1
|
Sharma M, Mittal A, Singh A, Jainarayanan AK, Sharma S, Paliwal S. Pharmacophore-driven identification of N-methyl-D-receptor antagonists as potent neuroprotective agents validated using in vivo studies. Biol Methods Protoc 2020; 5:bpaa013. [PMID: 32913897 PMCID: PMC7474860 DOI: 10.1093/biomethods/bpaa013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 06/25/2020] [Accepted: 07/02/2020] [Indexed: 01/18/2023] Open
Abstract
Alzheimer's disease (AD), apparently the most widespread reason behind dementia, is delineated by a continuous cognitive weakening in the aged. During its progression, N-methyl-D-aspartate receptor (NMDAR) antagonists are known to play a pivotal part in the mechanisms of learning and memory. Since there is an unmet medical need for the treatment of AD, we aim to identify possible chemical compounds targeted toward N-methyl-D-aspartate receptors. Three-dimensional models are developed to unveil some of the essential characteristics of the N-methyl-D-aspartate receptors by using a collection of already discovered N-methyl-D-aspartate receptor inhibitors. This is followed by virtual screening, which results in novel chemical compounds having the potential to inhibit N-methyl-D-aspartate receptors. Molecular docking studies and analysis promulgated two lead compounds with a high LibDock score. The compounds are shortlisted based on high estimated activity, fit values, LibDock score, no violation of Lipinski's, and availability for procuring. Finally, the shortlisted compounds are tested by employing in vivo studies, which we further propose as potential NMDA inhibitors for treating AD.
Collapse
Affiliation(s)
- Mukta Sharma
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, Rajasthan, India
| | - Anupama Mittal
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, Rajasthan, India
| | - Aarti Singh
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, Rajasthan, India
| | | | - Swapnil Sharma
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, Rajasthan, India
| | - Sarvesh Paliwal
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, Rajasthan, India
| |
Collapse
|
2
|
Fayyazi N, Esmaeili S, Taheri S, Ribeiro FF, Scotti MT, Scotti L, Ghasemi JB, Saghaei L, Fassihi A. Pharmacophore Modeling, Synthesis, Scaffold Hopping and Biological β- Hematin Inhibition Interaction Studies for Anti-malaria Compounds. Curr Top Med Chem 2020; 19:2743-2765. [DOI: 10.2174/1568026619666191116160326] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/02/2019] [Accepted: 10/01/2019] [Indexed: 01/23/2023]
Abstract
Backgound:Exploring potent compounds is critical to generating multi-target drug discovery. Hematin crystallization is an important mechanism of malaria.Methods:A series of chloroquine analogues were designed using a repositioning approach to develop new anticancer compounds. Protein-ligand interaction fingerprints and ADMET descriptors were used to assess docking performance in virtual screenings to design chloroquine hybrid β-hematin inhibitors. A PLS algorithm was applied to correlate the molecular descriptors to IC50 values. The modeling presented excellent predictive power with correlation coefficients for calibration and cross-validation of r2 = 0.93 and q2 = 0.72. Using the model, a series of 4-aminoquinlin hybrids were synthesized and evaluated for their biological activity as an external test series. These compounds were evaluated for cytotoxic cell lines and β-hematin inhibition.Results:The target compounds exhibited high β-hematin inhibition activity and were 3-9 times more active than the positive control. Furthermore, all the compounds exhibited moderate to high cytotoxic activity. The most potent compound in the dataset was docked with hemoglobin and its pharmacophore features were generated. These features were used as input to the Pharmit server for screening of six databases.Conclusion:The compound with the best score from ChEMBL was 2016904, previously reported as a VEGFR-2 inhibitor. The 11 compounds selected presented the best Gold scores with drug-like properties and can be used for drug development.
