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Mishra A, Jha V, Rajak H. Molecular structural investigations of quinoxaline derivatives through 3D-QSAR, molecular docking, ADME prediction and pharmacophore modeling studies for the search of novel antimalarial agent. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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2
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Chen G, Xie Y, Zhou D, Yang L, Zou L, Cheng M, Liu Y, Li N. In vivo evaluation and atom-based 3D-QSAR studies on saponins from shells of Xanthoceras sorbifolium Bunge as anti-AD agents. Bioorg Chem 2019; 94:103412. [PMID: 31812257 DOI: 10.1016/j.bioorg.2019.103412] [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: 09/10/2019] [Revised: 10/14/2019] [Accepted: 10/28/2019] [Indexed: 02/07/2023]
Abstract
A series of oleanane type of glycosides (1-19), including nine undescribed ones (1-9), were isolated and identified from Xanthoceras sorbifolium. Subsequently, an atom-based 3D-QSAR model was constructed based on results of the in vivo anti-AD evaluation of the isolates (2-3, 10-17) and nine literature-reported anti-AD oleanane type of glycosides to clarify the structure-anti-AD activity, and under the guidance of which 19 was predicted and proved to elicit a nearly equivalent in vivo anti-AD effect as xanthoceraside and donepezil that were used as positive drugs in the Y maze and Morris water maze test.
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Affiliation(s)
- Gang Chen
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
| | - Yumeng Xie
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
| | - Di Zhou
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
| | - Lei Yang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, China
| | - Libo Zou
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yang Liu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Ning Li
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China.
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Asirvatham S, Dhokchawle BV, Tauro SJ. Quantitative structure activity relationships studies of non-steroidal anti-inflammatory drugs: A review. ARAB J CHEM 2019. [DOI: 10.1016/j.arabjc.2016.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Rohini K, Ramanathan K, Shanthi V. Multi-Dimensional Screening Strategy for Drug Repurposing with Statistical Framework—A New Road to Influenza Drug discovery. Cell Biochem Biophys 2019; 77:319-333. [DOI: 10.1007/s12013-019-00887-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 09/16/2019] [Indexed: 12/17/2022]
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James N, Shanthi V, Ramanathan K. Discovery of novel anaplastic lymphoma kinase inhibitors: Structure and energy-based pharmacophore strategy. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The clinical outcomes in patients with non-small cell lung cancer have improved, as a result of anaplastic lymphoma kinase (ALK) inhibition. Therefore in the current study, substantial effort has been made to identify ALK inhibitors through systematic virtual screening experiment consisting of e-pharmacophore and pharmacophore perception techniques. Initially, a pharmacophore model (AAAHP.193) and an e-pharmacophore model (DDRRR) encompassing the whole dataset of 12 known ALK inhibitors were developed. The hypotheses could retrieve effective compounds from DrugBank database (8621 molecules), which were then subjected to molecular docking and ADME prediction. These approaches resulted in the identification of five hits, namely, nebivolol, HDY, D42, 796, and LZE having higher Glide docking scores and promising ADME properties with augmented CNS involvement. Moreover, molecular dynamics simulations were performed to validate the inhibitory activity of the hit compounds, and density functional theory calculations were carried out to scrutinize the chemical reactivity of the hits. Subsequent interaction and scaffold analysis identified prominent interactions of the hits with ALK kinase domain and scaffolds with anti-tumor activity against lung cancer cell lines. We strongly believe that the study provides an outlook for the sighting of novel and potent ALK inhibitors in the near future.
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Affiliation(s)
- Nivya James
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - V. Shanthi
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - K. Ramanathan
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
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Khan MF, Verma G, Alam P, Akhter M, Bakht MA, Hasan SM, Shaquiquzzaman M, Alam MM. Dibenzepinones, dibenzoxepines and benzosuberones based p38α MAP kinase inhibitors: Their pharmacophore modelling, 3D-QSAR and docking studies. Comput Biol Med 2019; 110:175-185. [PMID: 31173941 DOI: 10.1016/j.compbiomed.2019.05.023] [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: 12/03/2018] [Revised: 05/30/2019] [Accepted: 05/30/2019] [Indexed: 01/24/2023]
Abstract
In the present study, a series of dibenzepinones, dibenzoxepines, and benzosuberones targeting p38α MAP kinase were subjected to pharmacophore modelling, 3D-QSAR and molecular docking studies. The IC50 values for these 67 compounds ranged between 0.003 and 6.80 μM. A five-point model (DDHHR.8) was generated using these compounds. This model was found to be statistically significant and was found to have high correlation (R2 = 0.98), cross-validation coefficient (Q2 = 0.95) and F (330) values at six component PLS factor. Tests were performed to ascertain the efficacy of the generated model. These tests included external validation, Tropsha's test for predictive ability, Y-randomisation test and domain of applicability (APD). In order to check the restrictivity of the model, enrichment studies were performed with inactive compounds by using decoy set molecules. To evaluate the effectiveness of the docking protocol, the co-crystallised ligand was extracted from the ligand-binding domain of the protein and was re-docked into the same position. Both the conformers were then superimposed, suggesting satisfactory docking parameters with an RMSD value of less than 1.0 Å (0.853 Å). A 10 ns molecular dynamics simulation confirmed the docking results of the 3UVP-ligand complex and the presumed active conformation. The outcome of the present study provides insight into the molecular features that promote bioactivity and can be exploited for the prediction of novel potent p38α MAP kinase inhibitors before carrying out their synthesis and anticancer evaluation.
