1
|
Hossen SMM, Eva TA, Karim MS, Mamurat H, Rahat MHH, Nipun TS. Antimicrobial potential, GCMS analysis and molecular docking studies of Coelogyne suaveolens extracts: Identification of bioactive compounds with mechanism of action. Biochem Biophys Rep 2024; 37:101648. [PMID: 38314145 PMCID: PMC10834465 DOI: 10.1016/j.bbrep.2024.101648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 02/06/2024] Open
Abstract
Coelogyne suaveolens has been used as a traditional medicine for many years, and its potential as a natural source of antibacterial agents is of great interest. This investigation aimed to identify the bioactive compounds in the plant extract and assess their antibacterial properties. To achieve this, we identified the bioactive compounds using Gas chromatography mass spectrometry (GCMS) analysis on the extract's ethyl acetate fraction and used the disc diffusion method to determine the antibacterial effect. Additionally, molecular docking were performed to predict the binding affinities of selected phytochemicals against specific proteins in order to identify the root cause of bacterial inhibition. Our results revealed that the extract exhibited significant antibacterial activity against Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli, and Klebsiella pneumoniae, which are common and problematic pathogens. Furthermore, molecular docking studies identified eight best-selected compounds, of which {androstan-17-one, oxime, (5.alpha.)-}, diethofencarb, tetraconazole, {3,6-dimethyl-2,3,3a,4,5,7a-hexahydrobenzofuran}, and geranyl acetate showed a significant binding affinity with best binding interaction with the target enzymes. This suggests that binding to these specific proteins might lead to the mechanism of action of the evaluated antibacterial action. In conclusion, the present study contributes to the growing body of knowledge on natural antimicrobial agents and could have significant implications for the development of new and effective antibacterial agents.
Collapse
Affiliation(s)
- S M Moazzem Hossen
- Department of pharmacy, Faculty of Biological science, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Taslima Akter Eva
- Department of pharmacy, Faculty of Biological science, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Md Sifytul Karim
- Department of pharmacy, Faculty of Biological science, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Husnum Mamurat
- Department of pharmacy, Faculty of Biological science, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Md Habibul Hasan Rahat
- Department of pharmacy, Faculty of Biological science, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Tanzina Sharmin Nipun
- Department of pharmacy, Faculty of Biological science, University of Chittagong, Chittagong, 4331, Bangladesh
| |
Collapse
|
2
|
Liu M, Wang B, Liu H, Xia H, Ding L. Molecular docking, 3D-QASR and molecular dynamics simulations of benzimidazole Pin1 inhibitors. Phys Chem Chem Phys 2024; 26:4643-4656. [PMID: 38251755 DOI: 10.1039/d3cp05658a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Pin1 (protein interacting with never-in-mitosis akinase-1) is a member of the family of peptidylprolyl cis-trans isomerases (PPIases) that specifically recognize and isomerize substrates containing phosphorylated Ser/Thr-Pro sequences. Pin1 is involved in many cellular processes and plays a key role in the cell cycle, transcriptional regulation, cell metabolism, proliferation and differentiation, and its abnormalities lead to degenerative and neoplastic diseases. Pin1 is highly expressed in human cancers and promotes the development of tumors by activating multiple oncogenes and inactivating multiple tumor suppressor genes, making it an attractive target for cancer therapy. In this study, we investigated the binding mechanism and conformational relationship between benzimidazole Pin1 inhibitors and Pin1 proteins by molecular docking, three-dimensional quantitative structure-activity relationship (3D-QSAR) modeling, binding free energy calculations and decomposition, and molecular dynamics simulations. Molecular docking and molecular dynamics simulations disclosed the most likely binding pose of benzimidazoles with the Pin1 protein. The results of 3D-QSAR modeling indicated that electrostatic fields, hydrophobic fields and hydrogen bonding play important roles in the binding process of inhibitors to proteins. The binding free energy calculations and energy decomposition indicated that Lys63, Arg69, Cys113, Leu122, Met130, and Ser154 may be key residues in the binding of benzimidazole-based inhibitors to the Pin1 protein. This study provides an important theoretical basis for the design and optimization of benzimidazole compounds.