Collapse
Affiliation(s)
- Neda Fayyazi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan, Iran
| | - Somayeh Esmaeili
- Traditional Medicine and Medical Material Research Center (TMRC), Shahid beheshti University of Medical Sciences, Tehran, Iran
| | - Salman Taheri
- Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
| | - Frederico F. Ribeiro
- Synthesis and Drug Delivery Laboratory, Biological Sciences Department, Paraíba State University, João Pessoa, Brazil
| | | | | | - Jahan B. Ghasemi
- College of Sciences, Faculty of Chemistry, University of Tehran, Tehran, Iran
| | - Lotfollah Saghaei
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan, Iran
| | - Afshin Fassihi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan, Iran
| |
Collapse
|
3
|
Aggarwal S, Paliwal D, Kaushik D, Gupta GK, Kumar A. Synthesis, Antimalarial Evaluation and SAR Study of Some 1,3,5-Trisubstituted Pyrazoline Derivatives. LETT ORG CHEM 2019. [DOI: 10.2174/1570178616666190212145754] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The synthesis of a novel series of 1,3,5-trisubstitiuted pyrazoline was achieved by refluxing
chalcone derivative with different heteroaryl hydrazines. The newly synthesized compounds were
characterized by 1H NMR, 13CNMR, mass spectral and elemental analysis data. The synthetic series of
novel pyrazoline hybrids was screened for in vitro schizont maturation assay against chloroquine sensitive
3D7 strain of Plasmodium falciparum. Most of the compounds showed promising in vitro antimalarial
activity against CQ sensitive strain. The preliminary structure-activity relationship study showed
that quinoline substituted analog at position N-1 showed maximum activity followed by benzothiazole
substitution, while phenyl substitution lowers the antimalarial activity. The observed activity was persistent
by the docking study on P. falciparum cystein protease falcipain-2. The pharmacokinetic properties
were also studied using ADME prediction.
Collapse
Affiliation(s)
| | - Deepika Paliwal
- Institute of Pharmaceutical Sciences, Kurukshetra University, Kurukshetra 136119, India
| | - Dhirender Kaushik
- Institute of Pharmaceutical Sciences, Kurukshetra University, Kurukshetra 136119, India
| | - Girish Kumar Gupta
- Department of Pharmaceutical Chemistry, M.M. College of Pharmacy, Maharishi Markandeshwar University, Mullana, Ambala 133203, India
| | - Ajay Kumar
- Institute of Pharmaceutical Sciences, Kurukshetra University, Kurukshetra 136119, India
| |
Collapse
|
4
|
Mishra VK, Mishra M, Kashaw V, Kashaw SK. Synthesis of 1,3,5-trisubstituted pyrazolines as potential antimalarial and antimicrobial agents. Bioorg Med Chem 2017; 25:1949-1962. [DOI: 10.1016/j.bmc.2017.02.025] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 02/09/2017] [Accepted: 02/10/2017] [Indexed: 12/14/2022]
|
5
|
Paliwal S, Mittal A, Sharma M, pandey A, Singh A, Paliwal S. Pharmacophore and molecular docking based identification of novel structurally diverse PDE-5 inhibitors. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1144-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
6
|
Chandrasekaran M, Sakkiah S, Thangapandian S, Namadevan S, Kim HH, Kim YS, Lee KW. Pharmacophore Design for Anti-inflammatory Agent Targeting Interleukin-2 Inducible Tyrosine Kinase (Itk). B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.11.3333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
7
|
Frosch T, Popp J. Structural analysis of the antimalarial drug halofantrine by means of Raman spectroscopy and density functional theory calculations. JOURNAL OF BIOMEDICAL OPTICS 2010; 15:041516. [PMID: 20799794 DOI: 10.1117/1.3432656] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The structure of the antimalarial drug halofantrine is analyzed by means of density functional theory (DFT) calculations, IR, and Raman spectroscopy. Strong, selective enhancements of the Raman bands of halofantrine at 1621 and 1590 cm(-1) are discovered by means of UV resonance Raman spectroscopy with excitation wavelength lambda(exc)=244 nm. These signal enhancements can be exploited for a localization of small concentrations of halofantrine in a biological environment. The Raman spectrum of halofantrine is calculated by means of DFT calculations [B3LYP/6-311+G(d,p)]. The calculation is very useful for a thorough mode assignment of the Raman bands of halofantrine. The strong bands at 1621 and 1590 cm(-1) in the UV Raman spectrum are assigned to combined C[Double Bond]C stretching vibrations in the phenanthrene ring of halofantrine. These bands are considered as putative marker bands for pipi interactions with the biological target molecules. The calculation of the electron density demonstrates a strong distribution across the phenanthrene ring of halofantrine, besides the electron withdrawing effect of the Cl and CF(3) substituents. This strong and even electron density distribution supports the hypothesis of pipi stacking as a possible mode of action of halofantrine. Complementary IR spectroscopy is performed for an investigation of vibrations of polar functional groups of the halofantrine molecule.
