1
|
Modi P, Patel S, Chhabria M. Discovery of newer pyrazole derivatives with potential anti-tubercular activity via 3D-QSAR based pharmacophore modelling, virtual screening, molecular docking and molecular dynamics simulation studies. Mol Divers 2023; 27:1547-1566. [PMID: 35969333 DOI: 10.1007/s11030-022-10511-8] [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: 05/10/2022] [Accepted: 07/30/2022] [Indexed: 11/28/2022]
Abstract
Tuberculosis is one of the leading causes of death of at least one million people annually. The deadliest infectious disease has caused more than 120 million deaths in humans since 1882. The cell wall structure of Mycobacterium tuberculosis is important for survival in the host environment. InhA is the foremost target for the development of novel anti-tubercular agents. Therefore, we report pharmacophore-based virtual screening (ZINC and ASINEX databases) and molecular docking study (PDB Code: 4TZK) to identify and design potent inhibitors targeting to InhA. A five-point pharmacophore model AADHR_1 (with R2 = 0.97 and Q2 = 0.77) was developed by using 47 compounds with its reported MIC values. Further, to identify and design potent hit molecules based on lead identification and modification, generated hypothesis employed for virtual screening using ZINC and ASINEX databases. Predicted pyrazole derivatives further gauged for drug likeliness and docked against enoyl acyl carrier protein reductase to categorize the essential amino acid interactions to the active site of the enzyme. Structure elucidation of these synthesized compounds was carried out using IR, MS, 1H-NMR and 13C-NMR spectroscopy. Amongst all the synthesized compounds, some of the compounds 5a, 5c, 5d and 5e were found to be potent with their MIC ranging from 2.23 to 4.61 µM. Based on preliminary anti-tubercular activity synthesized potent molecules were further assessed for MDR-TB, XDR-TB and cytotoxic study.
Collapse
Affiliation(s)
- Palmi Modi
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Ahmedabad, Gujarat, 380009, India
- L. J. Institute of Pharmacy, L J University, Ahmedabad, Gujarat, 382 210, India
| | - Shivani Patel
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Ahmedabad, Gujarat, 380009, India
- Division of Biological and Life Sciences, Ahmedabad University, Ahmedabad, Gujarat, 380009, India
| | - Mahesh Chhabria
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Ahmedabad, Gujarat, 380009, India.
| |
Collapse
|
2
|
Shafiq N, Shahzad N, Rida F, Ahmad Z, Nazir HA, Arshad U, Zareen G, Attiq N, Parveen S, Rashid M, Ali B. One-pot multicomponent synthesis of novel pyridine derivatives for antidiabetic and antiproliferative activities. Future Med Chem 2023; 15:1069-1089. [PMID: 37503685 DOI: 10.4155/fmc-2023-0132] [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] [Indexed: 07/29/2023] Open
Abstract
Background: Due to the close relationship of diabetes with hypertension reported in various research, a set of pyridine derivatives with US FDA-approved drug cores were designed and integrated by artificial intelligence. Methods: Novel pyridines were designed and synthesized. Compounds MNS-1-MNS-4 were evaluated for their structure and were screened for their in vitro antidiabetic (α-amylase) activity and anticancer (HepG2) activity by methyl thiazolyl tetrazolium assay. Comparative 3D quantitative structure-activity relationship analysis and pharmacophore generation were carried out. Results: The study revealed MNS-1 and MNS-4 as good alternatives to acarbose as antidiabetic agents, and MNS-2 as a more viable, better alternative to doxorubicin in the methyl thiazolyl tetrazolium assay. Conclusion: This combination of studies identifies new and more active analogs of existing FDA-approved drugs for the treatment of diabetes.
