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Yunos NM, Wahab HA, Al-Thiabat MG, Sallehudin NJ, Jauri MH. In Vitro and In Silico Analysis of the Anticancer Effects of Eurycomanone and Eurycomalactone from Eurycoma longifolia. PLANTS (BASEL, SWITZERLAND) 2023; 12:2827. [PMID: 37570981 PMCID: PMC10421158 DOI: 10.3390/plants12152827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 08/13/2023]
Abstract
Eurycomanone and eurycomalactone are known quassinoids present in the roots and stems of Eurycoma longifolia. These compounds had been reported to have cytotoxic effects, however, their mechanism of action in a few cancer cell lines have yet to be elucidated. This study was aimed at investigating the anticancer effects and mechanisms of action of eurycomanone and eurycomalactone in cervical (HeLa), colorectal (HT29) and ovarian (A2780) cancer cell lines via Sulforhodamine B assay. Their mechanism of cell death was evaluated based on Hoechst 33342 assay and in silico molecular docking toward DHFR and TNF-α as putative protein targets. Eurycomanone and eurycomalactone exhibited in vitro anticancer effects manifesting IC50 values of 4.58 ± 0.090 µM and 1.60 ± 0.12 µM (HeLa), 1.22 ± 0.11 µM and 2.21 ± 0.049 µM (HT-29), and 1.37 ± 0.13 µM and 2.46 ± 0.081 µM (A2780), respectively. They induced apoptotic cancer cell death in dose- and time-dependent manners. Both eurycomanone and eurycomalactone were also predicted to have good inhibitory potential as demonstrated by the docking into TNF-α with binding affinity of -8.83 and -7.51 kcal/mol, respectively, as well as into DHFR with binding affinity results of -8.05 and -8.87 kcal/mol, respectively. These results support the evidence of eurycomanone and eurycomalactone as anticancer agents via apoptotic cell death mechanism that could be associated with TNF-α and DHFR inhibition as among possible protein targets.
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Affiliation(s)
- Nurhanan Murni Yunos
- Natural Products Division, Forest Research Institute Malaysia, Kepong 52109, Selangor, Malaysia; (N.J.S.); (M.H.J.)
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia;
| | - Habibah A. Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia;
| | - Mohammad G. Al-Thiabat
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia;
| | - Nor Jannah Sallehudin
- Natural Products Division, Forest Research Institute Malaysia, Kepong 52109, Selangor, Malaysia; (N.J.S.); (M.H.J.)
| | - Muhamad Haffiz Jauri
- Natural Products Division, Forest Research Institute Malaysia, Kepong 52109, Selangor, Malaysia; (N.J.S.); (M.H.J.)
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Praseetha NG, Divya UK, Nair S. Identifying the potential role of curcumin analogues as anti-breast cancer agents; an in silico approach. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00312-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Breast cancer ranks top among newly reported cancer cases and most of the women suffers from breast cancer. Development of target therapy using phytochemicals with minimal side effects is trending in health care research. Phytochemicals targets complex multiple signalling events in cancer and are pleiotropic in nature. Thus, the present study was conducted to check the effectivity of curcumin analogues (Capsaicin, Chlorogenic acid, Ferulic acid, Zingerone, Gingerol) against the receptors that are expressed in breast cancer cells and prove its ethno-medicinal value by using bioinformatic tools and softwares like PDB, Patch Dock, PubChem, Chimera and My Presto.
Result
Out of the various curcumin analogues studied, Ferulic acid showed best binding affinity with all the breast cancer cell specific receptors (FGF, MMP9, RNRM1, TGF-beta, DHFR, VEGF and aromatase) which was confirmed through the docking studies.
Conclusion
The current work was a preliminary step towards screening suitable drug candidate against breast cancer using in silico methods. This information can be used further to carry out in vivo studies using selected natural analogues of curcumin as a suitable drug candidate against breast cancer saving time and cost.