Collapse
Affiliation(s)
- Torsten Frosch
- Friedrich-Schiller-Universitat Jena, Institut fur Physikalische Chemie, Jena, Germany.
| | | |
Collapse
|
8
|
Nagarajan S, Ahmed A, Choo H, Cho YS, Oh KS, Lee BH, Shin KJ, Pae AN. 3D QSAR pharmacophore model based on diverse IKKβ inhibitors. J Mol Model 2010; 17:209-18. [PMID: 20419497 DOI: 10.1007/s00894-010-0714-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Accepted: 03/15/2010] [Indexed: 11/24/2022]
Abstract
The inhibitor kappaB kinase β (IKKβ) is a serine-threonine protein kinase that is critically involved in the activation of the transcription factor nuclear factor kappa B (NF-κB) in response to various inflammatory stimuli. IKKβ-selective inhibitors could prove useful for the treatment of inflammatory diseases. In the absence of structural information, a ligand-based approach can serve as an alternative to the virtual screening of large databases. We have developed a 3D QSAR pharmacophore model based on 23 IKKβ inhibitors with 3 nM ≤ IC(50) ≤ 50000 nM. A four-feature pharmacophore containing a hydrophobic (Hy) feature, two ring aromatic (RA) features, and a hydrogen bond donor (D) feature was constructed. It yielded a correlation coefficient of 0.93 with experimentally determined activity data, and a correlation coefficient of 0.77 with training set activity data. The best hypothesis, Hypo 1, was validated by estimating the activities of 136 compounds in a test set. As well as the correlation analysis and test set activity estimation, a Fisher's validation test was conducted at the 95% confidence level. The pharmacophore model's specificity and selectivity were determined in an exhaustive enrichment study.
Collapse
Affiliation(s)
- Shanthi Nagarajan
- Center for Chemoinformatics Research, Life Sciences Division, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Acharya BN, Saraswat D, Tiwari M, Shrivastava AK, Ghorpade R, Bapna S, Kaushik MP. Synthesis and antimalarial evaluation of 1, 3, 5-trisubstituted pyrazolines. Eur J Med Chem 2010; 45:430-8. [DOI: 10.1016/j.ejmech.2009.10.023] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Revised: 07/30/2009] [Accepted: 10/15/2009] [Indexed: 11/27/2022]
|
10
|
Recent advances in the discovery of haem-targeting drugs for malaria and schistosomiasis. Molecules 2009; 14:2868-87. [PMID: 19701131 PMCID: PMC6254801 DOI: 10.3390/molecules14082868] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 07/20/2009] [Accepted: 07/22/2009] [Indexed: 01/29/2023] Open
Abstract
Haem is believed to be the target of some of the historically most important antimalarial drugs, most notably chloroquine. This target is almost ideal as haem is host-derived and the process targeted, haemozoin formation, is a physico-chemical process with no equivalent in the host. The result is that the target remains viable despite resistance to current drugs, which arises from mutations in parasite membrane transport proteins. Recent advances in high-throughput screening methods, together with a better understanding of the interaction of existing drugs with this target, have created new prospects for discovering novel haem-targeting chemotypes and for target-based structural design of new drugs. Finally, the discovery that Schistosoma mansoni also produces haemozoin suggests that new drugs of this type may be chemotherapeutic not only for malaria, but also for schistosomiasis. These recent developments in the literature are reviewed.
Collapse
|
11
|
Acharya BN, Saraswat D, Kaushik MP. Pharmacophore based discovery of potential antimalarial agent targeting haem detoxification pathway. Eur J Med Chem 2008; 43:2840-52. [DOI: 10.1016/j.ejmech.2008.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 02/05/2008] [Accepted: 02/07/2008] [Indexed: 10/22/2022]
|