Collapse
Affiliation(s)
- Min Liu
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.
| | - Bingli Wang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.
| | - Huan Liu
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.
| | - Haolun Xia
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.
| | - Lina Ding
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.
| |
Collapse
|
3
|
Faris A, Ibrahim IM, Alnajjar R, Hadni H, Bhat MA, Yaseen M, Chakraborty S, Alsakhen N, Shamkh IM, Mabood F, M Naglah A, Ullah I, Ziedan N, Elhallaoui M. QSAR-driven screening uncovers and designs novel pyrimidine-4,6-diamine derivatives as potent JAK3 inhibitors. J Biomol Struct Dyn 2023:1-30. [PMID: 38059345 DOI: 10.1080/07391102.2023.2283168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/08/2023] [Indexed: 12/08/2023]
Abstract
This study presents a robust and integrated methodology that harnesses a range of computational techniques to facilitate the design and prediction of new inhibitors targeting the JAK3/STAT pathway. This methodology encompasses several strategies, including QSAR analysis, pharmacophore modeling, ADMET prediction, covalent docking, molecular dynamics (MD) simulations, and the calculation of binding free energies (MM/GBSA). An efficacious QSAR model was meticulously crafted through the employment of multiple linear regression (MLR). The initial MLR model underwent further refinement employing an artificial neural network (ANN) methodology aimed at minimizing predictive errors. Notably, both MLR and ANN exhibited commendable performance, showcasing R2 values of 0.89 and 0.95, respectively. The model's precision was assessed via leave-one-out cross-validation (CV) yielding a Q2 value of 0.65, supplemented by rigorous Y-randomization. , The pharmacophore model effectively differentiated between active and inactive drugs, identifying potential JAK3 inhibitors, and demonstrated validity with an ROC value of 0.86. The newly discovered and designed inhibitors exhibited high inhibitory potency, ranging from 6 to 8, as accurately predicted by the QSAR models. Comparative analysis with FDA-approved Tofacitinib revealed that the new compounds exhibited promising ADMET properties and strong covalent docking (CovDock) interactions. The stability of the new discovered and designed inhibitors within the JAK3 binding site was confirmed through 500 ns MD simulations, while MM/GBSA calculations supported their binding affinity. Additionally, a retrosynthetic study was conducted to facilitate the synthesis of these potential JAK3/STAT inhibitors. The overall integrated approach demonstrates the feasibility of designing novel JAK3/STAT inhibitors with robust efficacy and excellent ADMET characteristics that surpass Tofacitinib by a significant margin.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Abdelmoujoud Faris
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Ibrahim M Ibrahim
- Biophysics Department, Faculty of Science, Cairo University, Cairo, Egypt
| | - Radwan Alnajjar
- Department of Chemistry, Faculty of Science, University of Benghazi, Benghazi, Libya
| | - Hanine Hadni
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh, Swat, Pakistan
| | - Souvik Chakraborty
- Department of Physiology, Bhairab Ganguly College, Belghoria, Kolkata, West Bengal, India
| | - Nada Alsakhen
- Department of Chemistry, Faculty of Science, The Hashemite University, Zarqa, Jordan
| | - Israa M Shamkh
- Botany and Microbiology Department, Faculty of Science, Cairo University, Cairo, Egypt
| | - Fazal Mabood
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh, Swat, Pakistan
| | - Ahmed M Naglah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ihsan Ullah
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh, Swat, Pakistan
| | - Noha Ziedan
- Department of Physical, Mathematical and Engineering Science, Faculty of Science, Business and Enterprise, University of Chester, Chester, UK
| | - Menana Elhallaoui
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| |
Collapse
|
4
|
Hadni H, Elhallaoui M. Discovery of anti-colon cancer agents targeting wild-type and mutant p53 using computer-aided drug design. J Biomol Struct Dyn 2023; 41:10171-10189. [PMID: 36533393 DOI: 10.1080/07391102.2022.2153919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022]
Abstract