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Sharma S, Tyagi R, Srivastava M, Rani K, Kumar D, Asthana S, Raj VS. Identification and validation of potent inhibitor of Escherichia coli DHFR from MMV pathogen box. J Biomol Struct Dyn 2022:1-10. [PMID: 35652895 DOI: 10.1080/07391102.2022.2080113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The present study is conducted to find the solution of rising antimicrobial resistance (AMR) in Escherichia coli which is a pathogen responsible for fatal systemic infections in human and animals. The enzyme dihydrofolate reductase (DHFR) is found in all organisms. In this study DHFR of E. coli (ec-DHFR) and human DHFR (h-DHFR) is targeted by novel chemical entities (NCE) from the Pathogen box of Medicines for Malaria Venture, Switzerland (MMV) using molecular modelling. The in-silico studies were further validated by in-vitro assays. The virtual screening of 400 MMV compounds was conducted using PyRx standard tool followed by manual docking of selected compounds by Autodock vina and Ligplot program. The in-silico studies showed good binding energy and strong hydrogen bond in docking of MMV675968 with ec-DHFR and no hydrogen bond with h-DHFR. This was further validated by the Molecular dynamic studies that revealed high binding free energy in ec-DHFR and in-vitro assays that produced good synergy in combination study of MMV675968 with last line (meropenem) and last resort (colistin) antibiotics. The extensive MD simulation and energetic analysis thus concludes that MMV675968 targets ec-DHFR. The combination studies were conducted with MMV675968 and FDA approved drugs against a panel of multidrug resistant Escherichia coli isolates. The synergistic results obtained in combination studies concluded that in-vitro data is consistent with in-silico data and that MMV675968 is a potential lead for future process of antimicrobial drug development against the multidrug resistance E. coli.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shingini Sharma
- Centre for Drug Design Discovery and Development (C4D), SRM University, Sonepat, Haryana, India.,CCS National Institute of Animal Health, Baghpat, Uttar Pradesh, India
| | - Rashmi Tyagi
- Centre for Drug Design Discovery and Development (C4D), SRM University, Sonepat, Haryana, India
| | - Mitul Srivastava
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
| | - Kusum Rani
- Centre for Drug Design Discovery and Development (C4D), SRM University, Sonepat, Haryana, India
| | - Dhruv Kumar
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Noida, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
| | - V Samuel Raj
- Centre for Drug Design Discovery and Development (C4D), SRM University, Sonepat, Haryana, India
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Kumar A, Srivastava AK, Gangwar SK, Misra N, Brahmachari G, Mondal A, Mondal S. FT-IR, UV–visible, and NMR Spectral Analyses, Molecular Structure, and Properties of Nevadensin Revealed by Density Functional Theory and Molecular Docking. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2018.1458741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Abhishek Kumar
- Department of Physics, University of Lucknow, Lucknow, Uttar Pradesh, India
| | - Ambrish Kumar Srivastava
- P. G. Department of Physics, Veer Kunwar Singh University, Ara, Bihar, India
- Laboratory of Natural Products & Organic Synthesis, Department of Chemistry, Visva-Bharati (a Central University), Santiniketan, West Bengal, India
| | | | - Neeraj Misra
- Department of Physics, University of Lucknow, Lucknow, Uttar Pradesh, India
| | - Goutam Brahmachari
- P. G. Department of Physics, Veer Kunwar Singh University, Ara, Bihar, India
- Laboratory of Natural Products & Organic Synthesis, Department of Chemistry, Visva-Bharati (a Central University), Santiniketan, West Bengal, India
| | - Avijit Mondal
- P. G. Department of Physics, Veer Kunwar Singh University, Ara, Bihar, India
- Laboratory of Natural Products & Organic Synthesis, Department of Chemistry, Visva-Bharati (a Central University), Santiniketan, West Bengal, India
| | - Sadan Mondal
- P. G. Department of Physics, Veer Kunwar Singh University, Ara, Bihar, India
- Laboratory of Natural Products & Organic Synthesis, Department of Chemistry, Visva-Bharati (a Central University), Santiniketan, West Bengal, India
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Insights into the c-Jun N-terminal kinase 3 (JNK3) inhibitors: CoMFA, CoMSIA analyses and molecular docking studies. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02416-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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2,2′-(2-Oxopropane-1,3-diyl)bis-(2-hydroxy-1H-indene-1,3(2H)-dione): synthesis, crystal, electronic and molecular docking studies. SN APPLIED SCIENCES 2019. [DOI: 10.1007/s42452-019-0366-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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7
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Hasan T, Ghalib RM, Mehdi SH, Singh PK, Kumar A, Misra N. Vibrational Spectra, NBO and NLO Analyses, and A Molecular Docking Study of 3a,8a-Dihydroxy-2-Thioxo-1,3,3a,8a-Tetrahydroindeno[1,2-d]Imidazol-8(2H)-One Using DFT. J STRUCT CHEM+ 2018. [DOI: 10.1134/s0022476618050098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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Design and synthesis of some new piritrexim analogs as potential anticancer agents. RESEARCH ON CHEMICAL INTERMEDIATES 2018. [DOI: 10.1007/s11164-017-3132-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Mitra P, Rastogi A, Rajpoot M, Kumar A, Srivastava V. A QSAR model of Olanzapine derivatives as potential inhibitors for 5-HT2A Receptor. Bioinformation 2017; 13:339-342. [PMID: 29162966 PMCID: PMC5680715 DOI: 10.6026/97320630013339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 07/23/2017] [Indexed: 11/23/2022] Open
