1
|
Venanzi NE, Basciu A, Vargiu AV, Kiparissides A, Dalby PA, Dikicioglu D. Machine Learning Integrating Protein Structure, Sequence, and Dynamics to Predict the Enzyme Activity of Bovine Enterokinase Variants. J Chem Inf Model 2024; 64:2681-2694. [PMID: 38386417 PMCID: PMC11005043 DOI: 10.1021/acs.jcim.3c00999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
Despite recent advances in computational protein science, the dynamic behavior of proteins, which directly governs their biological activity, cannot be gleaned from sequence information alone. To overcome this challenge, we propose a framework that integrates the peptide sequence, protein structure, and protein dynamics descriptors into machine learning algorithms to enhance their predictive capabilities and achieve improved prediction of the protein variant function. The resulting machine learning pipeline integrates traditional sequence and structure information with molecular dynamics simulation data to predict the effects of multiple point mutations on the fold improvement of the activity of bovine enterokinase variants. This study highlights how the combination of structural and dynamic data can provide predictive insights into protein functionality and address protein engineering challenges in industrial contexts.
Collapse
Affiliation(s)
| | - Andrea Basciu
- Department
of Physics, University of Cagliari, Cittadella
Universitaria, I-09042 Monserrato, Cagliari, Italy
| | - Attilio Vittorio Vargiu
- Department
of Physics, University of Cagliari, Cittadella
Universitaria, I-09042 Monserrato, Cagliari, Italy
| | - Alexandros Kiparissides
- Department
of Biochemical Engineering, University College
London, Gower Street, WC1E 6BT London, U.K.
- Department
of Chemical Engineering, Aristotle University
of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Paul A. Dalby
- Department
of Biochemical Engineering, University College
London, Gower Street, WC1E 6BT London, U.K.
| | - Duygu Dikicioglu
- Department
of Biochemical Engineering, University College
London, Gower Street, WC1E 6BT London, U.K.
| |
Collapse
|
2
|
Ahmad B, Saeed A, Castrosanto MA, Amir Zia M, Farooq U, Abbas Z, Khan S. Identification of natural marine compounds as potential inhibitors of CDK2 using molecular docking and molecular dynamics simulation approach. J Biomol Struct Dyn 2023; 41:8506-8516. [PMID: 36300512 DOI: 10.1080/07391102.2022.2135594] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/08/2022] [Indexed: 10/31/2022]
Abstract
The multifunctional enzyme cyclin-dependent kinase 2 (CDK2) protein is essential for cell proliferation, transcription and modulation of the cell cycle. There is a dysfunction that is connected to various diseases, such as cancer, making it an important treatment target in oncology and beyond. The goal of this study is to identify novel CDK2 ATP binding site inhibitors using in silico drug designing. To find competitive inhibitors for the ATP site, molecular docking, molecular dynamics (MD) simulation and free-binding energy calculations were used. Natural compounds retrieved from marine sources (fungi and algae) were docked against protein, and the best-binding compounds were further evaluated using MD simulations. LIG1, LIG2 and LIG3 (ΔGPB = -19.98, -15.82 and -12.98 kcal/mol, respectively) were placed in the top positions based on their overall binding energy calculated using MMPBSA approach. Stability of the complexes was confirmed by carefully analyzing the rmsd and rmsf patterns retrieved from the MD trajectories. Several residues and areas (Leu124, Val123, Phe80, Leu83, Glu81, Arg 126, Asn132, Leu134, Gln131, Lys88 and Glu195) appear to be critical for inhibitor retention across the active pocket, according to RMSD and RMSF. The dynamics of the ligands inside the active pocket were mapped using principle component analysis. It has been observed that LIG1-3 appear to be the best possible inhibitors due to their high binding energies, interaction pattern and retention inside the active pocket.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Basharat Ahmad
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
- Department of Bioinformatics, Hazara University Mansehra, Mansehra, Pakistan
| | - Aamir Saeed
- Department of Bioinformatics, Hazara University Mansehra, Mansehra, Pakistan
| | - Melvin A Castrosanto
- College of Arts and Sciences, Institute of Chemistry, University of the Philippines Los Banos, Laguna, Philippines
| | - Muhammad Amir Zia
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Umar Farooq
- Department of Chemistry, COMSATS University Islamabad - Abbottabad Campus, Abbottabad, Pakistan
| | - Zaheer Abbas
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Sara Khan
- Department of Chemistry, COMSATS University Islamabad - Abbottabad Campus, Abbottabad, Pakistan
| |
Collapse
|
3
|
Wang D, Li L, Xu H, Sun Y, Li W, Liu T, Li Y, Shi X, He Z, Zhai Y, Sun B, Sun J. Rational Engineering Docetaxel Prodrug Nanoassemblies: Response Modules Guiding Efficacy Enhancement and Toxicity Reduction. NANO LETTERS 2023; 23:3549-3557. [PMID: 37053460 DOI: 10.1021/acs.nanolett.3c00704] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Prodrug-based nanoassemblies have been developed to solve the bottlenecks of chemotherapeutic drugs. The fabricated prodrugs usually consist of active drug modules, response modules, and modification modules. Among three modules, the response modules play a vital role in controlling the intelligent drug release at tumor sites. Herein, various locations of disulfide bond linkages were selected as response modules to construct three Docetaxel (DTX) prodrugs. Interestingly, the small structural difference caused by the length of response modules endowed corresponding prodrug nanoassemblies with unique characteristic. α-DTX-OD nanoparticles (NPs) possessed the advantages of high redox-responsiveness due to their shortest linkages. However, they were too sensitive to retain the intact structure in the blood circulation, leading to severe systematic toxicity. β-DTX-OD NPs significantly improved the pharmacokinetics of DTX but may induce damage to the liver. In comparison, γ-DTX-OD NPs with the longest linkages greatly ameliorated the delivery efficiency of DTX as well as improved DTX's tolerance dose.
