1
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Zheng W, Tu B, Zhang Z, Li J, Yan Z, Su K, Deng D, Sun Y, Wang X, Zhang B, Zhang K, Wong WL, Wu P, Hong WD, Ang S. Ligand and structure-based approaches for the exploration of structure-activity relationships of fusidic acid derivatives as antibacterial agents. Front Chem 2023; 10:1094841. [PMID: 36688047 PMCID: PMC9852990 DOI: 10.3389/fchem.2022.1094841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
Introduction: Fusidic acid (FA) has been widely applied in the clinical prevention and treatment of bacterial infections. Nonetheless, its clinical application has been limited due to its narrow antimicrobial spectrum and some side effects. Purpose: Therefore, it is necessary to explore the structure-activity relationships of FA derivatives as antibacterial agents to develop novel ones possessing a broad antimicrobial spectrum. Methods and result: First, a pharmacophore model was established on the nineteen FA derivatives with remarkable antibacterial activities reported in previous studies. The common structural characteristics of the pharmacophore emerging from the FA derivatives were determined as those of six hydrophobic centers, two atom centers of the hydrogen bond acceptor, and a negative electron center around the C-21 field. Then, seven FA derivatives have been designed according to the reported structure-activity relationships and the pharmacophore characteristics. The designed FA derivatives were mapped on the pharmacophore model, and the Qfit values of all FA derivatives were over 50 and FA-8 possessed the highest value of 82.66. The molecular docking studies of the partial target compounds were conducted with the elongation factor G (EF-G) of S. aureus. Furthermore, the designed FA derivatives have been prepared and their antibacterial activities were evaluated by the inhibition zone test and the minimum inhibitory concentration (MIC) test. The derivative FA-7 with a chlorine group as the substituent group at C-25 of FA displayed the best antibacterial property with an MIC of 3.125 µM. Subsequently, 3D-QSAR was carried on all the derivatives by using the CoMSIA mode of SYBYL-X 2.0. Conclusion: Hence, a computer-aided drug design model was developed for FA, which can be further used to optimize FA derivatives as highly potent antibacterial agents.
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Affiliation(s)
- Wende Zheng
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China,International Healthcare Innovation Institute, Jiangmen, China
| | - Borong Tu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China,International Healthcare Innovation Institute, Jiangmen, China
| | - Zhen Zhang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China,International Healthcare Innovation Institute, Jiangmen, China
| | - Jinxuan Li
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China,International Healthcare Innovation Institute, Jiangmen, China
| | - Zhenping Yan
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China,International Healthcare Innovation Institute, Jiangmen, China
| | - Kaize Su
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China,International Healthcare Innovation Institute, Jiangmen, China
| | - Duanyu Deng
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China,International Healthcare Innovation Institute, Jiangmen, China
| | - Ying Sun
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China,International Healthcare Innovation Institute, Jiangmen, China
| | - Xu Wang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China,International Healthcare Innovation Institute, Jiangmen, China
| | - Bingjie Zhang
- School of Biomedicine and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Kun Zhang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China,International Healthcare Innovation Institute, Jiangmen, China
| | - Wing-Leung Wong
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Panpan Wu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China,International Healthcare Innovation Institute, Jiangmen, China,*Correspondence: Panpan Wu, ; Weiqian David Hong, ; Song Ang,
| | - Weiqian David Hong
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China,International Healthcare Innovation Institute, Jiangmen, China,*Correspondence: Panpan Wu, ; Weiqian David Hong, ; Song Ang,
| | - Song Ang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China,International Healthcare Innovation Institute, Jiangmen, China,*Correspondence: Panpan Wu, ; Weiqian David Hong, ; Song Ang,
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2
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Kumar V, Ojha PK, Saha A, Roy K. Exploring 2D-QSAR for prediction of beta-secretase 1 (BACE1) inhibitory activity against Alzheimer's disease. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:87-133. [PMID: 31865778 DOI: 10.1080/1062936x.2019.1695226] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/17/2019] [Indexed: 06/10/2023]
Abstract
We have developed a robust quantitative structure-activity relationship (QSAR) model employing a dataset of 98 heterocycle compounds to identify structural features responsible for BACE1 (beta-secretase 1) enzyme inhibition. We have used only 2D descriptors for model development purpose thus avoiding the conformational complications arising due to 3D geometry considerations. Following the strict Organization for Economic Co-operation and Development (OECD) guidelines, we have developed models using stepwise regression analysis followed by the best subset selection, while the final model was developed by partial least squares regression technique. The model was validated using various internationally accepted stringent validation parameters. From the insights obtained from the developed model, we have concluded that heteroatoms (nitrogen, oxygen, etc.) present within to an aromatic nucleus and the structural features such as hydrophobic, ring aromatic and hydrogen bond acceptor/donor are responsible for the enhancement of the BACE1 enzyme inhibitory activity. Moreover, we have performed the pharmacophore modelling to unveil the structural requirements for the inhibitory activity against the BACE1 enzyme. Furthermore, molecular docking studies were carried out to understand the molecular interactions involved in binding, and the results are then correlated with the requisite structural features obtained from the QSAR and pharmacophore models.