Abstract
Schizophrenia is a complex, chronic mental disorder, affecting about 21 million people worldwide. It is characterized by symptoms, including distortions in thinking, perception, emotions, disorganized speech, sense of self and behavior. Recently, a numbers of marketed drugs for Schizophrenia are available against dopamine D2 and serotonin 5-HT2A receptors. Here, we docked Olanzapine derivatives (collected from literature) with 5-HT2A Receptor using the program AutoDock 4.2. The docked protein inhibitor complex structure was optimized using molecular dynamics simulation for 5ps with the CHARMM-22 force field using NAMD (NAnoscale Molecular Dynamics program) incorporated in visual molecular dynamics (VMD 1.9.2) and then evaluating the stability of complex structure by calculating RMSD values. NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. A quantitative structure activity relationship (QSAR) model was built using energy-based descriptors as independent variable and pKi value as dependent variable of eleven known Olanzapine derivatives with 5-HT2A Receptor, yielding correlation coefficient r2 of 0.63861. The predictive performance of QSAR model was assessed using different crossvalidation procedures. Our results suggest that a ligand-receptor binding interaction for 5-HT2A receptor using a QSAR model is promising approach to design more potent 5-HT2A receptor inhibitors prior to their synthesis.
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Affiliation(s)
- Pooja Mitra
- Department of Biotechnology, Rama University Uttar Pradesh, Kanpur, India
| | - Aishwarya Rastogi
- Department of Biotechnology, Rama University Uttar Pradesh, Kanpur, India
| | - Mayank Rajpoot
- Department of Biotechnology, Rama University Uttar Pradesh, Kanpur, India
| | - Ajay Kumar
- Department of Biotechnology, Rama University Uttar Pradesh, Kanpur, India
| | - Vivek Srivastava
- Department of Biotechnology, Rama University Uttar Pradesh, Kanpur, India
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Srivastava AK, Kumar A, Misra N. Quantum chemical studies on cocsuline using density functional theory and its docking into dihydrofolate reductase receptor. MAIN GROUP CHEMISTRY 2016. [DOI: 10.3233/mgc-150187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Srivastava AK, Kumar A, Misra N, Manjula P, Sarojini B, Narayana B. Synthesis, spectral (FT-IR, UV-visible, NMR) features, biological activity prediction and theoretical studies of 4-Amino-3-(4-hydroxybenzyl)-1H-1,2,4-triazole-5(4H)-thione and its tautomer. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.11.042] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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12
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Brahmachari G, Das S, Biswas (Sinha) M, Kumar A, Srivastava AK, Misra N. 3,5,7-Trimethoxyphenanthrene-1,4-dione: a new biologically relevant natural phenanthrenequinone derivative from Dioscorea prazeri and studies on its single X-ray crystallographic behavior, molecular docking and other physico-chemical properties. RSC Adv 2016. [DOI: 10.1039/c5ra21490d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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13
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Kumar A, Srivastava AK, Gangwar S, Misra N, Mondal A, Brahmachari G. Combined experimental (FT-IR, UV–visible spectra, NMR) and theoretical studies on the molecular structure, vibrational spectra, HOMO, LUMO, MESP surfaces, reactivity descriptor and molecular docking of Phomarin. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.04.031] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Khilari R, Thakur Y, Pardhi M, Pande R. RNA-Binding Efficacy of N-Phenylbenzohydroxamic Acid: An Invitro and Insilico Approach. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:332-47. [PMID: 25874942 DOI: 10.1080/15257770.2014.1001073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
RNA has attracted recent attention for its key role in gene expression and hence targeting by small molecules for therapeutic intervention. This study is aimed to elucidate the specificity of RNA binding affinity of parent compound of N-arylhydroxamic acids series, N-phenylbenzohydroxamic acid trivially named as PBHA,C6H5NOH.C6H5C˭O. The binding behavior was examined by various biophysical methods such as absorption, fluorescence, and viscosity measurements. Molecular docking was also done. The value of affinity constant and overall binding constant was calculated 5.79±0.03×10(4) M(-1) and K'=1.09±0.03×10(5) M(-1), respectively. The Stern-Volmer constant Ksv obtained was 2.28±0.04×10(4) M(-1). The compound (PBHA) shows a concentration-based enhancement of fluorescence intensity with increasing RNA concentration. Fluorescence quenching of PBHA-RNA complex in presence of K4 [Fe(CN)6] was also observed. Viscometric studies complimented the UV results where a continuous increase in relative viscosity of the RNA solution was observed with added optimal PBHA concentration. All the experimental evidences indicate that PBHA can strongly bind to RNA through an intercalative mode.