Collapse
Affiliation(s)
- Nusrat Shafiq
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Nabeel Shahzad
- Department of Chemistry, University of WAH, Wah Cantt, 44700, Pakistan
| | - Fatima Rida
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Zaheer Ahmad
- Department of Chemistry, University of WAH, Wah Cantt, 44700, Pakistan
| | - Hafiza Ayesha Nazir
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Uzma Arshad
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Gul Zareen
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Naila Attiq
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Shagufta Parveen
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Maryam Rashid
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Basharat Ali
- Department of Chemistry, Khawaja Fareed University of Engineering & Information Technology, Rahim Yar Khan, Punjab, 64200, Pakistan
| |
Collapse
|
3
|
Huo X, Gu Y, Zhang Y. The discovery of multi-target compounds with anti-inflammation activity from traditional Chinese medicine by TCM-target effects relationship spectrum. JOURNAL OF ETHNOPHARMACOLOGY 2022; 293:115289. [PMID: 35427724 DOI: 10.1016/j.jep.2022.115289] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/26/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Rhei Radix et Rhizoma, Lonicerae Japonicae Flos and Zingiberis Rhizoma was widely used in the treatment of inflammatory disease. The discovery of new multi-target compounds for new drug from the TCM was a possible direction. AIM OF THE STUDY Multi-target compounds screening based on polypharmacology was an effective method. As an interdisciplinary field, polypharmacology screen multi-target compounds by various methods. So, a flexible screening framework to avoid the disadvantage of single methods is considered to have great significance. MATERIALS AND METHODS The research propose a common framework called Traditional Chinese medicine target-effect relationship spectrum (TCM-TERS). TCM-TERS was constructed based on the pharmacophore and molecular docking models, which provided predicted activity by compounds screening. TCM-TERS merge the results of different models and visualize the targeted activity of each compounds. Then the TCM-TERS were analyzed by the analytic hierarchy process and active components were chosen by the contributing factors. The activity of components was verified on the RAW264.7 by RT-PCR. RESULTS This article constructed TCM-TERS of Rhei Radix et Rhizoma, Lonicerae Japonicae Flos and Zingiberis Rhizoma with the COX-2, mPGES-1, 5-LOX and SPLA2-IIA. Seven compounds were chosen with multiple targeted activity based on the TCM-TERS, which showed remarkable activity in RT-PCR. CONCLUSION The TCM-TERS was an efficient interdisciplinary method for drug discovery of the TCM, which provide a flexible method to the researcher that can screen specific compounds with multiple screening methods.
Collapse
Affiliation(s)
- Xiaoqian Huo
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China.
| | - Yu Gu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China.
| | - Yanling Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China.
| |
Collapse
|
4
|
Structure-Based Virtual Screening of Benzaldehyde Thiosemicarbazone Derivatives against DNA Gyrase B of Mycobacterium tuberculosis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:6140378. [PMID: 34938343 PMCID: PMC8687812 DOI: 10.1155/2021/6140378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/24/2021] [Indexed: 11/28/2022]
Abstract
Emergence of antibiotic-resistant Mycobacterium tuberculosis (M. tuberculosis) restricts the availability of drugs for the treatment of tuberculosis, which leads to the increased morbidity and mortality of the disease worldwide. There are many intrinsic and extrinsic factors that have been reported for the resistance mechanism. To overcome such mechanisms, chemically synthesized benzaldehyde thiosemicarbazone derivatives were screened against M. tuberculosis to find potential inhibitor for tuberculosis. Such filtering process resulted in compound 13, compound 21, and compound 20 as the best binding energy compounds against DNA gyrase B, an important protein in the replication process. The ADMET prediction has shown the oral bioavailability of the novel compounds.
