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Pharmacophore modeling and 3D-QSAR study for the design of novel α-synuclein aggregation inhibitors. J Mol Model 2021; 27:260. [PMID: 34432157 DOI: 10.1007/s00894-021-04881-3] [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: 05/19/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Alpha-synuclein (α-syn), as a highly soluble presynaptic protein expressed in the brain, plays an important role in recycling synaptic vesicles and regulating the synthesis, storage, and release of neurotransmitters. Accumulation of α-syn in Lewy bodies and Lewy neurites is the pathological hallmark of Parkinson's disease (PD), so inhibition of α-syn aggregation may provide a novel approach for treating PD. In this study, the 3D structure of α-syn was downloaded from Protein Data Bank (PDB ID: 2N0A). A ligand-based pharmacophore model was conducted on a set of 43 diverse α-syn ligands, and the results suggested that two hydrogen-bond acceptors, one hydrophobic group, and two aromatic rings were significant to the inhibition of α-syn aggregation. A ligand-based 3D-QSAR model was also established with good statistical significance (R2 = 0.920) and excellent predictive ability (Q2 = 0.752). Novel indolinone derivatives were designed and synthesized based on the pharmacophore model. Subsequently, the 3D-QSAR model was used to predict the inhibitory activities towards α-syn aggregation, and the actual inhibitory activities were evaluated by thioflavin-T assay in vitro with the best inhibitory activity reaching 45.08%. The fitting results indicated that the built pharmacophore and 3D-QSAR models provided better reliability and accuracy for compound modification and prediction of the activity thereof. A ligand-based pharmacophore modeling and 3D-QSAR study have been performed on a set of 43 diverse ligands for α-synuclein for the first time. Based on the best pharmacophore modeling, novel indolinone derivatives were designed and synthesized, and the inhibitory activities for α-synuclein aggregation were evaluated by thioflavin-T assay in vitro, which preliminary indicated that five pharmacophore sites (two hydrogen bond acceptors (A), a hydrophobic group (H), and two aromatic rings (R)) in compounds contribute to the inhibitory activities. In the study, the built pharmacophore modeling and 3D-QSAR provided better reliability and accuracy for compound modification and prediction of the activity thereof.
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da Costa CF, de Souza MVN, da Silva Lourenço MC, Coimbra ES, da Silva Lourenço Carvalho G, Wardell J, Calixto SL, da Trindade Granato J. Synthesis and SAR Study of Simple Aryl Oximes and Nitrofuranyl Derivatives with Potent Activity Against Mycobacterium tuberculosis. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180816666181227115738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Oximes and nitrofuranyl derivatives are particularly important compounds
in medicinal chemistry. Thus, many researchers have been reported to possess antibacterial,
antiparasitic, insecticidal and fungicidal activities.
Methods:
In this work, we report the synthesis and the biological activity against Mycobacterium
tuberculosis H37RV of a series of fifty aryl oximes, ArCH=N-OH, I, and eight nitrofuranyl compounds,
2-nitrofuranyl-X, II.
Results:
Among the oximes, I: Ar = 2-OH-4-OH, 42, and I: Ar = 5-nitrofuranyl, 46, possessed the
best activity at 3.74 and 32.0 µM, respectively. Also, 46, the nitrofuran compounds, II; X = MeO,
55, and II: X = NHCH2Ph, 58, (14.6 and 12.6 µM, respectively), exhibited excellent biological activities
and were non-cytotoxic.
Conclusion:
The compound 55 showed a selectivity index of 9.85. Further antibacterial tests were
performed with compound 55 which was inactive against Enterococcus faecalis, Klebisiella
pneumonae, Pseudomonas aeruginosa, Staphylococcus aureus, Salmonella typhymurium and Shigella
flexneri. This study adds important information to the rational design of new lead anti-TB drugs.
Structure-activity Relationship (SAR) is reported.