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Affiliation(s)
- Rubi Khilari
- a School of Studies in Chemistry, Pt. Ravishankar Shukla University , Raipur , Chhattisgarh , India
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15
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Brahmachari G, Kumar A, Srivastava AK, Gangwar S, Misra N, Gupta VK, Rajnikant R. Synthesis, spectroscopic characterization, X-ray analysis and theoretical studies on the spectral features (FT-IR, 1H-NMR), chemical reactivity, NBO analyses of 2-(4-fluorophenyl)-2-(4-fluorophenylamino)acetonitrile and its docking into IDO enzyme. RSC Adv 2015. [DOI: 10.1039/c5ra15797h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
One-pot green synthesis and combined spectral and theoretical studies of 2-(4-fluorophenyl)-2-(4-fluorophenylamino)acetonitrile along with its X-ray crystallographic properties are described.
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Affiliation(s)
- Goutam Brahmachari
- Laboratory of Natural Products & Organic Synthesis
- Department of Chemistry
- Visva-Bharati (a Central University)
- Santiniketan-731 235
- India
| | - Abhishek Kumar
- Department of Physics
- University of Lucknow
- Lucknow 226007
- India
| | | | - Shashi Gangwar
- Department of Physics
- University of Lucknow
- Lucknow 226007
- India
| | - Neeraj Misra
- Department of Physics
- University of Lucknow
- Lucknow 226007
- India
| | - Vivek K. Gupta
- Post-Graduate Department of Physics & Electronics
- University of Jammu
- Jammu Tawi-180 006
- India
| | - Rajnikant Rajnikant
- Post-Graduate Department of Physics & Electronics
- University of Jammu
- Jammu Tawi-180 006
- India
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In silico identification of potent inhibitors of alpha-synuclein aggregation and its in vivo evaluation using MPTP induced Parkinson mice model. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.biomag.2014.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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In silico designing and characterization of Amiloride derivatives as ion channel modulator. Med Chem Res 2013. [DOI: 10.1007/s00044-012-0096-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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18
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Computational molecular docking studies on anticancer drugs. ASIAN PACIFIC JOURNAL OF TROPICAL DISEASE 2012. [DOI: 10.1016/s2222-1808(12)60254-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Azam F, Prasad MVV, Thangavel N, Ali HI. Molecular docking studies of 1-(substituted phenyl)-3-(naphtha [1, 2-d] thiazol-2-yl) urea/thiourea derivatives with human adenosine A(2A) receptor. Bioinformation 2011; 6:330-4. [PMID: 21814389 PMCID: PMC3143394 DOI: 10.6026/97320630006330] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 06/28/2011] [Indexed: 12/02/2022] Open
Abstract
Computational assessment of the binding interactions of drugs is an important component of computer-aided drug design paradigms. In this perspective, a set of 30 1-(substituted phenyl)-3-(naphtha[1, 2-d] thiazol-2-yl) urea/thiourea derivatives showing antiparkinsonian activity were docked into inhibitor binding cavity of human adenosine A(2A) receptor (AA2AR) to understand their mode of binding interactions in silico. Lamarckian genetic algorithm methodology was employed for docking simulations using AutoDock 4.2 program. The results signify that the molecular docking approach is reliable and produces a good correlation coefficient (r(2) = 0.483) between docking score and antiparkinsonian activity (in terms of % reduction in catalepsy score). Potent antiparkinsonian agents carried methoxy group in the phenyl ring, exhibited both hydrophilic and lipophilic interactions with lower energy of binding at the AA(2A)R. These molecular docking analyses should, in our view, contribute for further development of selective AA(2A)R antagonists for the treatment of Parkinson's disease.