Collapse
Affiliation(s)
- Danping Wang
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Lingxiao Li
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Hezhen Xu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yixin Sun
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Wenxiao Li
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Tian Liu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yan Li
- Yantai Key Laboratory of Nanomedicine & Advanced Preparations, Yantai Institute of Materia Medica, Shandong 264000, China
| | - Xianbao Shi
- Department of Pharmacy, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121001, China
| | - Zhonggui He
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yinglei Zhai
- School of Medical Devices, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Bingjun Sun
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jin Sun
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| |
Collapse
|
4
|
Gangadhariah M, Pardhi T, Ravilla J, Chandra S, Singh SA. Citrus nutraceutical eriocitrin and its metabolites are partial agonists of peroxisome proliferator-activated receptor gamma (PPARγ): a molecular docking and molecular dynamics study. J Biomol Struct Dyn 2022; 41:11373-11393. [PMID: 36576222 DOI: 10.1080/07391102.2022.2162127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/18/2022] [Indexed: 12/29/2022]
Abstract
Peroxisome proliferator-activated receptor gamma (PPARγ) agonists are potent insulin sensitizers in treating type 2 diabetes. Despite being very effective in the fight against diabetes-mediated complications, PPARγ agonists are accompanied by severe side effects leading to complicated health problems, making the discovery of novel safe ligands highly pertinent. A significant intense research effort is in progress to explore the PPARγ activating potential of a wide range of natural compounds. Lemon (Citrus limon) contains various bioactive flavonoids, and eriocitrin is the major flavonoid. It possesses substantial antioxidant and anticancer, lipid-lowering activities and prevents obesity-associated metabolic diseases. Eriocitrin is metabolized to eriodictyol in the intestine, and the absorbed eriodictyol undergoes conversion to numerous metabolites in vivo. It is unclear if eriocitrin or its metabolites are responsible for their beneficial effects. We have used molecular docking, ADMET properties, drug-likeness score and molecular dynamics simulation study to find if eriocitrin and its metabolites are potent binders for PPARγ. Docking studies revealed that eriocitrin binds to PPARγ with the highest binding energy, but ADMET properties and in vivo studies show that the bioavailability of eriocitrin is very poor. Molecular dynamics studies were carried out to validate the docking results, and multiple parameters like RMSD, RMSF, Radius of gyration, SASA, hydrogen bond analysis, interaction energy, principal component analysis, Gibbs free energy and MM-PBSA were calculated. Based on our studies, eriodictyol, eriodictyol 7-O-glucuronide, eriodictyol 3'-O-glucuronide, homoeriodictyol and homoeriodictyol 7-O-glucuronide which are metabolites of eriocitrin appear to be potent partial agonists of PPARγ under physiological conditions.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Mahesha Gangadhariah
- Department of Traditional Foods and Applied Nutrition, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, India
| | - Triveni Pardhi
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland, OH, USA
| | - Jahnavi Ravilla
- Department of Traditional Foods and Applied Nutrition, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, India
| | - Subhash Chandra
- Computational Biology & Biotechnology Laboratory Department of Botany, Soban Singh Jeena University S.S.J. Campus, Almora, Uttarakhand, India
| | - Sridevi Annapurna Singh
- Department of Traditional Foods and Applied Nutrition, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, India
| |
Collapse
|
5
|
Purification of Two Taxanes from Taxus cuspidata by Preparative High-Performance Liquid Chromatography. SEPARATIONS 2022. [DOI: 10.3390/separations9120446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In the present study, an effective method of preparative high-performance liquid chromatography (Prep-HPLC) was established to purify two taxanes in Taxus cuspidata. During the experimental operation, the effects of flow rate, injection volume, and column temperature on the purity of 10-deacetyltaxol (10-DAT) and paclitaxel (PTX) were investigated, and the optimized conditions were as follows: flow rate of 10 mL/min, injection volume of 0.5 mL, and column temperature of 30 °C. Under these conditions, the purity of 10-DAT and PTX reached 95.33% and 99.15%, respectively. The purified products were characterized by scanning electron microscopy (SEM), high-performance liquid chromatography (HPLC), and electrospray ionization-high resolution mass spectrometry (ESI-HRMS). The results demonstrated that preparative HPLC can effectively purify 10-DAT and PTX from Taxus cuspidata with a purity of >95%, which was suitable for the large-scale preparation of 10-DAT and PTX.
Collapse
|
6
|
Separation and Purification of Taxanes from Crude Taxus cuspidata Extract by Antisolvent Recrystallization Method. SEPARATIONS 2022. [DOI: 10.3390/separations9100304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Taxanes are natural compounds with strong antitumor activity. In this study, we first enriched taxanes by ultrasonic extraction and liquid–liquid extraction from Taxus cuspidata, then purified these taxanes by the antisolvent recrystallization method, and discussed the effects of four recrystallization conditions on the purity of eight target compounds. The most promising purification results were obtained using methanol as a solvent and water as an antisolvent. Response surface methodology (RSM) was used to further optimize the optimal purification conditions: when the crude extraction concentration was 555.28 mg/mL, an antisolvent to solvent volume ratio was 28.16 times, the deposition temperature was 22.91 °C, and the deposition time was 1.76 min, the purity of the taxanes reached its maximum. The scanning electron microscopy (SEM) results showed that recrystallization could effectively reduce the particle size of crude Taxus cuspidata and control the particle morphology. X-ray diffraction (XRD) and Raman spectrum experiments demonstrated that the amorphous state of the crude Taxus cuspidata did not change during the recrystallization process, and always remained amorphous. This recrystallization method can effectively improve the purity of taxanes in Taxus cuspidata, and is suitable for the preliminary purification of taxanes.
Collapse
|
7
|
Alshehri NS, Sharfalddin AA, Domyati D, Basaleh AS, Hussien MA. Experiment versus theory of copper (II) complexes based imidazole derivatives as anti-cancer agents. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
|
8
|
Kumar Ys R, Rao Sj A, Bm U, Verma B, Mahadevappa P. Anti-proliferative activity of labdane diterpenes isolated from Polyalthia cerasoides and their molecular interaction studies. Curr Drug Discov Technol 2022; 19:e110522204615. [PMID: 35546742 DOI: 10.2174/1570163819666220511154837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/02/2022] [Accepted: 02/28/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Polyalthia cerasoides is well known for its therapeutic effects and is extensively used by the tribal people of South India and Africa to treat infertility, toothache, inflammation, rheumatism, fever, and to combat stress. OBJECTIVE In the present research, the anti-proliferative potential of two bioactive compounds isolated from the stem bark of P. cerasoides (Roxb.) Bedd. of the Annonaceae family were investigated. METHOD The dried stem bark was powdered and subjected to extraction using methanol and further partitioned using petroleum ether. Yellow viscous oil was isolated from the petroleum ether fraction using column and preparative thin-layer chromatography. The chromatographic fractions were characterized using GC-MS. The anti-proliferative effect of the isolated compounds was assessed against HepG2 Cells using MTT- Cytotoxicity test. Furthermore, comparative in-silico docking studies were performed to predict the binding pattern of isolated molecules individually, as well as simultaneously with α, β -tubulin, a critical protein involved in the molecular mechanism of microtubule formation. RESULTS GC-MS analysis of yellow viscous oil from petroleum fraction confirmed the presence of two labdane diterpenes and were identified as 12E-3,4-Seco-labda-4(18),8(17),12,14-tetraen-3-oic acid , and methyl harvadate C by mass fragmentation analysis. The MTT-Cytotoxicity assay showed the dose-dependent cytotoxic effect on HepG2 Cells. The comparative docking studies of the isolated compounds exhibited strong interactions with the α, β -tubulin protein. CONCLUSION The prominent anti-proliferative effect exhibited by the isolated compounds along with effective binding to α, β -tubulin protein encourages their future utilization as prominent anti-cancer molecules.
