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Morales N, Valdés-Muñoz E, González J, Valenzuela-Hormazábal P, Palma JM, Galarza C, Catagua-González Á, Yáñez O, Pereira A, Bustos D. Machine Learning-Driven Classification of Urease Inhibitors Leveraging Physicochemical Properties as Effective Filter Criteria. Int J Mol Sci 2024; 25:4303. [PMID: 38673888 PMCID: PMC11049951 DOI: 10.3390/ijms25084303] [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: 03/15/2024] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Urease, a pivotal enzyme in nitrogen metabolism, plays a crucial role in various microorganisms, including the pathogenic Helicobacter pylori. Inhibiting urease activity offers a promising approach to combating infections and associated ailments, such as chronic kidney diseases and gastric cancer. However, identifying potent urease inhibitors remains challenging due to resistance issues that hinder traditional approaches. Recently, machine learning (ML)-based models have demonstrated the ability to predict the bioactivity of molecules rapidly and effectively. In this study, we present ML models designed to predict urease inhibitors by leveraging essential physicochemical properties. The methodological approach involved constructing a dataset of urease inhibitors through an extensive literature search. Subsequently, these inhibitors were characterized based on physicochemical properties calculations. An exploratory data analysis was then conducted to identify and analyze critical features. Ultimately, 252 classification models were trained, utilizing a combination of seven ML algorithms, three attribute selection methods, and six different strategies for categorizing inhibitory activity. The investigation unveiled discernible trends distinguishing urease inhibitors from non-inhibitors. This differentiation enabled the identification of essential features that are crucial for precise classification. Through a comprehensive comparison of ML algorithms, tree-based methods like random forest, decision tree, and XGBoost exhibited superior performance. Additionally, incorporating the "chemical family type" attribute significantly enhanced model accuracy. Strategies involving a gray-zone categorization demonstrated marked improvements in predictive precision. This research underscores the transformative potential of ML in predicting urease inhibitors. The meticulous methodology outlined herein offers actionable insights for developing robust predictive models within biochemical systems.
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Affiliation(s)
- Natalia Morales
- Magíster en Ciencias de la Computación, Universidad Católica del Maule, Talca 3460000, Chile; (N.M.); (J.G.)
| | - Elizabeth Valdés-Muñoz
- Doctorado en Biotecnología Traslacional, Centro de Biotecnología de los Recursos Naturales, Universidad Católica del Maule, Talca 3480094, Chile;
| | - Jaime González
- Magíster en Ciencias de la Computación, Universidad Católica del Maule, Talca 3460000, Chile; (N.M.); (J.G.)
| | - Paulina Valenzuela-Hormazábal
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile;
| | - Jonathan M. Palma
- Facultad de Ingeniería, Universidad de Talca, Curicó 3344158, Chile;
| | - Christian Galarza
- Departamento de Matemáticas, Facultad de Ciencias Naturales y Matemáticas, Escuela Superior Politécnica del Litoral, Guayaquil EC090903, Ecuador; (C.G.); (Á.C.-G.)
| | - Ángel Catagua-González
- Departamento de Matemáticas, Facultad de Ciencias Naturales y Matemáticas, Escuela Superior Politécnica del Litoral, Guayaquil EC090903, Ecuador; (C.G.); (Á.C.-G.)
| | - Osvaldo Yáñez
- Núcleo de Investigación en Data Science, Facultad de Ingeniería y Negocios, Universidad de las Américas, Santiago 7500000, Chile;
| | - Alfredo Pereira
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Bellavista 7, Santiago 8420524, Chile
| | - Daniel Bustos
- Laboratorio de Bioinformática y Química Computacional, Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca 3480094, Chile
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Duan WL, Wang KT, Yan F, Luan J. Fabrication of multinuclear copper cluster-based coordination polymers as urease inhibitors. Dalton Trans 2024; 53:1336-1345. [PMID: 38124686 DOI: 10.1039/d3dt03459c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
This study focused on the design and synthesis of two Cu-based coordination polymers, [Cu2(4-dpye)(5-HSIP)(μ3-O)(H2O)2]·3H2O (Cu-CP-1) and [Cu(4-dpye)0.5(BCA)2] (Cu-CP-2), where 4-dpye = N,N'-bis(4-pyridinecarboxamide)-1,2-ethane, 5-H3SIP = 5-sulfoisophthalic acid, and HBCA = benzoic acid, by using a hydrothermal method. Single-crystal X-ray diffraction (SCXRD) study revealed that by adding various auxiliary ligands, the architectures of the Cu-CPs could be altered, yielding two distinct multinuclear Cu clusters. Moreover, the Cu-CPs can be used as urease inhibitors (UIs). In vitro experiments showed that the Cu-CPs had good urease inhibition effects with IC50 values of 0.53 ± 0.01 μM for Cu-CP-1 and 1.44 ± 0.01 μM for Cu-CP-2 and 98.48% (Cu-CP-1) and 96.27% (Cu-CP-2) inhibition of urease was achieved at a concentration of 100 μM, respectively. Furthermore, the inhibition effect of the tetranuclear Cu-CP was better than that of the binuclear Cu-CP. To better understand the potential mechanism of inhibition of the two copper complexes, we performed kinetic analysis using Lineweaver-Burk (L-B) plots in the presence of different concentrations of urea and different concentrations of inhibitors, and both Cu-CP-1 and Cu-CP-2 showed a non-competitive mode of inhibition. In addition, molecular docking analysis showed that the Cu-CPs were able to enter well into the urease binding pocket, thus interacting with key amino acid residues of urease to different degrees. Both kinetic and molecular docking studies theoretically explain and demonstrate the inhibition effect of both Cu-CPs on urease activity in vitro, which is expected to provide reasonable guidance and effective strategies for the development of novel, efficient, stable and safe CP-based UIs.