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Affiliation(s)
- Cristiane França da Costa
- Instituto de Tecnologia em Farmacos Farmanguinhos, FIOCRUZ Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Maria Cristina da Silva Lourenço
- Instituto de Pesquisas Clinicas Evandro Chagas, Departament of Bacteriology, FIOCRUZ Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Elaine Soares Coimbra
- Instituto de Ciencias Biologicas, Universidade Federal de Juiz de Fora, Juiz de Fora-MG, Brazil
| | | | - James Wardell
- Instituto de Tecnologia em Farmacos Farmanguinhos, FIOCRUZ Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Stephane Lima Calixto
- Instituto de Ciencias Biologicas, Universidade Federal de Juiz de Fora, Juiz de Fora-MG, Brazil
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Gumede NJ, Nxumalo W, Bisetty K, Escuder Gilabert L, Medina-Hernandez MJ, Sagrado S. Prospective computational design and in vitro bio-analytical tests of new chemical entities as potential selective CYP17A1 lyase inhibitors. Bioorg Chem 2019; 94:103462. [PMID: 31818479 DOI: 10.1016/j.bioorg.2019.103462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/27/2019] [Accepted: 11/20/2019] [Indexed: 10/25/2022]
Abstract
The development and advancement of prostate cancer (PCa) into stage 4, where it metastasize, is a major problem mostly in elder males. The growth of PCa cells is stirred up by androgens and androgen receptor (AR). Therefore, therapeutic strategies such as blocking androgens synthesis and inhibiting AR binding have been explored in recent years. However, recently approved drugs (or in clinical phase) failed in improving the expected survival rates for this metastatic-castration resistant prostate cancer (mCRPC) patients. The selective CYP17A1 inhibition of 17,20-lyase route has emerged as a novel strategy. Such inhibition blocks the production of androgens everywhere they are found in the body. In this work, a three dimensional-quantitative structure activity relationship (3D-QSAR) pharmacophore model is developed on a diverse set of non-steroidal inhibitors of CYP17A1 enzyme. Highly active compounds are selected to define a six-point pharmacophore hypothesis with a unique geometrical arrangement fitting the following description: two hydrogen bond acceptors (A), two hydrogen bond donors (D) and two aromatic rings (R). The QSAR model showed adequate predictive statistics. The 3D-QSAR model is further used for database virtual screening of potential inhibitory hit structures. Density functional theory (DFT) optimization provides the electronic properties explaining the reactivity of the hits. Docking simulations discovers hydrogen bonding and hydrophobic interactions as responsible for the binding affinities of hits to the CYP17A1 Protein Data Bank structure. 13 hits from the database search (including five derivatives) are then synthesized in the laboratory as different scaffolds. Ultra high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) in vitro experiments reveals three new chemical entities (NCEs) with half maximal inhibitory concentration (IC50) values against the lyase route at mid-micromolar range with favorable selectivity to the lyase over the hydroxylase route (one of them with null hydroxylase inhibition). Thus, prospective computational design has enabled the design of potential lead lyase-selective inhibitors for further studies.
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Affiliation(s)
- N J Gumede
- Department of Chemistry, Mangosuthu University of Technology, PO Box 12363, Jacobs 4026, South Africa.
| | - W Nxumalo
- Department of Chemistry, University of Limpopo, Private Bag X 1106, Sovenga 0727, South Africa
| | - K Bisetty
- Department of Chemistry, Durban University of Technology, PO Box 1334, Durban 4000, South Africa
| | - L Escuder Gilabert
- Departamento de Química Analítica, Facultad de Farmacia, Universidad de Valencia, Avda. Vicent Andrés Estellés, s/n, E-46100 Burjassot, Valencia, Spain
| | - M J Medina-Hernandez
- Departamento de Química Analítica, Facultad de Farmacia, Universidad de Valencia, Avda. Vicent Andrés Estellés, s/n, E-46100 Burjassot, Valencia, Spain
| | - S Sagrado
- Departamento de Química Analítica, Facultad de Farmacia, Universidad de Valencia, Avda. Vicent Andrés Estellés, s/n, E-46100 Burjassot, Valencia, Spain; Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Avda. Vicent Andrés Estellés, s/n, E-46100 Burjassot, Valencia, Spain
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Pagano A, Mancinelli M, Bianchi L, Giorgi G, Maccagno M, Petrillo G, Tavani C. Nitrobutadienes as powerful benzannulating agents: An unprecedented easy access to rare nitroindoles. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.06.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Zhang J, Ba Y, Wang S, Yang H, Hou X, Xu Z. Nitroimidazole-containing compounds and their antibacterial and antitubercular activities. Eur J Med Chem 2019; 179:376-388. [PMID: 31260891 DOI: 10.1016/j.ejmech.2019.06.068] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 06/23/2019] [Accepted: 06/24/2019] [Indexed: 11/24/2022]
Abstract
Infections especially tuberculosis caused by various bacteria including mycobacteria result in millions of lives every year, but the control of bacterial infections is challenged by the limitation of effective pharmaceuticals against drug-resistant pathogens. Nitroimidazoles belong to a group of nitroheterocyclic compounds that have broad-spectrum activity against a series of organisms such as mycobacteria, anaerobic Gram-positive and Gram-negative bacteria, and some of them have already been used in clinics or under clinical trials for the treatment of infectious diseases. In this review, we made an overview of the recent advances in nitroimidazole-containing compounds with antibacterial and antitubercular activity in the recent 20 years.