Collapse
Affiliation(s)
- Ravi Kumar Ys
- Department of Biotechnology, MS Ramaiah Institute of Technology, Bangalore, Karnataka, INDIA
| | - Aditya Rao Sj
- Kimberlite chemicals India Pvt. Ltd, KIADB III Phase, Doddaballapur, Bangalore-561203, Karnataka, INDIA
| | - Usha Bm
- Organic Chemistry Department, Indian Institute of Science, Bangalore, Karnataka, INDIA
| | - Bhupendra Verma
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, INDIA
| | - Paramesha Mahadevappa
- Department of Studies and Research in Food Technology, Davangere University, Shivagnagotri, Davangere, Karnataka, INDIA
| |
Collapse
|
9
|
Mao J, Luo QQ, Zhang HR, Zheng XH, Shen C, Qi HZ, Hu ML, Zhang H. Discovery of microtubule stabilizers with novel scaffold structures based on virtual screening, biological evaluation, and molecular dynamics simulation. Chem Biol Interact 2021; 352:109784. [PMID: 34932952 DOI: 10.1016/j.cbi.2021.109784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/20/2021] [Accepted: 12/16/2021] [Indexed: 02/08/2023]
Abstract
Disrupting the dynamics and structures of microtubules can perturb mitotic spindle formation, cause cell cycle arrest in G2/M phase, and subsequently lead to cellular death via apoptosis. In this investigation, the structure-based virtual screening methods, including molecular docking and rescoring, and similarity analysis of interaction molecular fingerprints, were developed to discover novel tubulin inhibitors from ChemDiv database with 1,601,806 compounds. The screened compounds were further filtered by PAINS, ADME/T, Toxscore, SAscore, and Drug-likeness analysis. Finally, 17 hit compounds were selected, and then submitted to the biologic evaluation. Among these hits, the P2 exhibited the strongest antiproliferative activity against four tumor cells including HeLa, HepG2, MCF-7, and A549. The in vitro tubulin polymerization assay revealed P2 could promote tubulin polymerization in a dose dependent manner. Finally, in order to analyze the interaction modes of complexes, the molecular dynamics simulation was performed to investigate the interactions between P2 and tubulin. The molecular dynamics simulation analysis showed that P2 could stably bind to taxane site, induced H6-H7, B9-B10, and M-loop regions changes. The ΔGbind energies of tubulin-P2 and tubulin-paclitaxel were -68.25 ± 12.98 and -146.05 ± 16.17 kJ mol-1, respectively, which were in line with the results of the experimental test. Therefore, P2 has been well characterized as lead compounds for developing new tubulin inhibitors with potential anticancer activity.
Collapse
Affiliation(s)
- Jun Mao
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Qing-Qing Luo
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Hong-Rui Zhang
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Xiu-He Zheng
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Chen Shen
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Hua-Zhao Qi
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Mei-Ling Hu
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Hui Zhang
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, 610041, PR China.
| |
Collapse
|
10
|
Mechanisms of influence of the microtubule over-stabilizing ligands on the structure and intrinsic dynamics of α,β-Tubulin. Comput Biol Chem 2021; 96:107617. [PMID: 34942453 DOI: 10.1016/j.compbiolchem.2021.107617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/24/2021] [Accepted: 12/06/2021] [Indexed: 11/23/2022]
Abstract
The intervention into the cell cycle progression by administering microtubule over-stabilizing ligands that arrest the mitotic cell division by preventing spindle dissociation, is a promising strategy to fight against cancers. The building blocks of the microtubules and the spindles, i.e. the α,β-tubulin dimer, upon binding of such ligands, stay more comfortably in the microtubular multimeric form; the phenomenon of which is the key to the said over-stabilization. Using two such over-stabilizing ligands, Taxol and Taxotere, the present work reports the collective changes that these ligands induce on the structure and dynamics of the α,β-tubulin dimer which could be reconciled as the molecular basis of the over-stabilization of the microtubules; the trends have been found to be statistically significant across all independent calculations on them. The ligand binding increases the coherence between the residue communities of the two opposite faces of the β-subunit, which in a periodic arrangement in microtubule are knwon to form intermolecular contact with each other. This is likely to create an indirect cooperativity between those structural regions and this is a consequence of the reshuffling of the internal network of interactions upon ligand binding. Such reorganizations are also complemented by the increased contributions of the softer modes of the intrinsic dynamics more, which is likely to increase the plasticity of the system favourable for making structural adjustments in a multimer. Further, the ligands are able to compensate the drawback of lacking one phosphate group in protein-GDP interactions compared to the same for protein-GTP and this is in agreement with the hints form the earlier reports. The findings form a mechanistic basis of the enhanced capacity of the α,β-tubulin dimer to get more favourably accommodated into the microtubule superstructure upon binding either of Taxol and Taxotere.