Mutations in the p53 gene are common and occur in over 50% of all cancers, as it is involved in DNA damage repair, cell cycle regulation and apoptosis. Moreover, the p53 gene is mutated in 70% of colon cancers. Therefore, the development of drugs to combat this mutation requires urgent attention. With this in mind, in silico drug design approaches were applied on quinoline derivatives with anticancer activity. In 3D-QSAR study, steric, electrostatic, hydrophobic and H-bond acceptor fields (SEHA) play an important role in prediction and design of new colon cancer compounds. Indeed, the two best CoMSIA/SEHA models with (Q2 = 0.737, R2 = 0.914, R pred 2 = 0.720) and (Q2 = 0.738, R2 = 0.919, R pred 2 = 0.739) show good prediction of human colon carcinoma HCT 116 (p53+/+) and (p53-/-) activities, respectively. Furthermore, the predictive ability and robustness of these models were tested by several validation methods. Molecular docking analyses reveal crucial interactions with the active sites of the p53 protein in both wild type and mutant. Based on these theoretical studies, we designed 10 new compounds with good anticancer activity potential, which were evaluated using ADMET properties. Molecular dynamics simulations were performed to confirm the detailed binding mode of the docking results. Finally, the MM-GBSA based on molecular dynamics simulation confirmed that the designed compounds were able to form stable hydrogen bonding interactions with the crucial residues, which are essential to overcome the p53 mutation in colon cancer.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Hanine Hadni
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Menana Elhallaoui
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| |
Collapse
|
5
|
Saha A, Choudhury AAK, Adhikari N, Ghosh SK, Shakya A, Patgiri SJ, Pratap Singh U, Bhat HR. Molecular docking and antimalarial evaluation of hybrid para-aminobenzoic acid 1,3,5 triazine derivatives via inhibition of Pf-DHFR. J Biomol Struct Dyn 2023; 41:15520-15534. [PMID: 37154740 DOI: 10.1080/07391102.2023.2208207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 03/03/2023] [Indexed: 05/10/2023]
Abstract
In this study, a structurally guided pharmacophore hybridization strategy is used to combine the two key structural scaffolds, para-aminobenzoic acid (PABA), and 1,3,5 triazine in search of new series of antimalarial agents. A combinatorial library of 100 compounds was prepared in five different series as [4A (1-22), 4B (1-21), 4 C (1-20), 4D (1-19) and 4E (1-18)] using different primary and secondary amines, from where 10 compounds were finally screened out through molecular property filter analysis and molecular docking study as promising PABA substituted 1,3,5-triazine scaffold as an antimalarial agent. The docking results showed that compounds 4A12 and 4A20 exhibited good binding interaction with Phe58, IIe164, Ser111, Arg122, Asp54 (-424.19 to -360.34 kcal/mol) and Arg122, Phe116, Ser111, Phe58 (-506.29 to -431.75 kcal/mol) against wild (1J3I) and quadruple mutant (1J3K) type of Pf-DHFR. These compounds were synthesized by conventional as well as microwave-assisted synthesis and characterized by different spectroscopic methods. In-vitro antimalarial activity results indicated that two compounds 4A12 and 4A20 showed promising antimalarial activity against chloroquine-sensitive (3D7) and chloroquine-resistant (Dd2) strains of Plasmodium falciparum with IC50 (1.24-4.77 μg mL-1) and (2.11-3.60 μg mL-1). These hybrid PABA substituted 1,3,5-triazine derivatives might be used in the lead discovery towards a new class of Pf-DHFR inhibitors.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Ashmita Saha
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, India
| | | | - Nayana Adhikari
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, India
| | - Surajit Kumar Ghosh
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, India
| | - Anshul Shakya
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, India
| | - Saurav Jyoti Patgiri
- Regional Medical Research Centre, Indian Council of Medical Research (ICMR), Dibrugarh, India
| | - Udaya Pratap Singh
- Drug Design & Discovery Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture, Technology & Sciences, Allahabad, India
| | - Hans Raj Bhat
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, India
| |
Collapse
|
6
|
Abdullahi M, Uzairu A, Eltayb WA, Shallangwa GA, Mamza PA, Ibrahim MT. 3D-QSAR, homology modelling of influenza hemagglutinin receptor (StrainA/WS/1933), molecular dynamics, DFT, and ADMET studies for newly designed inhibitors. J INDIAN CHEM SOC 2023. [DOI: 10.1016/j.jics.2023.100975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