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Affiliation(s)
- Wen-Long Duan
- College of Science, Shenyang University of Chemical Technology, Shenyang, 110142, P. R. China.
| | - Kai-Tong Wang
- College of Science, Shenyang University of Chemical Technology, Shenyang, 110142, P. R. China.
| | - Feng Yan
- College of Science, Shenyang University of Chemical Technology, Shenyang, 110142, P. R. China.
| | - Jian Luan
- College of Science, Shenyang University of Chemical Technology, Shenyang, 110142, P. R. China.
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Sepehri S, Khedmati M. An overview of the privileged synthetic heterocycles as urease enzyme inhibitors: Structure-activity relationship. Arch Pharm (Weinheim) 2023; 356:e2300252. [PMID: 37401193 DOI: 10.1002/ardp.202300252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 07/05/2023]
Abstract
Urease is a metalloenzyme including two Ni2+ ions, found in some plants, bacteria, fungi, microorganisms, invertebrate animals, and animal tissues. Urease acts as a significant virulence factor, mainly in catheter blockage and infective urolithiasis as well as in the pathogenesis of gastric infection. Therefore, studies on urease lead to novel synthetic inhibitors. In this review, the synthesis and antiurease activities of a collection of privileged synthetic heterocycles such as (thio)barbiturate, (thio)urea, dihydropyrimidine, and triazol derivatives were described and discussed according to structure-activity relationship findings in search of the best moieties and substituents that are answerable for encouraging the desired activity even more potent than the standard. It was found that linking substituted phenyl and benzyl rings to the heterocycles led to potent urease inhibitors.
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Affiliation(s)
- Saghi Sepehri
- Pharmaceutical Sciences Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Mina Khedmati
- Students Research Committee, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
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Mutahir S, Khan MA, Almehizia AA, Abouzied AS, Khalifa NE, Naglah AM, Deng H, Refat MS, Khojali WMA, Huwaimel B. Design, Synthesis, Characterization and Computational Studies of Mannich Bases Oxadiazole Derivatives as New Class of Jack Bean Urease Inhibitors. Chem Biodivers 2023; 20:e202300241. [PMID: 37344354 DOI: 10.1002/cbdv.202300241] [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: 02/18/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 06/23/2023]
Abstract
Mannich bases consisting of 1,3,4-oxadiazole-2-thione (3 a-3 l) bearing various substituents were synthesized and found potent jack bean urease inhibitors. The prepared compounds showed significantly good inhibitory activities with IC50 values from 9.45±0.05 to 267.42±0.23 μM. The compound 3 k containing 4-chlorophenyl (-R) and 4-hydroxyphenyl (-R') was most active with IC50 9.45±0.05 μM followed by 3 e (IC50 22.52±0.15 μM) in which -R was phenyl and -R' was isopropyl group. However, when both -R and -R' were either 4-chlorophenyl groups (3 l) or only -R' was 4-nitrophenyl (3 i), both compounds were found inactive. The detailed binding affinities of the produced compounds with protein were explored through molecular docking and data-supported in-vitro enzyme inhibition profiles. Drug likeness was confirmed by in silico ADME investigations and molecular orbital analysis (HOMO-LUMO) and electrostatic potential maps were got from DFT calculations. ESP maps exposed that there are two potential binding sites with the most positive and most negative parts.