Collapse
|
11
|
Jayaswal A, Pathak E, Mishra H, Shah K. Evaluation of binding of potential ADMET/tox screened saquinavir analogues for inhibition of HIV-protease via molecular dynamics and binding free energy calculations. J Biomol Struct Dyn 2021; 40:6439-6449. [PMID: 33663345 DOI: 10.1080/07391102.2021.1885496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Developing novel drug molecules against HIV is a scientific quest necessitated by development of drug resistance against used drugs. We report comparative results of molecular dynamics simulation studies on 11 structural analogues of Saquinavir (SQV) - against HIV-protease that were earlier examined for pharmacodynamic and pharmacokinetic properties. We reported analogues S1, S5 and S8 to qualify the ADMET criterion and may be considered as potential lead molecules. In this study the designed molecules were successively docked with native HIV-protease at AutoDock. Docking scores established relative goodness of the 11 analogues against the benchmark for Saquinavir. The docked complexes were subjected to molecular dynamics simulation studies using GROMACS 4.6.2. Four parameters viz. H-bonding, RMSD, Binding energy and Protein-Ligand Distance were used for comparative analyses of the analogues relative to Saquinavir. The comparison and analysis of the results are indicative that analogues S8, S9 and S1 are promising candidates among all the analogues studied. From our earlier work and present study it is evident that among the three S8 and S1 qualify the ADMET criterion and between S1 and S8, the analogue S8 shows more target efficacy and specificity over S1 and have better molecular dynamics simulation results. Thus, of the 11 de novo Saquinavir analogues, the S8 appears to be the most promising candidate as lead molecule for HIV-protease inhibitor and is best suited for testing under biological system. Further validation of the proposed lead molecules through wet lab studies involving antiviral assays however is required.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Amit Jayaswal
- Department of Bioinformatics, MMV, Banaras Hindu University, Varanasi, India
| | - Ekta Pathak
- Department of Bioinformatics, MMV, Banaras Hindu University, Varanasi, India
| | | | - Kavita Shah
- Institute of Environment and Sustainable Development, BHU, Varanasi, India
| |
Collapse
|
12
|
Zhao Y, Wang Y, Wang H, Hu B, Luo Z, Zhang F. A computational prospective on isoform-selective CB2 inhibitors. NEW J CHEM 2021. [DOI: 10.1039/d1nj02296b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The strategy of enlarging the molecular size, increasing hydrogen bond interactions with the key residues of CB2, and furthering geometric distribution of hydrophobic groups would improve the selectivity towards CB2 receptor.
Collapse
Affiliation(s)
- Yi Zhao
- School of Pharmacy
- Shenyang Pharmaceutical University
- Shenyang 110016
- People's Republic of China
| | - Ying Wang
- Wuya College of Innovation
- Shenyang Pharmaceutical University
- Shenyang 110016
- People's Republic of China
| | - Huibin Wang
- School of Pharmacy
- Shenyang Pharmaceutical University
- Shenyang 110016
- People's Republic of China
| | - Baichun Hu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education
- Shenyang Pharmaceutical University
- Shenyang 110016
- People's Republic of China
- School of Pharmaceutical Engineering
| | - Zhaohu Luo
- Wuya College of Innovation
- Shenyang Pharmaceutical University
- Shenyang 110016
- People's Republic of China
| | - Fengjiao Zhang
- Wuya College of Innovation
- Shenyang Pharmaceutical University
- Shenyang 110016
- People's Republic of China
| |
Collapse
|
13
|
Lee KE, Bharadwaj S, Yadava U, Kang SG. Computational and In Vitro Investigation of (-)-Epicatechin and Proanthocyanidin B2 as Inhibitors of Human Matrix Metalloproteinase 1. Biomolecules 2020; 10:biom10101379. [PMID: 32998374 PMCID: PMC7650666 DOI: 10.3390/biom10101379] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/17/2020] [Accepted: 09/24/2020] [Indexed: 01/16/2023] Open
Abstract
Matrix metalloproteinases 1 (MMP-1) energetically triggers the enzymatic proteolysis of extracellular matrix collagenase (ECM), resulting in progressive skin aging. Natural flavonoids are well known for their antioxidant properties and have been evaluated for inhibition of matrix metalloproteins in human. Recently, (-)-epicatechin and proanthocyanidin B2 were reported as essential flavanols from various natural reservoirs as potential anti-inflammatory and free radical scavengers. However, their molecular interactions and inhibitory potential against MMP-1 are not yet well studied. In this study, sequential absorption, distribution, metabolism, and excretion (ADME) profiling, quantum mechanics calculations, and molecular docking simulations by extra precision Glide protocol predicted the drug-likeness of (-)-epicatechin (−7.862 kcal/mol) and proanthocyanidin B2 (−8.145 kcal/mol) with the least reactivity and substantial binding affinity in the catalytic pocket of human MMP-1 by comparison to reference bioactive compound epigallocatechin gallate (−6.488 kcal/mol). These flavanols in docked complexes with MMP-1 were further studied by 500 ns molecular dynamics simulations that revealed substantial stability and intermolecular interactions, viz. hydrogen and ionic interactions, with essential residues, i.e., His218, Glu219, His222, and His228, in the active pocket of MMP-1. In addition, binding free energy calculations using the Molecular Mechanics Generalized Born Surface Area (MM/GBSA) method suggested the significant role of Coulomb interactions and van der Waals forces in the stability of respective docked MMP-1-flavonol complexes by comparison to MMP-1-epigallocatechin gallate; these observations were further supported by MMP-1 inhibition assay using zymography. Altogether with computational and MMP-1–zymography results, our findings support (-)-epicatechin as a comparatively strong inhibitor of human MMP-1 with considerable drug-likeness against proanthocyanidin B2 in reference to epigallocatechin gallate.
Collapse
Affiliation(s)
- Kyung Eun Lee
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Korea; (K.E.L.); (S.B.)
| | - Shiv Bharadwaj
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Korea; (K.E.L.); (S.B.)
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh 273009, India;
| | - Sang Gu Kang
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Korea; (K.E.L.); (S.B.)
- Stemforce, 313 Institute of Industrial Technology, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Korea
- Correspondence:
| |
Collapse
|
14
|
Density functional theory and molecular dynamics simulation support Ganoderma lucidum triterpenoids as broad range antagonist of matrix metalloproteinases. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113322] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
15
|
Jia WQ, Feng XY, Liu YY, Han ZZ, Jing Z, Xu WR, Cheng XC. Identification of Phosphoinositide-3 Kinases Delta and Gamma Dual Inhibitors Based on the p110δ/γ Crystal Structure. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180816666190730163431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Phosphoinositide-3 kinases (PI3Ks) are key signaling molecules that affect
a diverse array of biological processes in cells, including proliferation, differentiation, survival, and
metabolism. The abnormal activity of PI3K signals is closely related to the occurrence of many diseases,
which has become a very promising drug target, especially for the treatment of cancer.
PI3Kδ/γ inhibitors can reduce toxicity concerns for chronic indications such as asthma and rheumatoid
arthritis compared with pan PI3Ks inhibitors.
Methods:
With the aim of finding more effective PI3Kδ/γ dual inhibitors, virtual screening,
ADMET prediction Molecular Dynamics (MD) simulations and MM-GBSA were executed based
on the known p110δ/γ crystal structure. Compound ZINC28564067 with high docking score and
low toxicity was obtained.
