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Anyubaga SB, Shallangwa GA, Uzairu A, Abechi SE. Chemo-informatics applications in the design of novel 7-keto-sempervirol derivatives as SmCB1 inhibitors with potential for treatment of Schistosomiasis. Heliyon 2024; 10:e23115. [PMID: 38173516 PMCID: PMC10761359 DOI: 10.1016/j.heliyon.2023.e23115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
The quest for a sound treatment on the vulnerable population suffering and dying as a result of the blood flukes, S. mansoni is on the increase because both Praziquantel and Oxamniquine widely used for the treatment of Schistosomiasis for over 51 years suffer resistance and recurrence. Here-in, chemo-informatics techniques such as QSAR modeling, pharmacokinetic, docking alongside MD simulation were harnessed in designing novel 7-keto- sempevirolsempevirol derivatives that are more competent against S. mansoni. Upon QSAR screening, compound 15, which appears to be in the model's acceptability space, emerges the best with a high predicted activity. 5 new analogues with improved activity against Schistosomiasis better than the standard drug PZQ were designed from compound 15 (template 15*) on an account of the descriptors significance from the model with robust and validated parameters. Also their pharmacokinetic profiles indicates that the designed compounds have the characteristics of a good drug. Furthermore, docking evaluation fulfilled ranges from -113.121 to -100.79 kcal/mol (moldock score), with compound U1 being the best (least moldock score of -113.121 compared to PZQ and 15* (template) having a moldock score value of (-87.21 and -83.37 kcal/mol). 100-ns MD Simulation on the U1-docked complex was run using Desmond 2019-4 package. The nature and steadiness of U1 compound within the enzyme active site was further confirmed by RMSD, RMSF, RoG and H-bond assessment. Hence, we recommend compound U1 targeting the SmCB1 enzyme (6YI7) for Schistosomiasis treatment and for further medicinal evaluation and utilization.
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Affiliation(s)
| | | | - Adamu Uzairu
- Department of Chemistry Ahmadu Bello University, P.M.B. 1044, Zaria, Nigeria
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Okada T, Yamabe K, Jo M, Sakajiri Y, Shibata T, Sawada R, Yamanishi Y, Kanayama D, Mori H, Mizuguchi M, Obita T, Nabeshima Y, Koizumi K, Toyooka N. Design and structural optimization of thiadiazole derivatives with potent GLS1 inhibitory activity. Bioorg Med Chem Lett 2023; 93:129438. [PMID: 37549852 DOI: 10.1016/j.bmcl.2023.129438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
GLS1 is an attractive target not only as anticancer agents but also as candidates for various potential pharmaceutical applications such as anti-aging and anti-obesity treatments. We performed docking simulations based on the complex crystal structure of GLS1 and its inhibitor CB-839 and found that compound A bearing a thiadiazole skeleton exhibits GLS1 inhibition. Furthermore, we synthesized 27 thiadiazole derivatives in an effort to obtain a more potent GLS1 inhibitor. Among the synthesized derivatives, 4d showed more potent GLS1 inhibitory activity (IC50 of 46.7 µM) than known GLS1 inhibitor DON and A. Therefore, 4d is a very promising novel GLS1 inhibitor.
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Affiliation(s)
- Takuya Okada
- Faculty of Engineering, University of Toyama, Toyama 930-8555, Japan; Graduate School of Pharma-Medical Sciences, University of Toyama, Toyama 930-8555, Japan; Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan.
| | - Kaho Yamabe
- Graduate School of Pharma-Medical Sciences, University of Toyama, Toyama 930-8555, Japan
| | - Michiko Jo
- Division of Presymptomatic Disease, Institute of Natural Medicine, University of Toyama, Toyama 930‑0194, Japan.
| | - Yuko Sakajiri
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 804-8550, Japan; Graduate School of Informatics, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Tomokazu Shibata
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 804-8550, Japan
| | - Ryusuke Sawada
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 804-8550, Japan; Department of Pharmacology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 804-8550, Japan; Graduate School of Informatics, Nagoya University, Chikusa, Nagoya 464-8602, Japan.