|
7
|
Hadni H, Bakhouch M, Elhallaoui M. 3D-QSAR, molecular docking, DFT and ADMET studies on quinazoline derivatives to explore novel DHFR inhibitors. J Biomol Struct Dyn 2023; 41:161-175. [PMID: 34825630 DOI: 10.1080/07391102.2021.2004233] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Resistance to folate antagonists is caused by mutations in the dihydrofolate reductase (DHFR) genes. These mutations affect the amino acids at positions 51, 59, 108 and 164 of DHFR, which appear to play a major role in malaria treatment failure. Therefore, the design of new drugs able to overcome the problem of antifolate drug resistance should receive urgent attention. In this study, a three-dimensional quantitative structure-activity relationship (3 D-QSAR) and molecular docking studies have been performed on antimalarial quinazoline derivatives. The CoMFA (Q2 = 0.63, R2 = 0.83 and Rpred2 = 0.70) and the CoMSIA (Q2 = 0.584, R2 = 0.816, and Rpred2= 0.73) models show a good prediction of antimalarial activity. The reliability and robustness of the proposed models have been tested using several validation methods, which showed that the steric, electrostatic, hydrophobic and H-bond acceptor fields of the CoMSIA model play a key role in the prediction of antimalarial activity. Molecular docking studies reveal important interactions between two isomeric compounds (meta and para) and the DHFR receptor in its wild and mutant forms. The obtained outcomes of molecular docking studies have been validated using a new method based on visual inspection. The DFT study of the two isomeric compounds confirms clearly the trends of 3 D-QSAR and molecular docking for the design of new compounds. Moreover, the consistency between theoretical, 3 D-QSAR and molecular docking analysis provides guidance for the design of new drug candidates, which have been tested using ADMET properties and drug likeness analysis.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Hanine Hadni
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohamed Bakhouch
- Laboratory of Bioorganic Chemistry, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, El Jadida, Morocco.,Engineering Laboratory of Organometallic and Molecular Materials and Environment, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Menana Elhallaoui
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| |
Collapse
|
8
|
Zhao J, Liu M, Zang J, Yang S, Chen R, Zhao X, Ding L. Molecular docking, 3D-QASR and molecular dynamics simulations of thiazoles Pin1 inhibitors. J Biomol Struct Dyn 2022; 40:12699-12713. [PMID: 34499020 DOI: 10.1080/07391102.2021.1975568] [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: 12/27/2022]
Abstract
Pin1 (protein interacting with never-in-mitosis akinase-1) is a member of the PPIase (peptidylprolyl cis-trans isomerase) family. It can interact with a variety of carcinogenic or tumor suppressive phosphorylated proteins. The interaction results in the conformational changes of target proteins, and ultimately regulates the activity of these proteins. These activity changes play a key role in tumorigenesis. Pin1 is an attractive target for cancer therapy due to its over-expression and/or activation in various types of cancer and the disorder of Proline directed phosphorylation. In this study, molecular docking, three-dimensional quantitative structure-activity relationship (3D-QSAR) and molecular dynamics (MD) simulations were performed to investigate the structure-activity relationship and binding mechanism of 45 thiazole-class Pin1 inhibitors. Molecular docking studies predict the binding mode and the interactions between the ligand and the receptor protein. The results of the 3 D-QSAR model show that electrostatic field, hydrophobic field and hydrogen bond play important roles in the binding process of inhibitors to protein. Molecular dynamics simulation results reveal that the complex of the ligand and the receptor protein are stable at 300 K. The binding free energy calculation and energy decomposition results show that His59, Cys113, Ser114, Ser115, Leu122, Met130, Gln131, Phe134, Ser154 and His157 may be the key to the inhibitor binding to Pin1 protein. This study provides an important theoretical basis for further development of the new Pin1 inhibitor design. These results can provide more useful information for our further drug design. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Jiangheng Zhao