Results:
By MD simulations and MM-GBSA, we could observe that ZINC28564067 had more favorable
conformation binding to the PI3Kδ/γ than the original ligands.
Conclusion:
The results provided a rapid approach for the discovery of novel PI3Kδ/γ dual inhibitors
which might be a potential anti-tumor lead compound.
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 300070, China
| | - Xiao-Yan Feng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Ya-Ya Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Zhen-Zhen Han
- Baokang Hospital, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China
| | - Zhi Jing
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Wei-Ren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| |
Collapse
|
16
|
Sohraby F, Aryapour H. Rational drug repurposing for cancer by inclusion of the unbiased molecular dynamics simulation in the structure-based virtual screening approach: Challenges and breakthroughs. Semin Cancer Biol 2020; 68:249-257. [PMID: 32360530 DOI: 10.1016/j.semcancer.2020.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 03/07/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022]
Abstract
Managing cancer is now one of the biggest concerns of health organizations. Many strategies have been developed in drug discovery pipelines to help rectify this problem and two of the best ones are drug repurposing and computational methods. The combination of these approaches can have immense impact on the course of drug discovery. In silico drug repurposing can significantly reduce the time, the cost and the effort of drug development. Computational methods such as structure-based drug design (SBDD) and virtual screening can predict the potentials of small molecule binders, such as drugs, for having favorable effect on a particular molecular target. However, the demand for accuracy and efficiency of SBDD requires more sophisticated and complicated approaches such as unbiased molecular dynamics (UMD) simulation that has been recently introduced. As a complementary strategy, the knowledge acquired from UMD simulations can increase the chance of finding the right candidates and the pipeline of its administration is introduced and discussed in this review. An elaboration of this pipeline is also made by detailing an example, the binding and unbinding pathways of dasatinib-c-Src kinase complex, which shows that how influential this method can be in rational drug repurposing in cancer treatment.
Collapse
Affiliation(s)
- Farzin Sohraby
- Department of Biology, Faculty of Science, Golestan University, Gorgan, Iran
| | - Hassan Aryapour
- Department of Biology, Faculty of Science, Golestan University, Gorgan, Iran.
| |
Collapse
|
17
|
Bharadwaj S, Rao AK, Dwivedi VD, Mishra SK, Yadava U. Structure-based screening and validation of bioactive compounds as Zika virus methyltransferase (MTase) inhibitors through first-principle density functional theory, classical molecular simulation and QM/MM affinity estimation. J Biomol Struct Dyn 2020; 39:2338-2351. [PMID: 32216596 DOI: 10.1080/07391102.2020.1747545] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Recent Zika virus (ZIKV) outbreak and association with human diseases such as neurological disorders have raised global health concerns. However, in the absence of an approved anti-ZIKV drug has generated urgency for the drug development against ZIKV infection. Here, structure-based virtual screening of 8589 bioactive compounds, screened at the substrate-binding site of ZIKV nonstructural 5 (NS5)-based structure N-terminal methyltransferase (MTase) domain followed by ADMET (absorption, distribution, metabolism, excretion and toxicity) profiling concluded the four potential lead inhibitors, i.e. (4-acetylamino-benzenesulfonylamino)-acetic acid (F3342-0450), 3-(5-methylfuran-2-yl)-N-(4-sulfamoylphenyl)propanamide (F1736-0142), 8-(2-hydroxy-ethylamino)-1,3-dimethyl-7-(3-methyl-benzyl)-3,7-dihydro-purine-2,6-dione (F0886-0080) and N-[4-(aminosulfonyl)phenyl]-2,3-dihydro-1,4-benzodioxine-2-carboxamide (F0451-2187). Collectively, extra precision docking and Density Functional Theory(DFT) calculations studies identified the F3342-0450 molecule, having strong interactions on the active site of MTase, further supported by molecular dynamics simulation, binding affinity and hybrid QM/MM calculations, suggest a new drug molecule for the antiviral drug development against ZIKV infection. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shiv Bharadwaj
- Sabanci University Nanotechnology Research and Application Center, Istanbul, Turkey
| | - Akhilesh Kumar Rao
- Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, India
| | - Vivek Dhar Dwivedi
- Centre for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Sarad Kumar Mishra
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, India
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, India
| |
Collapse
|
18
|
|
19
|
Liao VWY, Kumari A, Narlawar R, Vignarajan S, Hibbs DE, Panda D, Groundwater PW. Tubulin-Binding 3,5-Bis(styryl)pyrazoles as Lead Compounds for the Treatment of Castration-Resistant Prostate Cancer. Mol Pharmacol 2020; 97:409-422. [PMID: 32241960 DOI: 10.1124/mol.119.118539] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/24/2020] [Indexed: 11/22/2022] Open
Abstract
The microtubule-binding taxanes, docetaxel and cabazitaxel, are administered intravenously for the treatment of castration-resistant prostate cancer (CRPC) as the oral administration of these drugs is largely hampered by their low and highly variable bioavailabilities. Using a simple, rapid, and environmentally friendly microwave-assisted protocol, we have synthesized a number of 3,5-bis(styryl)pyrazoles 2a-l, thus allowing for their screening for antiproliferative activity in the androgen-independent PC3 prostate cancer cell line. Surprisingly, two of these structurally simple 3,5-bis(styryl)pyrazoles (2a and 2l) had concentrations which gave 50% of the maximal inhibition of cell proliferation (GI50) in the low micromolar range in the PC3 cell line and were thus selected for extensive further biologic evaluation (apoptosis and cell cycle analysis, and effects on tubulin and microtubules). Our findings from these studies show that 3,5-bis[(1E)-2(2,6-dichlorophenyl)ethenyl]-1H-pyrazole 2l 1) caused significant effects on the cell cycle in PC3 cells, with the vast majority of treated cells in the G2/M phase (89%); 2) induces cell death in PC3 cells even after the removal of the compound; 3) binds to tubulin [dissociation constant (Kd) 0.4 ± 0.1 μM] and inhibits tubulin polymerization in vitro; 4) had no effect upon the polymerization of the bacterial cell division protein FtsZ (a homolog of tubulin); 5) is competitive with paclitaxel for binding to tubulin but not with vinblastine, crocin, or colchicine; and 6) leads to microtubule depolymerization in PC3 cells. Taken together, these results suggest that 3,5-bis(styryl)pyrazoles warrant further investigation as lead compounds for the treatment of CRPC. SIGNIFICANCE STATEMENT: The taxanes are important components of prostate cancer chemotherapy regimens, but their oral administration is hampered by very low and highly variable oral bioavailabilities resulting from their poor absorption, poor solubility, high first-pass metabolism, and efficient efflux by P-glycoprotein. New chemical entities for the treatment of prostate cancer are thus required, and we report here the synthesis and investigation of the mechanism of action of some bis(styryl)pyrazoles, demonstrating their potential as lead compounds for the treatment of prostate cancer.