Collapse
|
5
|
Arshad U, Ahmed S, Shafiq N, Ahmad Z, Hassan A, Akhtar N, Parveen S, Mehmood T. Structure-Based Designing, Solvent Less Synthesis of 1,2,3,4-Tetrahydropyrimidine-5-carboxylate Derivatives: A Combined In Vitro and In Silico Screening Approach. Molecules 2021; 26:molecules26154424. [PMID: 34361577 PMCID: PMC8348070 DOI: 10.3390/molecules26154424] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/02/2021] [Accepted: 07/18/2021] [Indexed: 11/16/2022] Open
Abstract
Objective: In this study, small molecules possessing tetrahydropyrimidine derivatives have been synthesized having halogenated benzyl derivatives and carboxylate linkage. As previously reported, FDA approved halogenated pyrimidine derivatives prompted us to synthesize novel compounds in order to evaluate their biological potential. Methodology: Eight pyrimidine derivatives have been synthesized from ethyl acetoacetate, secondary amine, aromatic benzaldehyde by adding catalytic amount of CuCl2·2H2O via solvent less Grindstone multicomponent reagent method. Molecular structure reactivity and virtual screening were performed to check their biological efficacy as an anti-oxidant, anti-cancer and anti-diabetic agent. These studies were supported by in vitro analysis and QSAR studies. Results: After combined experimental and virtual screening 5c, 5g and 5e could serve as lead compounds, having low IC50 and high binding affinity.
Collapse
Affiliation(s)
- Uzma Arshad
- Department of Chemistry, Government College Women University Faisalabad, Faisalabad 38000, Pakistan; (U.A.); (A.H.); (S.P.)
| | - Sibtain Ahmed
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
- Correspondence: (S.A.); or (N.S.)
| | - Nusrat Shafiq
- Department of Chemistry, Government College Women University Faisalabad, Faisalabad 38000, Pakistan; (U.A.); (A.H.); (S.P.)
- Correspondence: (S.A.); or (N.S.)
| | - Zaheer Ahmad
- Department of Chemistry, University of Wah, Rawalpindi 47000, Pakistan;
| | - Aqsa Hassan
- Department of Chemistry, Government College Women University Faisalabad, Faisalabad 38000, Pakistan; (U.A.); (A.H.); (S.P.)
| | - Naseem Akhtar
- Department of Chemistry, Government Sadiq College Women University, Bahawalpur 63000, Pakistan;
| | - Shagufta Parveen
- Department of Chemistry, Government College Women University Faisalabad, Faisalabad 38000, Pakistan; (U.A.); (A.H.); (S.P.)
| | - Tahir Mehmood
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan;
| |
Collapse
|
6
|
Al-Soliemy AM, Sabour R, Farghaly TA. Pyrazoles and fused pyrimidines: Synthesis, structure elucidation, antitubercular activity and molecular docking study. Med Chem 2021; 18:181-198. [PMID: 33761862 DOI: 10.2174/1573406417666210324131951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/21/2020] [Accepted: 12/14/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Synthesis of new heterocyclic drugs in short reaction time with sufficient quantity is considered as a target for several pharmaceutical scientists. Thus, organic reactions proceeded on the surface of nano-sized catalysts to speed up the stimulation process. OBJECTIVE we aimed in this research to synthesize a new series of heterocyclic compounds carrying pyrazole moiety in the presence of ZnO nano-catalyst to investigate their anti-tubercular activity. METHODS ZnO(NPs) was used in synthesis of novel series of thienylpyrazolopyrimidines bearing arylazo group by reaction of thiophene-enaminone and the amino-arylazopyrazoles in excellent yield. On the other hand, another series of theinyl-pyrazoles was synthesized through the reaction of the same enaminone with hydrazonoyl chlorides but the usage of ZnO(NPs) failed in such reactions. RESULTS The proposed structures of the products and the mechanistic pathways of the reactions were assured based on the spectral data and chemical evidences. Thienylpyrazole derivatives were assessed for their activity as Mycobacterium tuberculosis inhibitor and their results revealed that two thienylpyrazole derivatives 24d & 24f showed the most significant anti-mycobacterial activity with MIC values 0.70 & 1.29 µM/mL, respectively comparing with the MIC value = 0.60 µM/mL of the standard drug Rifampicin. Furthermore, the most active thienylpyrazole derivatives were investigated for their cytotoxic impact versus normal cells WI-38 (Normal human Lung fibroblast cells) using MTT assay. These thienylpyrazole derivatives exhibited good selective index profile. Moreover, 1,3,4-trisubstituted pyrazole analogues showed good interaction with the active site of enoyl-acyl carrier protein reductase (Mt InhA) through the molecular docking studies. CONCLUSION We succeeded to synthesis a new series of heterocyclic compounds carrying pyrazole moiety in the presence of ZnO nano-catalyst as anti-tubercular agents.