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Affiliation(s)
- Faizul Azam
- Department of Pharmaceutical Chemistry, NIMS Institute of Pharmacy, NIMS University, Jaipur-303121, Rajasthan, India
| | - Medapati Vijaya Vara Prasad
- Department of Pharmaceutical Chemistry, NIMS Institute of Pharmacy, NIMS University, Jaipur-303121, Rajasthan, India
| | - Neelaveni Thangavel
- Department of Pharmaceutical Chemistry, NIMS Institute of Pharmacy, NIMS University, Jaipur-303121, Rajasthan, India
| | - Hamed Ismail Ali
- Department of Pharmaceutical Chemistry, NIMS Institute of Pharmacy, NIMS University, Jaipur-303121, Rajasthan, India
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Algul O, Paulsen JL, Anderson AC. 2,4-Diamino-5-(2'-arylpropargyl)pyrimidine derivatives as new nonclassical antifolates for human dihydrofolate reductase inhibition. J Mol Graph Model 2010; 29:608-13. [PMID: 21146434 DOI: 10.1016/j.jmgm.2010.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 11/03/2010] [Accepted: 11/05/2010] [Indexed: 10/18/2022]
Abstract
Dihydrofolate reductase (DHFR) has been a well-recognized target for the development of therapeutics for human cancers for several decades. Classical inhibitors of DHFR use an active transport mechanism to gain access to the cell; disabling this mechanism creates a pathway for resistance. In response, recent research focuses on nonclassical lipid-soluble DHFR inhibitors that are designed to passively diffuse through the membrane. Here, a new series of propargyl-linked antifolates are investigated as potential nonclassical human DHFR inhibitors. Several of these compounds exhibit potent enzyme inhibition with 50% inhibition concentration values under 500 nM. Molecular docking investigations show that the compounds maintain conserved hydrogen bonds between the pyrimidine ring and the enzyme as well as form van der Waals interactions with critical residues in the active site. Interestingly, the most potent compound, 2,4-diamino-5-(3-(3,4,5-trimethoxyphenyl)prop-1-ynyl)-6-ethylpyrimidine (compound 35), is 3500-fold more potent than trimethoprim, a potent inhibitor of bacterial DHFR but weak inhibitor of human DHFR. The two structural differences between compound 35 and trimethoprim show that the propargyl linkage and the substitution at C6 of the pyrimidine ring are critical to the formation of contacts with Thr 56, Ser 59, Ile 60, Leu 22, Phe 31 and Phe 34 and hence, to enhancing potency. The propargyl-linked antifolates are efficient ligands with a high ratio of potency to the number of non-hydrogen atoms and represent a potentially fruitful avenue for future development of antineoplastic agents.
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Affiliation(s)
- Oztekin Algul
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd., Storrs, CT 06269, USA
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Srivastava V, Gupta SP, Siddiqi MI, Mishra BN. Molecular docking studies on quinazoline antifolate derivatives as human thymidylate synthase inhibitors. Bioinformation 2010; 4:357-65. [PMID: 20975900 PMCID: PMC2951674 DOI: 10.6026/97320630004357] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Accepted: 11/15/2009] [Indexed: 11/29/2022] Open
Abstract
We have performed molecular docking on quinazoline antifolates complexed with human thymidylate synthase to gain insight into the structural
preferences of these inhibitors. The study was conducted on a selected set of one hundred six compounds with variation in structure and activity.
The structural analyses indicate that the coordinate bond interactions, the hydrogen bond interactions, the van der Waals interactions as well as
the hydrophobic interactions between ligand and receptor are responsible simultaneously for the preference of inhibition and potency. In this
study, fast flexible docking simulations were performed on quinazoline antifolates derivatives as human thymidylate synthase inhibitors. The
results indicated that the quinazoline ring of the inhibitors forms hydrophobic contacts with Leu192, Leu221 and Tyr258 and stacking interaction
is conserved in complex with the inhibitor and cofactor.
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Affiliation(s)
- Vivek Srivastava
- Department of Biotechnology, Meerut Institute of Engineering & Technology, Meerut-250005; Department of Biotechnology, Institute of Engineering & Technology, UP Technical University, Sitapur Road, Lucknow 226021
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