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Bhati SK, Jain M, Muthukumaran J, Singh AK. Computational identification of candidate inhibitors for Dihydrofolate reductase in Acinetobacter baumannii. Curr Res Struct Biol 2024; 7:100127. [PMID: 38322649 PMCID: PMC10844809 DOI: 10.1016/j.crstbi.2024.100127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/08/2024] Open
Abstract
Acinetobacter baumannii is one of the emerging causes of hospital acquired infections and this bacterium, due to multi-drug resistant and Extensive Drug resistant has been able to develop resistance against the antimicrobial agents that are being used to eliminate it. A.baumannii has been the cause of death in immune compromised patients in hospitals. Hence it is the urgent need of time to find potential inhibitors for this bacterium to cease its virulence and affect its survival inside host organisms. The Dihydrofolate reductase enzyme, which is an important biocatalyst in the conversion of Dihydrofolate to Tetrahydrofolate, is an important drug target protein. In the present study high throughput screening is used to identify the inhibitors of this enzyme. The prioritized ligand molecular candidates identified through virtual screening for the substrate binding site of the predicted model are Z1447621107, Z2604448220 and Z1830442365. The Molecular Dynamics Simulation study suggests that potential inhibitor of the Dihydrofolate reductase enzyme would prevent bacteria from completing its life cycle, affecting its survival. Finally the complexes were analysed for binding free energy of the Dihydrofolate reductase enzyme complexes with the ligands.
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Affiliation(s)
- Saurabh Kumar Bhati
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Monika Jain
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Jayaraman Muthukumaran
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Amit Kumar Singh
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, India
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Reang J, Sharma K, Sharma PC, Yadav V, Sharma V, Majeed J. Discovery of VEGFR inhibitors through virtual screening and energy assessment. J Biochem Mol Toxicol 2023; 37:e23321. [PMID: 36808794 DOI: 10.1002/jbt.23321] [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: 06/23/2022] [Revised: 12/05/2022] [Accepted: 02/08/2023] [Indexed: 02/22/2023]
Abstract
Vascular endothelial growth factor receptor-2 (VEGFR-2) is crucial in promoting tumor angiogenesis and cancer metastasis. Thus, inhibition of VEGFR-2 has appeared as a good tactic for cancer treatment. To find out novel VEGFR-2 inhibitors, first, the PDB structure of VEGFR-2, 6GQO, was selected based on atomic nonlocal environment assessment (ANOLEA) and PROCHECK assessment. 6GQO was then further used for structure-based virtual screening (SBVS) of different molecular databases, including US-FDA approved drugs, US-FDA withdrawn drugs, may bridge, MDPI, and Specs databases using Glide. Based on SBVS, receptor fit, drug-like filters, and absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis of 427877 compounds, the best 22 hits were selected. From the 22 hits, hit 5 complex with 6GQO was put through molecular mechanics/generalized born surface area (MM/GBSA) study and hERG binding. The MM/GBSA study revealed that hit 5 possesses lesser binding free energy with more inferior stability in the receptor pocket than the reference compound. The VEGFR-2 inhibition assay of hit 5 disclosed an IC50 of 165.23 nM against VEGFR-2, which can be possibly enhanced through structural modifications.
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Affiliation(s)
- Jurnal Reang
- Department of Pharmaceutical Chemistry, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Kalicharan Sharma
- Department of Pharmaceutical Chemistry, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Prabodh C Sharma
- Department of Pharmaceutical Chemistry, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Vivek Yadav
- Department of Pharmaceutical Chemistry, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Vinita Sharma
- Department of Pharmaceutical Chemistry, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Jaseela Majeed
- Department of Pharmaceutical Management, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
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Snizhko AD, Kyrychenko AV, Gladkov ES. Synthesis of Novel Derivatives of 5,6,7,8-Tetrahydroquinazolines Using α-Aminoamidines and In Silico Screening of Their Biological Activity. Int J Mol Sci 2022; 23:ijms23073781. [PMID: 35409144 PMCID: PMC8999073 DOI: 10.3390/ijms23073781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 02/05/2023] Open
Abstract
α-Aminoamidines are promising reagents for the synthesis of a diverse family of pyrimidine ring derivatives. Here, we demonstrate the use of α-aminoamidines for the synthesis of a new series of 5,6,7,8-tetrahydroquinazolines by their reaction with bis-benzylidene cyclohexanones. The reaction occurs in mild conditions and is characterized by excellent yields. It has easy workup, as compared to the existing methods of tetrahydroquinazoline preparation. Newly synthesized derivatives of 5,6,7,8-tetrahydroquinazoline bear protecting groups at the C2-tert-butyl moiety of a quinazoline ring, which can be easily cleaved, opening up further opportunities for their functionalization. Moreover, molecular docking studies indicate that the synthesized compounds reveal high binding affinity toward some essential enzymes of Mycobacterial tuberculosis, such as dihydrofolate reductase (DHFR), pantothenate kinase (MtPanK), and FAD-containing oxidoreductase DprE1 (MtDprE1), so that they may be promising candidates for the molecular design and the development of new antitubercular agents against multidrug-resistant strains of the Tubercle bacillus. Finally, the high inhibition activity of the synthesized compounds was also predicted against β-glucosidase, suggesting a novel tetrahydroquinazoline scaffold for the treatment of diabetes.