Collapse
Affiliation(s)
- Amerah M Al-Soliemy
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah. Saudi Arabia
| | - Rehab Sabour
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo. Egypt
| | - Thoraya A Farghaly
- Department of Chemistry, Faculty of Science, University of Cairo, Giza, 12613. Egypt
| |
Collapse
|
7
|
Profiling of Potential Antibacterial Compounds of Lactic Acid Bacteria against Extremely Drug Resistant (XDR) Acinetobacter baumannii. Molecules 2021; 26:molecules26061727. [PMID: 33808805 PMCID: PMC8003687 DOI: 10.3390/molecules26061727] [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: 01/29/2021] [Revised: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 11/17/2022] Open
Abstract
A total of 20 of isolates of lactic acid bacteria (LAB) were selected and screened for antagonistic activity against clinical strains of 30 clinical isolates of extremely drug-resistant (XDR) Acinetobacter baumannii using the well diffusion assay method. Results showed that 50% of the highly LAB strains possessed inhibitory activity against (up to 66%) of the XDR A. baumannii strains tested. The supernatant of the twenty LAB strains was subjected to gas chromatography mass spectrometry (GCMS) revealed that the common compound found in the active isolates against XDR A. baumannii was 3-Isobutyl-2,3,6,7,8,8a-hexahydropyrrolo[1,2-a]pyrazine-1,4-dione, a known potential diketopiperazine group. The molecular docking study against potential antibacterial targets with selected ligands was performed to predict the binding mode of interactions, which is responsible for antibacterial activity. The docking analysis of the potent compounds supported the potential antibacterial activity exhibiting high inhibition constant and binding affinity in silico.
Collapse
|
8
|
Peytam F, Adib M, Shourgeshty R, Firoozpour L, Rahmanian-Jazi M, Jahani M, Moghimi S, Divsalar K, Faramarzi MA, Mojtabavi S, Safari F, Mahdavi M, Foroumadi A. An efficient and targeted synthetic approach towards new highly substituted 6-amino-pyrazolo[1,5-a]pyrimidines with α-glucosidase inhibitory activity. Sci Rep 2020; 10:2595. [PMID: 32054916 PMCID: PMC7018746 DOI: 10.1038/s41598-020-59079-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/16/2019] [Indexed: 01/10/2023] Open
Abstract
In an attempt to find novel α-glucosidase inhibitors, an efficient, straightforward reaction to synthesize a library of fully substituted 6-amino-pyrazolo[1,5-a]pyrimidines 3 has been investigated. Heating a mixture of α-azidochalcones 1 and 3-aminopyrazoles 2 under the mild condition afforded desired compounds with a large substrate scope in good to excellent yields. All obtained products were evaluated as α-glucosidase inhibitors and exhibited excellent potency with IC50 values ranging from 15.2 ± 0.4 µM to 201.3 ± 4.2 µM. Among them, compound 3d was around 50-fold more potent than acarbose (IC50 = 750.0 ± 1.5 µM) as standard inhibitor. Regarding product structures, kinetic study and molecular docking were carried out for two of the most potent ones.