Collapse
Affiliation(s)
- Vivian W Y Liao
- Sydney Pharmacy School, Faculty of Medicine and Health (V.W.Y.L., R.N., D.E.H., P.W.G.) and Charles Perkins Centre (S.V.), The University of Sydney, Sydney, New South Wales, Australia; and Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India (A.K., D.P.)
| | - Anuradha Kumari
- Sydney Pharmacy School, Faculty of Medicine and Health (V.W.Y.L., R.N., D.E.H., P.W.G.) and Charles Perkins Centre (S.V.), The University of Sydney, Sydney, New South Wales, Australia; and Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India (A.K., D.P.)
| | - Rajeshwar Narlawar
- Sydney Pharmacy School, Faculty of Medicine and Health (V.W.Y.L., R.N., D.E.H., P.W.G.) and Charles Perkins Centre (S.V.), The University of Sydney, Sydney, New South Wales, Australia; and Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India (A.K., D.P.)
| | - Soma Vignarajan
- Sydney Pharmacy School, Faculty of Medicine and Health (V.W.Y.L., R.N., D.E.H., P.W.G.) and Charles Perkins Centre (S.V.), The University of Sydney, Sydney, New South Wales, Australia; and Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India (A.K., D.P.)
| | - David E Hibbs
- Sydney Pharmacy School, Faculty of Medicine and Health (V.W.Y.L., R.N., D.E.H., P.W.G.) and Charles Perkins Centre (S.V.), The University of Sydney, Sydney, New South Wales, Australia; and Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India (A.K., D.P.)
| | - Dulal Panda
- Sydney Pharmacy School, Faculty of Medicine and Health (V.W.Y.L., R.N., D.E.H., P.W.G.) and Charles Perkins Centre (S.V.), The University of Sydney, Sydney, New South Wales, Australia; and Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India (A.K., D.P.)
| | - Paul W Groundwater
- Sydney Pharmacy School, Faculty of Medicine and Health (V.W.Y.L., R.N., D.E.H., P.W.G.) and Charles Perkins Centre (S.V.), The University of Sydney, Sydney, New South Wales, Australia; and Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India (A.K., D.P.)
| |
Collapse
|
20
|
Feng XY, Ding TT, Liu YY, Xu WR, Cheng XC. In-silico identification of peroxisome proliferator-activated receptor (PPAR)α/γ agonists from Ligand Expo Components database. J Biomol Struct Dyn 2020; 39:1853-1864. [DOI: 10.1080/07391102.2020.1745279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Xiao-Yan Feng
- 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
| | - Ya-Ya Liu
- 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
|
21
|
Discovery of Ganoderma lucidum triterpenoids as potential inhibitors against Dengue virus NS2B-NS3 protease. Sci Rep 2019; 9:19059. [PMID: 31836806 PMCID: PMC6911040 DOI: 10.1038/s41598-019-55723-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 11/30/2019] [Indexed: 12/05/2022] Open
Abstract
Dengue virus (DENV) infection causes serious health problems in humans for which no drug is currently available. Recently, DENV NS2B-NS3 protease has been proposed as a primary target for anti-dengue drug discovery due to its important role in new virus particle formation by conducting DENV polyprotein cleavage. Triterpenoids from the medicinal fungus Ganoderma lucidum have been suggested as pharmacologically bioactive compounds and tested as anti-viral agents against various viral pathogens including human immunodeficiency virus. However, no reports are available concerning the anti-viral activity of triterpenoids from Ganoderma lucidum against DENV. Therefore, we employed a virtual screening approach to predict the functional triterpenoids from Ganoderma lucidum as potential inhibitors of DENV NS2B-NS3 protease, followed by an in vitro assay. From in silico analysis of twenty-two triterpenoids of Ganoderma lucidum, four triterpenoids, viz. Ganodermanontriol (−6.291 kcal/mol), Lucidumol A (−5.993 kcal/mol), Ganoderic acid C2 (−5.948 kcal/mol) and Ganosporeric acid A (−5.983 kcal/mol) were predicted to be viral protease inhibitors by comparison to reference inhibitor 1,8-Dihydroxy-4,5-dinitroanthraquinone (−5.377 kcal/mol). These results were further studied for binding affinity and stability using the molecular mechanics/generalized Born surface area method and Molecular Dynamics simulations, respectively. Also, in vitro viral infection inhibition suggested that Ganodermanontriol is a potent bioactive triterpenoid.
Collapse
|
22
|
Su Y, Song P, Wang H, Hu B, Wang J, Cheng MS. Precise design of highly isoform-selective p21-activated kinase 4 inhibitors: computational insights into the selectivity mechanism through molecular dynamics simulation and binding free energy calculation. J Biomol Struct Dyn 2019; 38:3825-3837. [DOI: 10.1080/07391102.2019.1664330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yuan Su
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Peilu Song
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Hanxun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Baichun Hu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Mao-Sheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| |
Collapse
|
23
|
Bharadwaj S, Lee KE, Dwivedi VD, Yadava U, Kang SG. Computational aided mechanistic understanding of Camellia sinensis bioactive compounds against co-chaperone p23 as potential anticancer agent. J Cell Biochem 2019; 120:19064-19075. [PMID: 31257629 DOI: 10.1002/jcb.29229] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 11/08/2022]
Abstract
Co-chaperon p23 has been well established as molecular chaperon for the heat shock protein 90 (Hsp90) that further leads to immorality in cancer cells by providing defense against Hsp90 inhibitors, and as stimulating agent for generating overexpressed antiapoptotic proteins, that is, Hsp70 and Hsp27. The natural compounds such as catechins from Camellia sinensis (green tea) are also well known for inhibition activity against various cancer. However, molecular interaction profile and potential lead bioactive compounds against co-chaperon p23 from green tea are not yet reported. To this context, we study the various secondary metabolites of green tea against co-chaperon p23 using structure-based virtual screening from Traditional Chinese Medicine (TCM) database. Following 26 compounds were obtained from TCM database and further studied for extra precision molecular docking that showed binding score between -10.221 and -2.276 kcal/mol with co-chaperon p23. However, relative docking score to known inhibitors, that is, ailanthone (-4.54 kcal/mol) and gedunin ( 3.60 kcal/mol) along with ADME profile analysis concluded epicatechin (-7.013 kcal/mol) and cis-theaspirone (-4.495 kcal/mol) as potential lead inhibitors from green tea against co-chaperone p23. Furthermore, molecular dynamics simulation and molecular mechanics generalized born surface area calculations validated that epicatechin and cis-theaspirone have significantly occupied the active region of co-chaperone p23 by hydrogen and hydrophobic interactions with various residues including most substantial amino acids, that is, Thr90, Ala94, and Lys95. Hence, these results supported the fact that green tea contained potential compounds with an ability to inhibit the cancer by disrupting the co-chaperon p23 activity.
