding and van der Waals interactions with the target protein.
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Affiliation(s)
- Maja Molnar
- Faculty of Food Technology Osijek, Josip Juraj Strossmayer University of Osijek, Franje Kuhaca 20, 31000 Osijek, Croatia.
| | - Harshad Brahmbhatt
- Faculty of Food Technology Osijek, Josip Juraj Strossmayer University of Osijek, Franje Kuhaca 20, 31000 Osijek, Croatia.
| | - Vesna Rastija
- Faculty of Agriculture, Josip Juraj Strossmayer University of Osijek, Vladimira Preloga 1, 31000 Osijek, Croatia.
| | - Valentina Pavić
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Cara Hadrijana 8/A, 31000 Osijek, Croatia.
| | - Mario Komar
- Faculty of Food Technology Osijek, Josip Juraj Strossmayer University of Osijek, Franje Kuhaca 20, 31000 Osijek, Croatia.
| | - Maja Karnaš
- Faculty of Agriculture, Josip Juraj Strossmayer University of Osijek, Vladimira Preloga 1, 31000 Osijek, Croatia.
| | - Jurislav Babić
- Faculty of Food Technology Osijek, Josip Juraj Strossmayer University of Osijek, Franje Kuhaca 20, 31000 Osijek, Croatia.
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Khalili B. Structural and energetic quantum chemical investigations into how the bioactive thiazolidinedione and rhodanine scaffolds interact with cytosine to form part of DNA. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2017.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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15
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S. Alneyadi S. Rhodanine as a Scaffold: A Short Review on Its Synthesis and Anti-Diabetic Activities. HETEROCYCLES 2018. [DOI: 10.3987/rev-17-878] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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16
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Kaur Manjal S, Kaur R, Bhatia R, Kumar K, Singh V, Shankar R, Kaur R, Rawal RK. Synthetic and medicinal perspective of thiazolidinones: A review. Bioorg Chem 2017; 75:406-423. [DOI: 10.1016/j.bioorg.2017.10.014] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 09/29/2017] [Accepted: 10/22/2017] [Indexed: 02/04/2023]
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17
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Yan Y, Wang W, Sun Z, Zhang JZH, Ji C. Protein-Ligand Empirical Interaction Components for Virtual Screening. J Chem Inf Model 2017; 57:1793-1806. [PMID: 28678484 DOI: 10.1021/acs.jcim.7b00017] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A major shortcoming of empirical scoring functions is that they often fail to predict binding affinity properly. Removing false positives of docking results is one of the most challenging works in structure-based virtual screening. Postdocking filters, making use of all kinds of experimental structure and activity information, may help in solving the issue. We describe a new method based on detailed protein-ligand interaction decomposition and machine learning. Protein-ligand empirical interaction components (PLEIC) are used as descriptors for support vector machine learning to develop a classification model (PLEIC-SVM) to discriminate false positives from true positives. Experimentally derived activity information is used for model training. An extensive benchmark study on 36 diverse data sets from the DUD-E database has been performed to evaluate the performance of the new method. The results show that the new method performs much better than standard empirical scoring functions in structure-based virtual screening. The trained PLEIC-SVM model is able to capture important interaction patterns between ligand and protein residues for one specific target, which is helpful in discarding false positives in postdocking filtering.
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Affiliation(s)
- Yuna Yan
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.,State Key Laboratory of Precision Spectroscopy, East China Normal University , Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China
| | - Weijun Wang
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.,State Key Laboratory of Precision Spectroscopy, East China Normal University , Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China
| | - Zhaoxi Sun
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.,State Key Laboratory of Precision Spectroscopy, East China Normal University , Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China
| | - John Z H Zhang
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.,State Key Laboratory of Precision Spectroscopy, East China Normal University , Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China
| | - Changge Ji
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.,State Key Laboratory of Precision Spectroscopy, East China Normal University , Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China
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Akhavan M, Foroughifar N, Pasdar H, Khajeh-Amiri A, Bekhradnia A. Copper(II)-complex functionalized magnetite nanoparticles: a highly efficient heterogeneous nanocatalyst for the synthesis of 5-arylidenthiazolidine-2,4-diones and 5-arylidene-2-thioxothiazolidin-4-one. TRANSIT METAL CHEM 2017. [DOI: 10.1007/s11243-017-0159-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Andleeb H, Khan I, Bauzá A, Tahir MN, Simpson J, Hameed S, Frontera A. Synthesis and supramolecular self-assembly of thioxothiazolidinone derivatives driven by H-bonding and diverse π–hole interactions: A combined experimental and theoretical analysis. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.03.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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20
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Muhammad SA, Ravi S, Thangamani A, Chandrasekaran B, Ramesh M. Synthesis, antiproliferative activity and docking study of novel rhodanine derivatives as Bcr-Abl T1351 inhibitors. RESEARCH ON CHEMICAL INTERMEDIATES 2017. [DOI: 10.1007/s11164-017-2968-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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21
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Synthesis and evaluation of some novel N-substituted rhodanines for their anticancer activity. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1545-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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22
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Andleeb H, Tehseen Y, Ali Shah SJ, Khan I, Iqbal J, Hameed S. Identification of novel pyrazole–rhodanine hybrid scaffolds as potent inhibitors of aldose reductase: design, synthesis, biological evaluation and molecular docking analysis. RSC Adv 2016. [DOI: 10.1039/c6ra14531k] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A series of novel pyrazole–rhodanine derivatives was designed, synthesized, and biologically evaluated for their potential inhibitory effect on both aldehyde reductase (ALR1) and aldose reductase (ALR2).