Collapse
Affiliation(s)
- Fariba Peytam
- School of Chemistry, College of Science, University of Tehran, Tehran, Iran.,Department of Medicinal Chemistry, Faculty of Pharmacy and The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Adib
- School of Chemistry, College of Science, University of Tehran, Tehran, Iran.
| | - Reihaneh Shourgeshty
- School of Chemistry, College of Science, University of Tehran, Tehran, Iran.,Department of Medicinal Chemistry, Faculty of Pharmacy and The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Loghman Firoozpour
- Department of Medicinal Chemistry, Faculty of Pharmacy and The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Mahmoud Rahmanian-Jazi
- Department of Medicinal Chemistry, Faculty of Pharmacy and The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Jahani
- School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Setareh Moghimi
- Department of Medicinal Chemistry, Faculty of Pharmacy and The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Kouros Divsalar
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Ali Faramarzi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Somayeh Mojtabavi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Safari
- Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran
| | - Mohammad Mahdavi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Foroumadi
- Department of Medicinal Chemistry, Faculty of Pharmacy and The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran. .,Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran.
| |
Collapse
|
9
|
Du S, Yang B, Wang X, Li WY, Lu XH, Zheng ZH, Ma Y, Wang RL. Identification of potential leukocyte antigen-related protein (PTP-LAR) inhibitors through 3D QSAR pharmacophore-based virtual screening and molecular dynamics simulation. J Biomol Struct Dyn 2019; 38:4232-4245. [PMID: 31588870 DOI: 10.1080/07391102.2019.1676825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Owing to its negative regulatory role in insulin signaling, protein tyrosine phosphatase of leukocyte antigen-related protein (PTP-LAR) was widely thought as a potential drug target for diabetes. Now, it was urgent to search for potential LAR inhibitors targeting diabetes. Initially, the pharmacophore models of LAR inhibitors were established with the application of the HypoGen module. The cost analysis, test set validation, as well as Fischer's test was used to verify the efficiency of pharmacophore model. Then, the best pharmacophore model (Hypo-1-LAR) was applied for the virtual screening of the ZINC database. And 30 compounds met the Lipinski's rule of five. Among them, 10 compounds with better binding affinity than the known LAR inhibitor (BDBM50296375) were discovered by docking studies. Finally, molecular dynamics simulations and post-analysis experiments (RMSD, RMSF, PCA, DCCM and RIN) were conducted to explore the effect of ligands (ZINC97018474 and Compound 1) on LAR and preliminary understand why ZINC97018474 had better inhibitory activity than Compound 1 (BDBM50296375). Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shan Du
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Bing Yang
- Department of Cell Biology, School of Basic Medical Science, Tianjin Medical University, Tianjin, China
| | - Xin Wang
- Tasly Pharmaceutical Group Co., Ltd, Tianjin, China
| | - Wei-Ya Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xin-Hua Lu
- Key Laboratory for New Drug Screening Technology of Shijiazhuang City, New Drug Research & Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering & Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Shijiazhuang, Hebei, China
| | - Zhi-Hui Zheng
- Key Laboratory for New Drug Screening Technology of Shijiazhuang City, New Drug Research & Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering & Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Shijiazhuang, Hebei, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| |
Collapse
|
10
|
Liu YY, Ding TT, Feng XY, Xu WR, Cheng XC. Virtual identification of novel peroxisome proliferator-activated receptor (PPAR) α/δ dual antagonist by 3D-QSAR, molecule docking, and molecule dynamics simulation. J Biomol Struct Dyn 2019; 38:4143-4161. [PMID: 31556349 DOI: 10.1080/07391102.2019.1673211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The therapeutic potential of PPARs antagonists extends beyond diabetes. PPARs antagonists represent a new drug class that holds promise as a broadly applicable therapeutic approach for cancer treatment. Thus, there is a strong need to develop a rational design strategy for creating PPARs antagonists. In this study, three-dimensional quantitative