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Affiliation(s)
- Mohemmed Faraz Khan
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Garima Verma
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Perwez Alam
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mymoona Akhter
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Md Afroz Bakht
- Department of Chemistry, College of Science and Humanities, Prince Sattam Bin Abdulaziz University, P.O. Box- 173, Al-Kharj, Saudi Arabia
| | - Syed Misbahul Hasan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Integral University, Lucknow, 226026, India
| | - Mohammad Shaquiquzzaman
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Mohammad Mumtaz Alam
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India.
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Hyphenated 3D-QSAR statistical model-drug repurposing analysis for the identification of potent neuraminidase inhibitor. Cell Biochem Biophys 2018; 76:357-376. [PMID: 29687225 DOI: 10.1007/s12013-018-0844-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 04/10/2018] [Indexed: 01/30/2023]
Abstract
The Influenza A virus is one of the principle causes of respiratory illness in human. The surface glycoprotein of the influenza virus, neuraminidase (NA), has a vital role in the release of new viral particle and spreads infection in the respiratory tract. It has been long recognized as a valid drug target for influenza A virus infection. Oseltamivir is used as a standard drug of choice for the treatment of influenza. However, the emergence of mutants with novel mutations has increased the resistance to potent NA inhibitor. In the present investigation, we have employed computer-assisted combinatorial techniques in the screening of 8621 molecules from Drug Bank to find potent NA inhibitors. A three-dimensional pharmacophore model was generated from the previously reported 28 carbocylic influenza NA inhibitors along with oseltamivir using PHASE module of Schrödinger Suite. The model generated consists of one hydrogen bond acceptor (A), one hydrogen bond donors (D), one hydrophobic group (H), and one positively charged group (P), ADHP. The hypothesis was further validated for its integrity and significance using enrichment analysis. Subsequently, an atom-based 3D-QSAR model was built using the common pharmacophore hypothesis (CPH). The developed 3D-QSAR model was found to be statistically significant with R2 value of 0.9866 and Q2 value of 0.7629. Further screening was accomplished using three-stage docking process using the Glide algorithm. The resultant lead molecules were examined for its drug-like properties using the Qikprop algorithm. Finally, the calculated pIC50 values of the lead compounds were validated by the AutoQSAR algorithm. Overall, the results from our analysis highlights that lisinopril (DB00722) is predicted to bind better with NA than currently approved drug. In addition, it has the best match in binding geometry conformations with the existing NA inhibitor. Note that the antiviral activity of lisinopril is reported in the literature. However, our paper is the first report on lisinopril activity against influenza A virus infection. These results are envisioned to help design the novel NA inhibitors with an increased antiviral efficacy.
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Bhadoriya KS, Sharma MC, Jain SV. 2,4-Dihydropyrano[2,3-c]pyrazole: Discovery of new lead as through pharmacophore modelling, atom-based 3D-QSAR, virtual screening and docking strategies for improved anti-HIV-1 chemotherapy. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2018. [DOI: 10.1016/j.jtusci.2014.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Kamlendra Singh Bhadoriya
- Department of Pharmaceutical Chemistry, Sri Aurobindo Institute of Pharmacy (SAIP)Indore-Ujjain State Highway, Near MR-10 Crossing, Sanwer RoadIndoreMP 453111India
| | - Mukesh C. Sharma
- School of Pharmacy, Devi Ahilya VishwavidyalayaTakshashila Campus, Ring RoadIndoreMP 452017India
| | - Shailesh V. Jain
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma UniversityS.G. HighwayAhmedabadGujarat 382481India
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Hadaji EG, Bourass M, Ouammou A, Bouachrine M. 3D-QSAR models to predict anti-cancer activity on a series of protein P38 MAP kinase inhibitors. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2018. [DOI: 10.1016/j.jtusci.2016.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- El Ghalia Hadaji
- Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdallah, Fez, Morocco
| | - Mohamed Bourass
- Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdallah, Fez, Morocco
| | - Abdelkarim Ouammou
- Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdallah, Fez, Morocco
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