Collapse
Affiliation(s)
- Shiv Bharadwaj
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
| | - Kyung Eun Lee
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
| | - Vivek Dhar Dwivedi
- Centre for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, India
| | - Sang Gu Kang
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea.,Stemforce, 313 Institute of Industrial Technology, Yeungnam University, Gyeongbuk, Gyeongsan, Republic of Korea
| |
Collapse
|
24
|
Liu TT, Yang T, Gao MN, Chen KX, Yang S, Yu KQ, Jiang HL. The inhibitory mechanism of aurintricarboxylic acid targeting serine/threonine phosphatase Stp1 in Staphylococcus aureus: insights from molecular dynamics simulations. Acta Pharmacol Sin 2019; 40:850-858. [PMID: 30796354 PMCID: PMC6786342 DOI: 10.1038/s41401-019-0216-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/17/2019] [Indexed: 12/19/2022] Open
Abstract
Serine/threonine phosphatase (Stp1) is a member of the bacterial Mg2+- or Mn2+- dependent protein phosphatase/protein phosphatase 2C family, which is involved in the regulation of Staphylococcus aureus virulence. Aurintricarboxylic acid (ATA) is a known Stp1 inhibitor with an IC50 of 1.03 μM, but its inhibitory mechanism has not been elucidated in detail because the Stp1-ATA cocrystal structure has not been determined thus far. In this study, we performed 400 ns molecular dynamics (MD) simulations of the apo-Stp1 and Stp1-ATA complex models. During MD simulations, the flap subdomain of the Stp1-ATA complex experienced a clear conformational transition from an open state to a closed state, whereas the flap domain of apo-Stp1 changed from an open state to a semi-open state. In the Stp1-ATA complex model, the hydrogen bond (H-bond) between D137 and N142 disappeared, whereas critical H-bond interactions were formed between Q160 and H13, Q160/R161 and ATA, as well as N162 and D198. Finally, four residues (D137, N142, Q160, and R161) in Stp1 were mutated to alanine and the mutant enzymes were assessed using phosphate enzyme activity assays, which confirmed their important roles in maintaining Stp1 activity. This study indicated the inhibitory mechanism of ATA targeting Stp1 using MD simulations and sheds light on the future design of allosteric Stp1 inhibitors.
Collapse
Affiliation(s)
- Ting-Ting Liu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Teng Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang, 550025, China
| | - Mei-Na Gao
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai-Xian Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang, 550025, China.
| | - Kun-Qian Yu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hua-Liang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| |
Collapse
|
25
|
Eun Lee K, Bharadwaj S, Yadava U, Gu Kang S. Evaluation of caffeine as inhibitor against collagenase, elastase and tyrosinase using in silico and in vitro approach. J Enzyme Inhib Med Chem 2019; 34:927-936. [PMID: 31039625 PMCID: PMC6493221 DOI: 10.1080/14756366.2019.1596904] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Skin ageing results from enhanced activation of intracellular enzymes such as collagenases, elastases and tyrosinase, stimulated by intrinsic ageing and photoageing factors. Recently, caffeine-based cosmetics are introduced that demonstrates to slow down skin photoageing process. However, no attempts have been done so for to understand caffeine functional inhibitory activity against photoageing related enzymes. Hence, this study established the caffeine molecular interaction and inhibition activity profiles against respective enzymes using in silico and in vitro methods, respectively. Results from in silico study indicates that caffeine has comparatively good affinity with collagenase (−4.6 kcal/mol), elastase (−3.36 kcal/mol) and tyrosinase (−2.86 kcal/mol) and formed the stable protein-ligand complex as validated by molecular dynamics simulation (protein-ligand contacts, RMSD, RMSF and secondary structure changes analysis). Moreover, in vitro data showed that caffeine (1000 µg/mL) has statistically significant maximum inhibition activity of 41.86, 36.44 and 13.72% for collagenase, elastase and tyrosinase, respectively.
Collapse
Affiliation(s)
- Kyung Eun Lee
- a Department of Biotechnology , Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University , Gyeongsan , Republic of Korea
| | - Shiv Bharadwaj
- a Department of Biotechnology , Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University , Gyeongsan , Republic of Korea
| | - Umesh Yadava
- b Department of Physics , Deen Dayal Upadhyay Gorakhpur University , Gorakhpur , India
| | - Sang Gu Kang
- a Department of Biotechnology , Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University , Gyeongsan , Republic of Korea.,c Stemforce, 313 Institute of Industrial Technology, Yeungnam University , Gyeongsan , Republic of Korea
| |
Collapse
|
26
|
Arif R, Nayab PS, Akrema, Abid M, Yadava U, Rahisuddin. Investigation of DNA binding and molecular docking propensity of phthalimide derivatives: in vitro antibacterial and antioxidant assay. J Anal Sci Technol 2019. [DOI: 10.1186/s40543-019-0177-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
|
27
|
Kumar A, Mehta V, Raj U, Varadwaj PK, Udayabanu M, Yennamalli RM, Singh TR. Computational and In-Vitro Validation of Natural Molecules as Potential Acetylcholinesterase Inhibitors and Neuroprotective Agents. Curr Alzheimer Res 2019; 16:116-127. [DOI: 10.2174/1567205016666181212155147] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/04/2018] [Accepted: 12/11/2018] [Indexed: 01/07/2023]
Abstract
Background:
Cholinesterase inhibitors are the first line of therapy for the management of
Alzheimer’s disease (AD), however, it is now established that they provide only temporary and symptomatic
relief, besides, having several inherited side-effects. Therefore, an alternative drug discovery
method is used to identify new and safer ‘disease-modifying drugs’.