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Affiliation(s)
- V Kumar
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - P K Ojha
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - A Saha
- Department of Chemical Technology, University of Calcutta, Kolkata, India
| | - K Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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3
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Sharma T, Harioudh MK, Kuldeep J, Kumar S, Banerjee D, Ghosh JK, Siddiqi MI. Identification of Potential Inhibitors of Cathepsin-B using Shape & Pharmacophore-based Virtual Screening, Molecular Docking and Explicit Water Thermodynamics. Mol Inform 2019; 39:e1900023. [PMID: 31648416 DOI: 10.1002/minf.201900023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 09/18/2019] [Indexed: 12/12/2022]
Abstract
Lysosome has been long understood as a vital digestive organelle. Increasing reports indicate that the lysosome also plays a crucial role in the pathogenesis of a variety of neurodegenerative diseases, including Huntington's disease, Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. Abnormal protein degradation and deposition stimulated by lysosomal dysfunction may cause age-related neurodegeneration. Enormous efforts have been devoted to the development of effective therapeutics against Alzheimer's disease, the most debilitating neurodegenerative disease. Endopeptidase activity of the Cathepsin-B is associated with the pathological processes. Work presented here focuses on identification of new inhibitors against Cathepsin-B protein using diverse computational approaches together. The inhibitors identified were further tested for in-vitro activity using enzyme based assay method. The identified inhibitors provided interesting understanding on how the water thermodynamic properties along with hydrophobic, steric, electronic, and structural requirements contribute to cathepsin-B inhibitory activity. These water thermodynamic studies, may further be used in computer aided drug discovery pipeline to design and predict more potent derivatives of various scaffolds as cathepsin-B inhibitors.
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Affiliation(s)
- Tanuj Sharma
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Munesh Kumar Harioudh
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Jitendra Kuldeep
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Sushil Kumar
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Dibyendu Banerjee
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Central Drug Research Institute, Campus, Lucknow, 226031, India
| | - Jimut Kanti Ghosh
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Central Drug Research Institute, Campus, Lucknow, 226031, India
| | - Mohammad Imran Siddiqi
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Central Drug Research Institute, Campus, Lucknow, 226031, India
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4
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Synthesis, molecular modeling and BACE-1 inhibitory study of tetrahydrobenzo[b] pyran derivatives. Bioorg Chem 2019; 84:202-210. [DOI: 10.1016/j.bioorg.2018.11.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 11/16/2018] [Accepted: 11/17/2018] [Indexed: 11/24/2022]
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5
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Xu X, Lü P, Wang J, Xu F, Liang L, Wang C, Niu Y, Xu P. Design, synthesis, and biological evaluation of 4‐aminopyrimidine or 4,6‐diaminopyrimidine derivatives as beta amyloid cleaving enzyme‐1 inhibitors. Chem Biol Drug Des 2019; 93:926-933. [DOI: 10.1111/cbdd.13489] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 12/14/2018] [Accepted: 01/09/2019] [Indexed: 02/02/2023]
Affiliation(s)
- Xiufeng Xu
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Peng Lü
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Junjie Wang
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Fengrong Xu
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Lei Liang
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Chao Wang
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Yan Niu
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Ping Xu
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
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6
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Yan G, Hao L, Niu Y, Huang W, Wang W, Xu F, Liang L, Wang C, Jin H, Xu P. 2-Substituted-thio-N-(4-substituted-thiazol/1H-imidazol-2-yl)acetamides as BACE1 inhibitors: Synthesis, biological evaluation and docking studies. Eur J Med Chem 2017. [PMID: 28624701 DOI: 10.1016/j.ejmech.2017.06.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this work, a series of 2-substituted-thio-N-(4-substituted-thiazol/1H-imidazol-2-yl)acetamide derivatives were developed as β-secretase (BACE-1) inhibitors. Supported by docking study, a small library of derivatives were designed, synthesized and biologically evaluated in vitro. In addition, the selected compounds were tested with affinity (KD) towards BACE-1, blood brain barrier (BBB) permeability and cytotoxicity. The studies revealed that the most potent analog 41 (IC50 = 4.6 μM) with high predicted BBB permeability and low cellular cytotoxicity, could serve as a good lead structure for further optimization.
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Affiliation(s)
- Gang Yan
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Lina Hao
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Yan Niu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China.
| | - Wenjie Huang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Wei Wang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Fengrong Xu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Lei Liang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Chao Wang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Ping Xu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China.