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Min Liu
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Jieying Zang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Shuangshuang Yang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Ruiyou Chen
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Xin Zhao
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Lina Ding
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| |
Collapse
|
9
|
Adhikari N, Choudhury AAK, Shakya A, Ghosh SK, Patgiri SJ, Singh UP, Bhat HR. Design and development of novel
N
‐(4‐aminobenzoyl)‐
l
‐glutamic acid conjugated 1,3,5‐triazine derivatives as
Pf
‐DHFR inhibitor: An
in‐silico
and
in‐vitro
study. J Biochem Mol Toxicol 2022; 37:e23290. [PMID: 36541419 DOI: 10.1002/jbt.23290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 10/17/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
In the present work, a library of 120 compounds was prepared using various aliphatic and aromatic amines. Finally, 10 compounds were selected through in silico screening carrying 4-aminobenzoyl-l-glutamic acid and 1,3,5-triazine moiety. The docking results of compounds 4d16 and 4d38 revealed higher binding interaction with amino acids Asp54 (-537.96 kcal/mol) and Asp54, Phe116 (-618.22 kcal/mol) against wild (1J3I) and quadruple mutant (1J3K) type of Pf-DHFR inhibitors and were comparable to standard WR99210. These compounds were developed by facile and microwave-assisted synthesis via nucleophilic substitution reaction and characterized by different spectroscopic methods. In vitro antimalarial assay results also suggested that these two compounds were having higher antimalarial activity against chloroquine-sensitive (3D7) and chloroquine-resistant (Dd2) strain out of the ten synthesized compounds with IC50 13.25 μM and 14.72 μM, respectively. These hybrid scaffolds might be useful in the lead discovery of a new class of Pf-DHFR inhibitors.
Collapse
Affiliation(s)
- Nayana Adhikari
- Department of Pharmaceutical Sciences Dibrugarh University Dibrugarh Assam India
| | | | - Anshul Shakya
- Department of Pharmaceutical Sciences Dibrugarh University Dibrugarh Assam India
| | - Surajit K. Ghosh
- Department of Pharmaceutical Sciences Dibrugarh University Dibrugarh Assam India
| | - Saurav J. Patgiri
- Regional Medical Research Centre, Indian Council of Medical Research (ICMR) Dibrugarh Assam India
| | - Udaya P. Singh
- Drug Design & Discovery Laboratory, Department of Pharmaceutical Sciences Sam Higginbottom University of Agriculture, Technology & Sciences Prayagraj Uttar Pradesh India
| | - Hans R. Bhat
- Department of Pharmaceutical Sciences Dibrugarh University Dibrugarh Assam India
| |
Collapse
|
10
|
El Rhabori S, El Aissouq A, Chtita S, Khalil F. QSAR, molecular docking and ADMET studies of quinoline, isoquinoline and quinazoline derivatives against Plasmodium falciparum malaria. Struct Chem 2022. [DOI: 10.1007/s11224-022-01988-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
11
|
Er-rajy M, El Fadili M, Hadni H, Mrabti NN, Zarougui S, Elhallaoui M. 2D-QSAR modeling, drug-likeness studies, ADMET prediction, and molecular docking for anti-lung cancer activity of 3-substituted-5-(phenylamino) indolone derivatives. Struct Chem 2022. [DOI: 10.1007/s11224-022-01913-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
12
|
Density functional theory calculations and molecular docking of 2-phenylbenzimidazoles with estrogen receptor for quantitative structure-activity relationship studies. JOURNAL OF THE SERBIAN CHEMICAL SOCIETY 2022. [DOI: 10.2298/jsc210302044m] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Benzimidazole derivatives, especially 2-phenylbenzimidazole with various substituents on the C-5, C-2 and C-6 positions, are so important in pharmaceutical chemistry. Multiple linear regression was applied to predict the activity of 27 novel 2-phenylbenzimidazole derivatives as anticancer agents. At first, we made an effort to create a QSAR model for a selected series of novel 2-phenylbenzimidazole with density functional theory and molecular docking descriptors. Then, we tried to investigate the nature of the interactions between 2-phenylbenzimidazole derivatives and the estrogen receptor using the molecular docking method. Six descriptors of MATS4e, GATS5e, R6v, R1v+, dipole moment, and torsional free energy were selected for modelling. Due to docking results, increase in the binding energy, and decrease in the dipole moment could increase inhibitor activity.