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Affiliation(s)
- Jingyu Zhang
- Pharmacy College, Henan University of Chinese Medicine, 450046, Zhengzhou, PR China
| | - Yanyan Ba
- Pharmacy College, Henan University of Chinese Medicine, 450046, Zhengzhou, PR China
| | - Su Wang
- Pharmacy College, Henan University of Chinese Medicine, 450046, Zhengzhou, PR China
| | - Huaixia Yang
- Pharmacy College, Henan University of Chinese Medicine, 450046, Zhengzhou, PR China
| | - Xuehui Hou
- Faculty of Science, Henan University of Animal Husbandry and Economy, 450046, Zhengzhou, PR China.
| | - Zhi Xu
- Huanghuai University, College of Chemistry and Pharmaceutical Engineering, Zhumadian, PR China.
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Suryanarayanan V, Rajavel T, Devi KP, Singh SK. Structure based identification and biological evaluation of novel and potent inhibitors of PCAF catalytic domain. Int J Biol Macromol 2018; 120:823-834. [PMID: 30118769 DOI: 10.1016/j.ijbiomac.2018.08.052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 08/08/2018] [Accepted: 08/09/2018] [Indexed: 12/14/2022]
Abstract
p300/CBP Associated Factor (PCAF), a GNAT family member protein, represent a valid target for therapeutic interventions since its dysfunction has implicated in variety of diseases like cancer, diabetes, inflammatory diseases, etc. Despite its potential for therapeutics, only a small number of PCAF inhibitors were reported. Hence, in this study, the catalytic domain of PCAF was explored to screen novel, potent and cell permeable inhibitor from three small molecule databases like Life Chemical, Maybridge and Chembridge by using Structure Based Virtual Screening (SBVS) method. Further, Induced Fit Docking, Binding Free Energy calculation, Single Point Energy calculation and Molecular Dynamics Simulation were performed on selected hits. In silico results revealed that F2209-0381 has higher binding energy of -109.722 and have greater cell permeability (QPPCaco = 1456.764; QPPMDCK = 742.941) than rest of hits. Cytotoxicity effect and protein expression analysis of F2209-0381 on A549 cells reveals that it exhibited strong inhibition with IC50 value of 58.31 μg/ml and significantly reduced the expression of PCAF after 72 h time point. Thus, this study warrants that F2209-0381 could become a novel, potent and cell permeable drug of PCAF thereby it could combat its mediated diseases.
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Affiliation(s)
- Venkatesan Suryanarayanan
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi 630 004, Tamil Nadu, India
| | - Tamilselvam Rajavel
- Department of Biotechnology, Alagappa University, Karaikudi, 630 004, Tamil Nadu, India
| | - Kasi Pandima Devi
- Department of Biotechnology, Alagappa University, Karaikudi, 630 004, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi 630 004, Tamil Nadu, India.