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Affiliation(s)
- Arsenii D. Snizhko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody Sq., 61022 Kharkiv, Ukraine; (A.D.S.); (A.V.K.)
| | - Alexander V. Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody Sq., 61022 Kharkiv, Ukraine; (A.D.S.); (A.V.K.)
| | - Eugene S. Gladkov
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody Sq., 61022 Kharkiv, Ukraine; (A.D.S.); (A.V.K.)
- State Scientific Institution “Institute for Single Crystals”, National Academy of Sciences of Ukraine, 60 Nauky Ave, 61072 Kharkiv, Ukraine
- Correspondence:
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Zhou BD, Li JL, Ruan ZP, Xu GF, Fang YY, Lin J, Zhang XL, Hu DB. Efficient synthesis, and antitumor and antioxidant activities of polyhydroxybenzophenone. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2021; 23:1171-1181. [PMID: 33334137 DOI: 10.1080/10286020.2020.1856096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Five polyhydroxybenzophenones were synthesized, then their antitumor and antioxidant activities were evaluated. Compounds 1-3 and 5 exhibited obvious antitumor activity. Among them, compounds 1 and 2 exhibited stronger cytotoxicity against hepatocarcinoma SMMC-7721 cells than cisplatin, with half maximal inhibitory concentrations (IC50) of approximately 3.86 and 5.32 μM, respectively. Compounds 1, 2, and 3 exhibited stronger antioxidant activity than trolox, with IC50 values of 11.15, 10.15, and 8.91 μM, respectively, and the antioxidant mechanism and strength of all compounds were further verified using computational chemistry. These results demonstrated that compounds 1-3 and 5 were very promising leads for further structural modification.
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Affiliation(s)
- Bei-Dou Zhou
- School of Pharmacy and Medical Technology, Putian University, Putian 351100, China
- Key Laboratory of Pharmaceutical Analysis and Laboratory Medicine, Putian University, Fujian Province University, Putian 351100, China
- Fujian Tianquan Pharmaceutical Co., Ltd, Longyan 364000, China
| | - Jia-Li Li
- School of Pharmacy and Medical Technology, Putian University, Putian 351100, China
- Key Laboratory of Pharmaceutical Analysis and Laboratory Medicine, Putian University, Fujian Province University, Putian 351100, China
| | - Zhi-Peng Ruan
- School of Pharmacy and Medical Technology, Putian University, Putian 351100, China
- Key Laboratory of Pharmaceutical Analysis and Laboratory Medicine, Putian University, Fujian Province University, Putian 351100, China
| | - Gui-Fen Xu
- School of Pharmacy and Medical Technology, Putian University, Putian 351100, China
- Key Laboratory of Pharmaceutical Analysis and Laboratory Medicine, Putian University, Fujian Province University, Putian 351100, China
| | - Yuan-Yuan Fang
- School of Pharmacy and Medical Technology, Putian University, Putian 351100, China
- Key Laboratory of Pharmaceutical Analysis and Laboratory Medicine, Putian University, Fujian Province University, Putian 351100, China
| | - Jian Lin
- School of Pharmacy and Medical Technology, Putian University, Putian 351100, China
- Key Laboratory of Pharmaceutical Analysis and Laboratory Medicine, Putian University, Fujian Province University, Putian 351100, China
| | - Xiao-Ling Zhang
- Fujian Key Laboratory of Drug Target Discovery and Structural and Functional Research, School of Pharmacy, Fujian Medical University, Fuzhou 350108, China
| | - Dong-Bao Hu
- School of Chemical Biology and Environment, Yuxi Normal University, Yuxi 653100, China
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Bolz SN, Adasme MF, Schroeder M. Toward an Understanding of Pan-Assay Interference Compounds and Promiscuity: A Structural Perspective on Binding Modes. J Chem Inf Model 2021; 61:2248-2262. [PMID: 33899463 DOI: 10.1021/acs.jcim.0c01227] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Pan-assay interference compounds (PAINS) are promiscuous compound classes that produce false positive hits in high-throughput screenings. Yet, the mechanisms of PAINS activity are poorly understood. Although PAINS are often associated with protein reactivity, several recent studies have shown that they also mediate noncovalent interactions. Aiming at a deep understanding of PAINS promiscuity, we performed an analysis of the Protein Data Bank to characterize the binding modes of PAINS. We explored the binding mode conservation of 34 PAINS classes present in 871 ligands and among 517 protein targets. The two major findings of this work are the following: First, different PAINS classes exhibit different levels of binding mode conservation. Our novel classification of PAINS based on binding mode similarity enables a rational assessment of PAINS from a structural perspective. Second, PAINS classes with variable binding modes can bind with high affinity. The evaluation of noncovalent binding modes of PAINS-like compounds sheds light on the mechanisms of promiscuous binding. Our findings could facilitate the decisions on how to deal with PAINS and help scientists to understand why PAINS produce hits in their screenings.
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Affiliation(s)
- Sarah Naomi Bolz
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany
| | - Melissa F Adasme
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany
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