Collapse
|
13
|
Ibrahim ZY, Uzairu A, Shallangwa GA, Abechi SE. Molecular modeling and design of some β-amino alcohol grafted 1,4,5-trisubstituted 1,2,3-triazoles derivatives against chloroquine sensitive, 3D7 strain of Plasmodium falciparum. Heliyon 2021; 7:e05924. [PMID: 33553724 PMCID: PMC7851792 DOI: 10.1016/j.heliyon.2021.e05924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/13/2020] [Accepted: 01/06/2021] [Indexed: 11/16/2022] Open
Abstract
Resistance nature of Plasmodium falciparum (P. falciparum) to the most effective antimalarial drug, Artemisinin, intimidate the global goal of total eradication of malarial. In an attempt to overcome this challenge, the research was aimed at designing derivatives of β-amino alcohol grafted 1,4,5-trisubstituted 1,2,3-triazoles with improve activity against the P. falciparum through structural modifications of the most active compound (design template), and their activity determined using the developed theoretical predictive model. To achieve this, the geometries were optimized via density functional theory (DFT) using B3LYP/6-31G∗ basis set to generate molecular descriptors for model development. Analysis of the developed model and the descriptors mean effect lead to the design of derivatives with improved activity. Five (5) theoretical models were developed, where the model {pIC50 = 5.95067(SpMin5_Bhi) - 0.0323461(RDF45m) + 0.0203865 (RDF95e) + 0.0499285 (L1m) - 3.50822} with the highest coefficient of determination (R2) of 0.9367, cross-validated R2 (Q2cv) of 0.8242, and the external validated R2 (R2pred) of 0.9462, selected as the best model. The mean effect analysis revealed descriptor SpMin5_Bhi as the most contributive. The descriptor encodes the first ionization potentials of the compounds and are influenced by electron-withdrawing/donating substituents. Hence, structural modifications of the compound with the highest activity (a design template) using electron-withdrawing substituents such as –NO2, –SO3H, -Br, –I, –CH2CH3, and –CH3 was done at a different positions, to obtain five (5) hypothetical novel compounds. The statistical results, shows the robustness, excellent prediction power, and validity of the selected model. Descriptor analysis revealed the first ionization potential (SpMin5_Bhi) to play a significant role in the activity of β-amino alcohol grafted 1,4,5-trisubstituted 1,2,3-triazoles derivatives. The five design derivatives of β-amino alcohol grafted 1,4,5-trisubstituted 1,2,3-triazoles with higher activities revealed compound 21C to have an antimalarial activity of pIC50 = 6.7573 higher than it co-designed compounds and even the standard drug. This claim could be verified through molecular docking to determine their interaction with the target protein.
Collapse
Affiliation(s)
- Zakari Ya'u Ibrahim
- Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, P.M.B, 1045, Zaria, Nigeria
| | - Adamu Uzairu
- Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, P.M.B, 1045, Zaria, Nigeria
| | - Gideon Adamu Shallangwa
- Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, P.M.B, 1045, Zaria, Nigeria
| | - Stephen Eyije Abechi
- Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, P.M.B, 1045, Zaria, Nigeria
| |
Collapse
|
14
|
Prasher P, Sharma M, Aljabali AAA, Gupta G, Negi P, Kapoor DN, Singh I, Zacconi FC, Jesus Andreoli Pinto T, Silva MW, Bakshi HA, Chellappan DK, Tambuwala MM, Dua K. Hybrid molecules based on 1,3,5‐triazine as potential therapeutics: A focused review. Drug Dev Res 2020; 81:837-858. [DOI: 10.1002/ddr.21704] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/25/2020] [Accepted: 05/29/2020] [Indexed: 12/30/2022]
Affiliation(s)
- Parteek Prasher
- UGC‐Sponsored Centre for Advanced Studies, Department of Chemistry Guru Nanak Dev University Amritsar India
- Department of Chemistry University of Petroleum & Energy Studies Dehradun India
| | - Mousmee Sharma
- UGC‐Sponsored Centre for Advanced Studies, Department of Chemistry Guru Nanak Dev University Amritsar India
- Department of Chemistry Uttaranchal University Dehradun India