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Suryanarayanan V, Singh SK. Deciphering the binding mode and mechanistic insights of pentadecylidenemalonate (1b) as activator of histone acetyltransferase PCAF. J Biomol Struct Dyn 2018; 37:2296-2309. [PMID: 30044210 DOI: 10.1080/07391102.2018.1479658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Histone acetyltransferases (HATs) is one among the conspicuous posttranslational modification in eukaryotic cells. p300/CBP Associated Factor (PCAF) and CREB-binding protein (CBP) are the two highly homologous HAT family which are vastly implicated in several diseases like cancer, diabetes, etc. Pentadecylidenemalonate, a simplified analog of anacardic acid, was reported as first mixed inhibitor/activator of HATs which inhibits p300/CBP and activates PCAF. It was appointed earlier as a valuable biological tool to understand the mechanism of lysine acetyltransferases due to its powerful apoptotic effect. In this study, pentadecylidenemalonate was taken for deciphering the binding mode, key interacting residues as well as mechanistic insights on PCAF and CBP as activator and inhibitor, respectively. This study is highly believed to help in rational design on antineoplastic drugs against PCAF. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Venkatesan Suryanarayanan
- a Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics , Alagappa University , Karaikudi , India Communicated by Ramaswamy H. Sarma
| | - Sanjeev Kumar Singh
- a Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics , Alagappa University , Karaikudi , India Communicated by Ramaswamy H. Sarma
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Suryanarayanan V, Singh SK. Unravelling novel congeners from acetyllysine mimicking ligand targeting a lysine acetyltransferase PCAF bromodomain. J Biomol Struct Dyn 2018; 36:4303-4319. [DOI: 10.1080/07391102.2017.1415820] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Venkatesan Suryanarayanan
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu 630004, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu 630004, India
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Suryanarayanan V, Singh SK. Assessment of dual inhibition property of newly discovered inhibitors against PCAF and GCN5 throughin silicoscreening, molecular dynamics simulation and DFT approach. J Recept Signal Transduct Res 2014; 35:370-80. [DOI: 10.3109/10799893.2014.956756] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Suryanarayanan V, Singh SK, Tripathi SK, Selvaraj C, Reddy KK, Karthiga A. A three-dimensional chemical phase pharmacophore mapping, QSAR modelling and electronic feature analysis of benzofuran salicylic acid derivatives as LYP inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2013; 24:1025-1040. [PMID: 23987088 DOI: 10.1080/1062936x.2013.821421] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Lymphoid tyrosine phosphatase (LYP), encoded by the PTPN22 gene, has a critical negative regulatory role in T-cell antigen receptor (TCR) and emerged as a promising drug target for human autoimmune diseases. A five-point pharmacophore with two hydrogen bond acceptors, one hydrogen bond donor and two aromatic ring features was generated for a series of benzofuran salicylic acid derivatives as LYP inhibitors in order to elucidate their anti-autoimmune activity. The generated pharmacophore yielded a significant 3D-QSAR model with r(2) of 0.9146 for a training set of 27 compounds. The model also showed excellent predictive power with Q(2) of 0.7068 for a test set of eight compounds. The investigation of the 3D-QSAR model has revealed the structural insights which could lead to more potent analogues. The most active and inactive compounds were further subjected to electronic structure analysis using density functional theory (DFT) at B3LYP/3-21(∗)G level to support the 3D-QSAR predictions. The results obtained from this study are expected to be useful in the proficient design and development of benzofuran salicylic acid derivatives as inhibitors of LYP.
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Affiliation(s)
- V Suryanarayanan
- a Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics , Alagappa University , Tamil Nadu , India
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Yang Y, Zhang W, Cheng J, Tang Y, Peng Y, Li Z. Pharmacophore, 3D-QSAR, and Bayesian Model Analysis for Ligands Binding at the Benzodiazepine Site of GABAAReceptors: the Key Roles of Amino Group and Hydrophobic Sites. Chem Biol Drug Des 2013; 81:583-90. [DOI: 10.1111/cbdd.12100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/07/2012] [Accepted: 12/12/2012] [Indexed: 01/19/2023]
Affiliation(s)
- Ying Yang
- Shanghai Key Laboratory of Chemical Biology; School of Pharmacy; East China University of Science and Technology; Shanghai; China
| | - Wei Zhang
- Shanghai Key Laboratory of Chemical Biology; School of Pharmacy; East China University of Science and Technology; Shanghai; China
| | | | - Yun Tang
- Shanghai Key Laboratory of New Drug Design; School of Pharmacy; East China University of Science and Technology; PO Box 544, 130 Meilong Road; Shanghai; 200237; China
| | - Yanqing Peng
- Shanghai Key Laboratory of Chemical Biology; School of Pharmacy; East China University of Science and Technology; Shanghai; China
| | - Zhong Li
- Shanghai Key Laboratory of Chemical Biology; School of Pharmacy; East China University of Science and Technology; Shanghai; China
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