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Affiliation(s)
- Hina Andleeb
- Department of Chemistry
- Quaid-i-Azam University
- Islamabad-45320
- Pakistan
| | - Yildiz Tehseen
- Centre for Advanced Drug Research
- COMSATS Institute of Information Technology
- Abbottabad-22060
- Pakistan
| | - Syed Jawad Ali Shah
- Centre for Advanced Drug Research
- COMSATS Institute of Information Technology
- Abbottabad-22060
- Pakistan
| | - Imtiaz Khan
- Department of Chemistry
- Quaid-i-Azam University
- Islamabad-45320
- Pakistan
| | - Jamshed Iqbal
- Centre for Advanced Drug Research
- COMSATS Institute of Information Technology
- Abbottabad-22060
- Pakistan
| | - Shahid Hameed
- Department of Chemistry
- Quaid-i-Azam University
- Islamabad-45320
- Pakistan
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Mehrabi H, Esfandiarpour Z. A facile and effective procedure for the synthesis of new 1,3-thiazine-2-thione derivatives. J Sulphur Chem 2015. [DOI: 10.1080/17415993.2015.1072718] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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24
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A facile and efficient one-pot synthesis of 6-amino-2-oxo-4-aryl-4H-1,3-dithiine-5-carbonitrile derivatives in water. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2015. [DOI: 10.1007/s13738-015-0681-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Hou X, Li R, Li K, Yu X, Sun JP, Fang H. Fast Identification of Novel Lymphoid Tyrosine Phosphatase Inhibitors Using Target–Ligand Interaction-Based Virtual Screening. J Med Chem 2014; 57:9309-22. [DOI: 10.1021/jm500692u] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Xuben Hou
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Rong Li
- Key
Laboratory Experimental Teratology of the Ministry of Education and
Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Kangshuai Li
- Department
of Physiology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Xiao Yu
- Department
of Physiology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Jin-Peng Sun
- Key
Laboratory Experimental Teratology of the Ministry of Education and
Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Hao Fang
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
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26
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Guiheneuf S, Paquin L, Carreaux F, Durieu E, Roisnel T, Meijer L, Bazureau JP. New 5-ylidene rhodanine derivatives based on the dispacamide A model. Mol Divers 2014; 18:375-88. [PMID: 24584455 DOI: 10.1007/s11030-014-9509-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 02/04/2014] [Indexed: 01/01/2023]
Abstract
A practical approach for the preparation of (5Z) 5-ylidene rhodanine derivatives bearing the (4,5-dihalogeno-pyrrol-2-yl)carbamoyl fragment of dispacamide A is reported. The new compounds were obtained in good yields (19-88 %) by Knoevenagel condensation according to a solution-phase microwave dielectric heating protocol in the presence of organic bases (piperidine, TEA, and AcONa) from a set of N-substituted rhodanines 2(a-i). The ten synthetic products 3(a-j) have been synthesized with a Z-geometry about their exocyclic double bond and the structure of one of these compounds (3) was confirmed by a single X-ray diffraction analysis. The new (5Z) 5-ylidene rhodanine derivatives 3(a-j) were tested against eight protein kinases.
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Affiliation(s)
- Solene Guiheneuf
- Université de Rennes 1 Institut des Sciences Chimiques de Rennes ISCR UMR CNRS 6226, groupe Ingénierie Chimique et Molécules pour le Vivant (ICMV), Bât. 10 A, Campus de Beaulieu, CS 74205, 263 Avenue du Général Leclerc, 35042, Rennes Cedex, France
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27
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Nitsche C, Schreier VN, Behnam MAM, Kumar A, Bartenschlager R, Klein CD. Thiazolidinone-peptide hybrids as dengue virus protease inhibitors with antiviral activity in cell culture. J Med Chem 2013; 56:8389-403. [PMID: 24083834 DOI: 10.1021/jm400828u] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The protease of dengue virus is a promising target for antiviral drug discovery. We here report a new generation of peptide-hybrid inhibitors of dengue protease that incorporate N-substituted 5-arylidenethiazolidinone heterocycles (rhodanines and thiazolidinediones) as N-terminal capping groups of the peptide moiety. The compounds were extensively characterized with respect to inhibition of various proteases, inhibition mechanisms, membrane permeability, antiviral activity, and cytotoxicity in cell culture. A sulfur/oxygen exchange in position 2 of the capping heterocycle (thiazolidinedione-capped vs rhodanine-capped peptide hybrids) has a significant effect on these properties and activities. The most promising in vitro affinities were observed for thiazolidinedione-based peptide hybrids containing hydrophobic groups with Ki values between 1.5 and 1.8 μM and competitive inhibition mechanisms. Rhodanine-capped peptide hybrids with hydrophobic substituents have, in correlation with their membrane permeability, a more pronounced antiviral activity in cell culture than the thiazolidinediones.
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Affiliation(s)
- Christoph Nitsche
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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28
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Yu C, Yao C, Li T, Wang X. An aqueous, catalyst-free and three-component synthesis of 6-amino-3-(trifluoromethyl)-1,4-dihydro-1-phenyl-4-arylpyrano[2,3-c]pyrazole-5-carbonitriles. RESEARCH ON CHEMICAL INTERMEDIATES 2013. [DOI: 10.1007/s11164-013-1058-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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29
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Deng QG, Gao Y, Zhao B, Ruan YY, Ma MJ, Wang LY, Feng YQ. ONE-POT SYNTHESIS OF 11,23-BIS(IMIDAZOL-1-YL)CALIX[4]ARENE DERIVATIVES BASED ON THE UPPER RIM OF BIS-AMINOCALIX[4]ARENE. HETEROCYCLES 2013. [DOI: 10.3987/com-13-12771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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