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7
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Palakurti R, Vadrevu R. Pharmacophore based 3D-QSAR modeling, virtual screening and docking for identification of potential inhibitors of β-secretase. Comput Biol Chem 2017; 68:107-117. [DOI: 10.1016/j.compbiolchem.2017.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 02/07/2017] [Accepted: 03/01/2017] [Indexed: 12/19/2022]
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8
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Affiliation(s)
- Rodrigo Aguayo-Ortiz
- Departamento de Fisicoquímica; Universidad Nacional Autónoma de México; Ciudad de México 04510 México
| | - Laura Dominguez
- Departamento de Fisicoquímica; Universidad Nacional Autónoma de México; Ciudad de México 04510 México
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9
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Semighini EP. In SilicoDesign of Beta-Secretase Inhibitors in Alzheimer's Disease. Chem Biol Drug Des 2014; 86:284-90. [DOI: 10.1111/cbdd.12492] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 11/24/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Evandro Pizeta Semighini
- Faculdade de Medicina de Ribeirão Preto; USP; Av. Bandeirantes, 3900, Monte Alegre Ribeirão Preto SP 14049-900 Brazil
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10
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Vuorinen A, Schuster D. Methods for generating and applying pharmacophore models as virtual screening filters and for bioactivity profiling. Methods 2014; 71:113-34. [PMID: 25461773 DOI: 10.1016/j.ymeth.2014.10.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Revised: 09/29/2014] [Accepted: 10/14/2014] [Indexed: 01/03/2023] Open
Abstract
Biological effects of small molecules in an organism result from favorable interactions between the molecules and their target proteins. These interactions depend on chemical functionalities, bonds, and their 3D-orientations towards each other. These 3D-arrangements of chemical functionalities that make a small molecule active towards its target can be described by pharmacophore models. In these models, chemical functionalities are represented as so-called features. Commonly, they are obtained either from a set of active compounds or directly from the observed protein-ligand interactions as present in X-ray crystal structures, NMR structures, or docking poses. In this review, we explain the basics of pharmacophore modeling including dataset generation, 3D-representations and conformational analysis of small molecules, pharmacophore model construction, model validation, and its benefits to virtual screening and other applications.
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Affiliation(s)
- Anna Vuorinen
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck - CMBI, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Daniela Schuster
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck - CMBI, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
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11
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4-Oxo-1,4-dihydro-quinoline-3-carboxamides as BACE-1 inhibitors: Synthesis, biological evaluation and docking studies. Eur J Med Chem 2014; 79:413-21. [DOI: 10.1016/j.ejmech.2014.04.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 04/07/2014] [Accepted: 04/07/2014] [Indexed: 11/18/2022]
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12
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Dhanjal JK, Goyal S, Sharma S, Hamid R, Grover A. Mechanistic insights into mode of action of potent natural antagonists of BACE-1 for checking Alzheimer's plaque pathology. Biochem Biophys Res Commun 2013; 443:1054-9. [PMID: 24365147 DOI: 10.1016/j.bbrc.2013.12.088] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 12/17/2013] [Indexed: 11/16/2022]
Abstract
Alzheimer's is a neurodegenerative disorder resulting in memory loss and decline in cognitive abilities. Accumulation of extracellular beta amyloidal plaques is one of the major pathology associated with this disease. β-Secretase or BACE-1 performs the initial and rate limiting step of amyloidic pathway in which 37-43 amino acid long peptides are generated which aggregate to form plaques. Inhibition of this enzyme offers a viable prospect to check the growth of these plaques. Numerous efforts have been made in recent years for the generation of BACE-1 inhibitors but many of them failed during the preclinical or clinical trials due to drug related or drug induced toxicity. In the present work, we have used computational methods to screen a large dataset of natural compounds to search for small molecules having BACE-1 inhibitory activity with low toxicity to normal cells. Molecular dynamics simulations were performed to analyze molecular interactions between the screened compounds and the active residues of the enzyme. Herein, we report two natural compounds of inhibitory nature active against β-secretase enzyme of amyloidic pathway and are potent lead molecules against Alzheimer's disease.
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Affiliation(s)
| | - Sukriti Goyal
- Apaji Institute of Mathematics & Applied Computer Technology, Banasthali University, Tonk 304022, Rajasthan, India
| | - Sudhanshu Sharma
- Department of Biotechnology, Delhi Technological University, New Delhi 110042, India
| | - Rabia Hamid
- Department of Biochemistry, University of Kashmir, Srinagar 190006, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
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13
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Honarparvar B, Govender T, Maguire GEM, Soliman MES, Kruger HG. Integrated Approach to Structure-Based Enzymatic Drug Design: Molecular Modeling, Spectroscopy, and Experimental Bioactivity. Chem Rev 2013; 114:493-537. [DOI: 10.1021/cr300314q] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Bahareh Honarparvar
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Thavendran Govender
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Glenn E. M. Maguire
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Mahmoud E. S. Soliman
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Hendrik G. Kruger
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
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