| | - Alaa A. A. Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology Faculty of Pharmacy, Yarmouk University Irbid Jordan
| | - Gaurav Gupta
- School of Pharmacy Suresh Gyan Vihar University Jaipur India
| | - Poonam Negi
- School of Pharmaceutical Sciences Shoolini University of Biotechnology and Management Sciences Solan India
| | - Deepak N. Kapoor
- School of Pharmaceutical Sciences Shoolini University of Biotechnology and Management Sciences Solan India
| | - Inderbir Singh
- Chitkara College of Pharmacy Chitkara University Punjab India
| | - Flavia C. Zacconi
- Departamento de Organica, faculdad de Quimica y de Farmacia, Pontificia Universidad Catolica de Chile Santiago Chile
| | | | - Mateus Webba Silva
- School of Pharmacy and Pharmaceutical Science Ulster University Coleraine United Kingdom
| | - Hamid A. Bakshi
- School of Pharmacy and Pharmaceutical Science Ulster University Coleraine United Kingdom
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy International Medical University Kuala Lumpur Malaysia
| | - Murtaza M. Tambuwala
- School of Pharmacy and Pharmaceutical Science Ulster University Coleraine United Kingdom
| | - Kamal Dua
- School of Pharmaceutical Sciences Shoolini University of Biotechnology and Management Sciences Solan India
- Discipline of Pharmacy, Graduate School of Health University of Technology Sydney Sydney New South Wales Australia
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute (HMRI) & School of Biomedical Sciences and Pharmacy University of Newcastle Callaghan New South Wales Australia
- Centre for Inflammation, Centenary Institute Royal Prince Alfred Hospital Sydney New South Wales Australia
| |
Collapse
|
15
|
Hadni H, Elhallaoui M. 3D-QSAR, docking and ADMET properties of aurone analogues as antimalarial agents. Heliyon 2020; 6:e03580. [PMID: 32322700 PMCID: PMC7168746 DOI: 10.1016/j.heliyon.2020.e03580] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/27/2020] [Accepted: 03/09/2020] [Indexed: 01/26/2023] Open
Abstract
The development of multi-resistant strains of plasmodium parasite has become a global problem, therefore, the discovery of new antimalarial agents is the only available solution. In order to improve and propose new compounds with antimalarial activity, the three-dimensional quantitative structure-activity relationship (3D-QSAR) and molecular docking studies were carried on aurone analogues acting as Qo site inhibitors in cytochrome b. The 3D-QSAR model was established in this study based on the Comparative Molecular Field Analysis (CoMFA) and the Comparative Molecular Similarity Indices Analysis (CoMSIA). The good predictability was obtained using the CoMFA model (Q2 = 0.5; R2 = 0.97;R pred 2 = 0.72) and the best CoMSIA model (Q2 = 0.526; R2 = 0.915;R pred 2 = 0.765). The predictive capacity of the developed model was evaluated through external validation using a test set compound and an applicability domain technique. In this study, the Steric, electrostatic and hydrogen bond acceptor fields played a key role in antimalarial activity. The results of the molecular docking revealed theoretically the importance of the residues his183 and his82 in the active site of the heme bL, this result was validated by a new assessment method. Based on the previous results, we designed several new potent Cytochrome b inhibitors and their inhibitory activities were predicted by the best model. Furthermore, these new inhibitors were analyzed for their ADMET properties and drug likeness. These results would be of great help in leading optimization for new drug discovery that can solve the problem of multiple drug resistance.
Collapse
Affiliation(s)
- Hanine Hadni
- Engineering Materials, Modeling and Environmental Laboratory, Faculty of Sciences Dhar El mahraz, Sidi Mohammed Ben Abdellah University, B.P. 1796, Atlas, Fes, Morocco
| | | |
Collapse
|
16
|
Hadni H, Elhallaoui M. 2D and 3D-QSAR, molecular docking and ADMET properties in silico studies of azaaurones as antimalarial agents. NEW J CHEM 2020. [DOI: 10.1039/c9nj05767f] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Malaria persists as the most infectious vector-borne disease in the world.