structure-activity relationship (3D-QSAR) models of PPARα receptor (CoMFA-1, q 2 = 0.636, r 2 = 0.953; CoMSIA-1, q 2 = 0.779, r 2 = 0.999) and PPARδ receptor (CoMFA-2, q 2 = 0.624, r 2 = 0.906; CoMSIA-2, q 2 = 0.627, r 2 = 0.959) were successfully constructed using 35 triazolone ring derivatives. Contour map analysis revealed that the electrostatic and hydrophobic fields played vital roles in the bioactivity of dual antagonists. Molecular docking studies suggested that the hydrogen bonding, electrostatic and hydrophobic interactions all influenced the binding of receptor-ligand complex. Based on the information obtained above, we designed a series of compounds. The docking results were mutually validated with 3D-QSAR results. Three-dimensional-QSAR and absorption, distribution, metabolism, excretion and toxicity (ADMET) predictions indicated that 19 newly designed compounds possessed excellent biological activity and physicochemical properties. In summary, this research could provide theoretical guidance for the structural optimization of novel PPARα and δ dual antagonists. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Ya-Ya Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ting-Ting Ding
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xiao-Yan Feng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| |
Collapse
|
11
|
Liu YY, Feng XY, Jia WQ, Jing Z, Xu WR, Cheng XC. Virtual identification of novel PPARα/γ dual agonists by 3D-QSAR, molecule docking and molecular dynamics studies. J Biomol Struct Dyn 2019; 38:2672-2685. [DOI: 10.1080/07391102.2019.1656110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Ya-Ya Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xiao-Yan Feng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wen-Qing Jia
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Zhi Jing
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| |
Collapse
|
12
|
Jia WQ, Liu YY, Feng XY, Xu WR, Cheng XC. Discovery of novel and highly selective PI3Kδ inhibitors based on the p110δ crystal structure. J Biomol Struct Dyn 2019; 38:2499-2508. [PMID: 31232196 DOI: 10.1080/07391102.2019.1635531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Wen-Qing Jia
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ya-Ya Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xiao-Yan Feng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| |
Collapse
|
13
|
Manhas A, Lone MY, Jha PC. Multicomplex-based pharmacophore modeling in conjunction with multi-target docking and molecular dynamics simulations for the identification of PfDHFR inhibitors. J Biomol Struct Dyn 2019; 37:4181-4199. [DOI: 10.1080/07391102.2018.1540362] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Anu Manhas
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
| | - Mohsin Y. Lone
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, India
| | - Prakash C. Jha
- Centre for Applied Chemistry, Central University of Gujarat, Gandhinagar, Gujarat, India
| |
Collapse
|
14
|
Novel Transforming Growth Factor-Beta Receptor 1 Antagonists through a Pharmacophore-Based Virtual Screening Approach. Molecules 2018; 23:molecules23112824. [PMID: 30384428 PMCID: PMC6278322 DOI: 10.3390/molecules23112824] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 10/27/2018] [Accepted: 10/29/2018] [Indexed: 12/27/2022] Open
Abstract
As new drugs for the treatment of malignant tumors, transforming growth factor-beta receptor 1 (TGFβR1) antagonists have attracted wide attention. Based on the crystal structure of TGFβR1-BMS22 complex, the pharmacophore model A02 with two hydrogen bond acceptors (HBAs) and four hydrophobic (HYD) properties was constructed. From the common features of active ligands reported in the literature, pharmacophore model B10 was also generated, which has two aromatic ring centers (RAs) and two HYD properties. The two models have high sensitivity and specificity to the training set, and they are highly consistent in spatial structure. Combining the two pharmacophore models, two novel skeleton structures with potential activity were selected by virtual screening from the DruglikeDiverse, MiniMaybridge, and ZINC Drug-Like databases. Four compounds (YXY01⁻YXY04) with potential anti-TGFβR1 activity were designed based on the new skeleton structures. In combination with Lipinski's rules; absorption, distribution, metabolism, excretion, and toxicity (ADMET); and, toxicological properties predicted in the study, YXY01-03 with the novel skeleton, good drug-like properties, and potential activity were finally discovered and may have higher safety relative to BMS22, which may be valuable for further research.
Collapse
|