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Affiliation(s)
- Sadaf Mutahir
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, 276000, China
| | - Muhammad Asim Khan
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, 276000, China
| | - Abdulrahman Abdulaziz Almehizia
- Drug Exploration and Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Amr Salah Abouzied
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail, 81442, Saudi Arabia
- Department of Pharmaceutical Chemistry, National Organization for Drug Control and Research (NODCAR), Giza, 12553, Egypt
| | - Nasrin Eldirdiri Khalifa
- Department of pharmaceutics, College of Pharmacy, University of Hail, Hail, 81442, Saudi Arabia
- Department of pharmaceutics, Faculty of Pharmacy, University of Khartoum, Khartoum, 11115, Sudan
| | - Ahmed Mohamed Naglah
- Drug Exploration and Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Haishan Deng
- School of Pharmacy, Nanjing University of Traditional Chinese Medicine, Nanjing, 210094, China
| | - Moamen Salaheldeen Refat
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Weam Mohamed Ali Khojali
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail, 81442, Saudi Arabia
- Department of pharmaceutical chemistry, faculty of pharmacy, Omdurman Islamic University, Omdurman, 14415, Sudan
| | - Bader Huwaimel
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail, 81442, Saudi Arabia
- Medical and Diagnostic Research Center, University of Hail, Hail, 81442, Saudi Arabia
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Singh R, Kumar P, Devi M, Sindhu J, Kumar A, Lal S, Singh D, Kumar H, Kumar S. Urease Inhibition and Structure‐Activity Relationship Study of Thiazolidinone‐, Triazole‐, and Benzothiazole‐Based Heterocyclic Derivatives: A Focus Review. ChemistrySelect 2023. [DOI: 10.1002/slct.202300244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- Rahul Singh
- Department of Chemistry Kurukshetra University Kurukshetra 136119 India
| | - Parvin Kumar
- Department of Chemistry Kurukshetra University Kurukshetra 136119 India
| | - Meena Devi
- Department of Chemistry Kurukshetra University Kurukshetra 136119 India
| | - Jayant Sindhu
- Department of Chemistry COBS&H, CCS Haryana gricultural University Hisar 125004 India
| | - Ashwani Kumar
- Department of Pharmaceutical Sciences GJUS&T Hisar 125001 India
| | - Sohan Lal
- Department of Chemistry Kurukshetra University Kurukshetra 136119 India
| | - Devender Singh
- Department of Chemistry Maharshi Dayanand University Rohtak 124001 India
| | - Harish Kumar
- Department of Chemistry, School of Basic Sciences Central university Haryana Mahendergarh India
| | - Sumit Kumar
- Department of Chemistry DCR University of Science & Technology, Murthal Haryana 131039 India
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Yang W, Feng Q, Peng Z, Wang G. An overview on the synthetic urease inhibitors with structure-activity relationship and molecular docking. Eur J Med Chem 2022; 234:114273. [PMID: 35305460 DOI: 10.1016/j.ejmech.2022.114273] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/04/2022] [Accepted: 03/08/2022] [Indexed: 01/06/2023]
Abstract
Urease is a kind of enzyme which could be found in various bacteria, fungi, plants, and algae, which can quickly catalyze the hydrolysis of urea into ammonia and carbon dioxide. With the ammonia concentration increasing, the activity of Helicobacter pylori has got an obvious enhancement and leads to mucosal damage in the stomach, gastroduodenal infection, peptic ulcers, and gastric cancer. The infectious diseases caused by Helicobacter pylori can be controlled to a certain extent by inhibiting urease activity with urease inhibitors. Hence, studies of urease inhibitors have attracted great attention all over the world and a variety of effective urease inhibitors have been synthesized in recent years. In this review, we will draw summaries for these inhibitors including urease inhibitory activity, inhibition kinetics, structure-activity relationship, and molecular docking. The collected information is expected to provide rational guidance and effective strategy to develop novel, potent, and safe urease inhibitors for better practical applications in the future.
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Affiliation(s)
- Wei Yang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang, China; Teaching and Research Section of Natural Medicinal Chemistry, School of Pharmacy, Guizhou Medical University, Guiyang, China
| | - Qianqian Feng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang, China; Teaching and Research Section of Natural Medicinal Chemistry, School of Pharmacy, Guizhou Medical University, Guiyang, China
| | - Zhiyun Peng
- Office of Drug Clinical Trial Institutions, The Affiliated Hospital of Guizhou Medical University, Guiyang, China.
| | - Guangcheng Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang, China; Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University, Guiyang, China.
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Song WQ, Liu ML, Li SY, Xiao ZP. Recent Efforts in the Discovery of Urease Inhibitor Identifications. Curr Top Med Chem 2021; 22:95-107. [PMID: 34844543 DOI: 10.2174/1568026621666211129095441] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/22/2022]
Abstract
Urease is an attractive drug target for designing anti-infective agents against pathogens such as Helicobacter pylori, Proteus mirabilis, and Ureaplasma urealyticum. In the past century, hundreds of medicinal chemists focused their efforts on explorations of urease inhibitors. Despite the FDA's approval of acetohydroxamic acid as a urease inhibitor for the treatment of struvite nephrolithiasis and the widespread use of N-(n-butyl)thiophosphoric triamide as a soil urease inhibitor as nitrogen fertilizer synergists in agriculture, urease inhibitors with high potency and safety are urgently needed. Exploration of novel urease inhibitors has therefore become a hot research topic recently. Herein, inhibitors identified worldwide from 2016 to 2021 have been reviewed. They structurally belong to more than 20 classes of compounds such as urea/thioure analogues, hydroxamic acids, sulfonamides, metal complexes, and triazoles. Some inhibitors showed excellent potency with IC50 values lower than 10 nM, having 10000-fold higher potency than the positive control thiourea.
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Affiliation(s)
- Wan-Qin Song
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, Jishou 416000. China
| | - Mei-Ling Liu
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, Jishou 416000. China
| | - Su-Ya Li
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, Jishou 416000. China
| | - Zhu-Ping Xiao
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, Jishou 416000. China
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