Collapse
Affiliation(s)
- Hanine Hadni
- Engineering Materials
- Modeling and Environmental Laboratory
- Faculty of Sciences Dhar El mahraz
- Sidi Mohammed Ben Abdellah University
- Atlas
| | - Menana Elhallaoui
- Engineering Materials
- Modeling and Environmental Laboratory
- Faculty of Sciences Dhar El mahraz
- Sidi Mohammed Ben Abdellah University
- Atlas
| |
Collapse
|
17
|
Yadav BS, Chaturvedi N, Marina N. Recent Advances in System Based Study for Anti-Malarial Drug Development Process. Curr Pharm Des 2019; 25:3367-3377. [DOI: 10.2174/1381612825666190902162105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 08/30/2019] [Indexed: 12/22/2022]
Abstract
Background:
Presently, malaria is one of the most prevalent and deadly infectious disease across Africa,
Asia, and America that has now started to spread in Europe. Despite large research being carried out in the
field, still, there is a lack of efficient anti-malarial therapeutics. In this paper, we highlight the increasing efforts
that are urgently needed towards the development and discovery of potential antimalarial drugs, which must be
safe and affordable. The new drugs thus mentioned are also able to counter the spread of malaria parasites that
have been resistant to the existing agents.
Objective:
The main objective of the review is to highlight the recent development in the use of system biologybased
approaches towards the design and discovery of novel anti-malarial inhibitors.
Method:
A huge literature survey was performed to gain advance knowledge about the global persistence of
malaria, its available treatment and shortcomings of the available inhibitors. Literature search and depth analysis
were also done to gain insight into the use of system biology in drug discovery and how this approach could be
utilized towards the development of the novel anti-malarial drug.
Results:
The system-based analysis has made easy to understand large scale sequencing data, find candidate
genes expression during malaria disease progression further design of drug molecules those are complementary of
the target proteins in term of shape and configuration.
Conclusion:
The review article focused on the recent computational advances in new generation sequencing,
molecular modeling, and docking related to malaria disease and utilization of the modern system and network
biology approach to antimalarial potential drug discovery and development.
Collapse
Affiliation(s)
- Brijesh S. Yadav
- Department of Bioengineering, University of Information Science and Technology, Partizahska, Ohrid, Macedonia, the Former Yugoslav Republic of
| | - Navaneet Chaturvedi
- Department of Bioengineering, University of Information Science and Technology, Partizahska, Ohrid, Macedonia, the Former Yugoslav Republic of
| | - Ninoslav Marina
- Department of Bioengineering, University of Information Science and Technology, Partizahska, Ohrid, Macedonia, the Former Yugoslav Republic of
| |
Collapse
|
18
|
Hadni H, Elhallaoui M. Molecular docking and QSAR studies for modeling the antimalarial activity of hybrids 4-anilinoquinoline-triazines derivatives with the wild-type and mutant receptor pf-DHFR. Heliyon 2019; 5:e02357. [PMID: 31485537 PMCID: PMC6717158 DOI: 10.1016/j.heliyon.2019.e02357] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 08/12/2019] [Accepted: 08/20/2019] [Indexed: 12/20/2022] Open
Abstract
Plasmodium falciparum dihydrofolate reductase (pf-DHFR) is one of the several targets in the treatment of malaria. Double and quadruple mutations at residues 51, 59, 108, and 164 of pf-DHFR have been linked to antifolate resistance. Several efforts are underway to overcome this drug resistance and to produce potential inhibitors. In this regard, the quantitative structure-activity relationship (QSAR) and docking studies were performed for previously reported 4-anilinoquinoline and 1,3,5-triazines based molecular hybrids. The generated model showed good correlation coefficients (R2 = 0.70) and test set prediction coefficient (R2 = 0.74). These outcomes showed the good predictive competence of the established QSAR model. Based on these results we docked into active site of pf-DHFR protein with the most active (4) and the less active (5) compounds. The docking results revealed that these molecules interact specifically with SER108 and ILE164 in the pf-DHFR binding pocket as that of best active compound but also showed additional interactions with LEU40 and GLY44.
Collapse
Affiliation(s)
- Hanine Hadni
- Engineering Materials, Modeling and Environmental Laboratory, Faculty of Sciences Dhar El mahraz, Sidi Mohammed Ben Abdellah University, B.P. 1796, Atlas, Fes, Morocco
| | | |
Collapse
|