| | - Daisuke Kanayama
- Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Hisashi Mori
- Department of Molecular Neuroscience, Faculty of Medicine, University of Toyama, Toyama 930-0194, Japan; Research Center for Pre-Disease Science, University of Toyama, Toyama 930-0194, Japan
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Takayuki Obita
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Yuko Nabeshima
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Keiichi Koizumi
- Division of Presymptomatic Disease, Institute of Natural Medicine, University of Toyama, Toyama 930‑0194, Japan; Research Center for Pre-Disease Science, University of Toyama, Toyama 930-0194, Japan
| | - Naoki Toyooka
- Faculty of Engineering, University of Toyama, Toyama 930-8555, Japan; Graduate School of Pharma-Medical Sciences, University of Toyama, Toyama 930-8555, Japan; Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
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Kushveer JS, Sharma R, Samantaray M, Amutha R, Sarma VV. Purification and evaluation of 2, 4-di-tert butylphenol (DTBP) as a biocontrol agent against phyto-pathogenic fungi. Fungal Biol 2023; 127:1067-1074. [PMID: 37344008 DOI: 10.1016/j.funbio.2023.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 05/14/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023]
Abstract
A fungal strain, Marasmiellus sp (PUK64), isolated from the mangrove forests in Muthupet, Tamil Nadu, East coast of India, along with others were screened for the search of potent bioactive compounds. A phenolic compound, 2,4-di-tert-butylphenol (DTBP), was isolated from the most promising strain PUK64 and its chemical structure was ascertained. DTBP demonstrated remarkable antifungal activity against the phytopathogenic fungi Aspergillus oryzae, Curvularia lunata and Fusarium verticillioides. In an in-vitro experimental setup, DTBP suppressed the growth of all three fungi, among which F. verticillioides was found to be highly susceptible. This effect relates with the inhibition of spore germination and hyphal growth that we observed. DTBP showed high affinity with the F. verticillioides's β-tubulin protein (determined by ligand-protein docking) as compared to the standard fungicide carbendazim (CBZ). Molecular docking and simulation studies of DTBP with target β-tubulin further confirmed the potential of β-tubulin binding in F. verticillioides. To our knowledge, this is the first report on DTBP-mediated biocontrol of phytopathogenic fungi, produced by Marasmiellus sp. PUK64 that can be potent inhibitor of β-tubulin protein of F. verticillioides.
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Affiliation(s)
- J S Kushveer
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Rahul Sharma
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Mahesh Samantaray
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - R Amutha
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
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Koh DH, Song WS, Kim EY. Multi-step structure-activity relationship screening efficiently predicts diverse PPARγ antagonists. Chemosphere 2022; 286:131540. [PMID: 34346341 DOI: 10.1016/j.chemosphere.2021.131540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/08/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
In discovering the potential antagonist of peroxisome proliferator-activated receptor gamma (PPARγ), the structure-activity relationship (SAR) is a useful in silico method. However, it is difficult for conventional SAR approaches to predict the activities of antagonists owing to the large structural diversity of antagonistic compounds. This study provides evidence that multi-step SAR screening is applicable for predicting PPARγ antagonists by combining different complementary methodologies. We constructed three models: read-across-like SAR, docking-simulation-interpreting SAR, and deep-learning-based SAR. To provide user-customized prediction results, our multi-step SAR screening model combined the three SAR models in a stepwise manner, which subdivided them according to potential levels of the PPARγ antagonist. The read-across-like SAR, which considered specific antagonist scaffolds, revealed the highest positive predictive value (PPV). The docking-simulation-interpreting SAR, which considered the molecular surface features, revealed high statistics for the PPV and the true-positive rate (TPR). The deep-learning-based SAR showed the highest TPR at the last classification step. This multi-step SAR screening covered the antagonists of high reliability provided by a read-across-like SAR, as well as the antagonists of diverse scaffolds provided by docking-simulation-interpreting SAR and deep-learning-based SAR. Therefore, to predict PPARγ antagonists, multi-step SAR screening could be as a useful tool.
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Affiliation(s)
- Dong-Hee Koh
- Department of Life and Nanopharmaceutical Science, South Korea
| | - Woo-Seon Song
- Department of Life and Nanopharmaceutical Science, South Korea
| | - Eun-Young Kim
- Department of Life and Nanopharmaceutical Science, South Korea; Department of Biology, Kyung Hee University, Hoegi-Dong, Dongdaemun-Gu, Seoul, 130-701, South Korea.
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