Methods:
Herein, we screened 646 small molecules of natural origin having reported pharmacological
and functional values through in-silico docking studies to predict safer neuromodulatory molecules with
potential to modulate acetylcholine metabolism. Further, the potential of the predicted molecules to inhibit
acetylcholinesterase (AChE) activity and their ability to protect neurons from degeneration was
determined through in-vitro assays.
Results:
Based on in-silico AChE interaction studies, we predicted quercetin, caffeine, ascorbic acid and
gallic acid to be potential AChE inhibitors. We confirmed the AChE inhibitory potential of these molecules
through in-vitro AChE inhibition assay and compared results with donepezil and begacestat. Herbal
molecules significantly inhibited enzyme activity and inhibition for quercetin and caffeine did not show
any significant difference from donepezil. Further, the tested molecules did not show any neurotoxicity
against primary (E18) hippocampal neurons. We observed that quercetin and caffeine significantly improved
neuronal survival and efficiently protected hippocampal neurons from HgCl2 induced neurodegeneration,
which other molecules, including donepezil and begacestat, failed to do.
Conclusion:
Quercetin and caffeine have the potential as “disease-modifying drugs” and may find application
in the management of neurological disorders such as AD.
Collapse
Affiliation(s)
- Ashwani Kumar
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173234, India
| | - Vineet Mehta
- Department of Pharmacy, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173234, India
| | - Utkarsh Raj
- Indian Institute of Information Technology-Allahabad, Allahabad, Uttar Pradesh - 211012, India
| | - Pritish Kumar Varadwaj
- Indian Institute of Information Technology-Allahabad, Allahabad, Uttar Pradesh - 211012, India
| | - Malairaman Udayabanu
- Department of Pharmacy, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173234, India
| | - Ragothaman M. Yennamalli
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173234, India
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173234, India
| |
Collapse
|
28
|
Identification of novel PPARα/γ dual agonists by pharmacophore screening, docking analysis, ADMET prediction and molecular dynamics simulations. Comput Biol Chem 2019; 78:178-189. [DOI: 10.1016/j.compbiolchem.2018.11.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/20/2018] [Accepted: 11/25/2018] [Indexed: 01/05/2023]
|
29
|
Liu X, Li W, Hu B, Wang M, Wang J, Guan L. Identification of isobavachalcone as a potential drug for rice blast disease caused by the fungus Magnaporthe grisea. J Biomol Struct Dyn 2018; 37:3399-3409. [PMID: 30132740 DOI: 10.1080/07391102.2018.1515117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The rice blast disease caused by the fungus Magnaporthe grisea is one of the most devastating rice diseases, but there is no effective fungicide toward chitinase which is a key enzyme of M. grisea. In this study, we observed that distortion and cell-wall damage of M. grisea hyphae were significantly under the scanning electron micrograph after a 24-h treatment with 10 mg/L isobavachalcone (IBC) extracted from Psoralea corylifolia L. To further explore the effect of IBC on the cell wall of M. grisea, we examined changes in enzymes associated with cell wall degradation by enzyme activity experiments, treated liquid culture mycelia with 10 mg/L IBC for 1 h. Results displayed that chitinase was obviously more active than control group. To illustrate the interactions between IBC and chitinase, the studies of homology modeling and molecular docking were carried out successively. The results revealed that IBC had hydrogen bonds with residues ASP267 and ARG276 of chitinase. Besides, these nonpolar residues TYR270, PRO271, VAL272, LEU310, PRO311, TYR316, and LEU317 were able to form strong hydrophobic interactions. Binding energies of the chitinase-IBC complexes were calculated by MM-GBSA showed that the ΔGbind score of molecular dynamics had lower binding energy and more stable than docking complexes. All above, IBC owns significant agonistic activity in chitinase and would be a potent fungicide to inhibit the growth of M. grisea. We hope the above information provides an important insight for understanding the interactions between IBC and chitinase, which may be useful in the discovery of a novel potent agonist. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Xue Liu
- a Department of Pharmaceutical and Biological Engineering , Shenyang University of Chemical Technology , Shenyang , China
| | - Wei Li
- a Department of Pharmaceutical and Biological Engineering , Shenyang University of Chemical Technology , Shenyang , China
| | - Baichun Hu
- b Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education , Shenyang Pharmaceutical University , Shenyang , China
| | - Mingxing Wang
- b Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education , Shenyang Pharmaceutical University , Shenyang , China
| | - Jian Wang
- b Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education , Shenyang Pharmaceutical University , Shenyang , China
| | - Lijie Guan
- a Department of Pharmaceutical and Biological Engineering , Shenyang University of Chemical Technology , Shenyang , China
| |
Collapse
|
30
|
Tümer Y, Asmafiliz N, Zeyrek CT, Kılıç Z, Açık L, Çelik SP, Türk M, Çağdaş Tunalı B, Ünver H, Hökelek T. Syntheses, spectroscopic and crystallographic characterizations of cis- and trans-dispirocyclic ferrocenylphosphazenes: molecular dockings, cytotoxic and antimicrobial activities. NEW J CHEM 2018. [DOI: 10.1039/c7nj03643d] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The crystallographic and molecular docking investigations and the determinations of the cytotoxic activities of the dispirocyclic ferrocenylphosphazenes were performed.
Collapse
Affiliation(s)
- Yasemin Tümer
- Department of Chemistry
- Karabük University
- 78050 Karabük
- Turkey
| | | | - C. Tuğrul Zeyrek
- Department of Training and Application
- Ankara Nuclear Research and Training Center
- Turkish Atomic Energy Authority
- TR-06100 Beşevler
- Turkey
| | - Zeynel Kılıç
- Department of Chemistry
- Ankara University
- 06100 Ankara
- Turkey
| | - Leyla Açık
- Department of Biology
- Gazi University
- 06500 Ankara
- Turkey
| | | | - Mustafa Türk
- Department of Bioengineering
- Kırıkkale University
- 71450 Yahşihan-Kırıkkale
- Turkey
| | - B. Çağdaş Tunalı
- Department of Bioengineering
- Kırıkkale University
- 71450 Yahşihan-Kırıkkale
- Turkey
| | - Hüseyin Ünver
- Department of Physics
- Faculty of Sciences
- Ankara University
- Beşevler
- Turkey
| | - Tuncer Hökelek
- Department of Physics
- Hacettepe University
- 06800 Ankara
- Turkey
| |
Collapse
|
31
|
Jia WQ, Jing Z, Liu X, Feng XY, Liu YY, Wang SQ, Xu WR, Liu JW, Cheng XC. Virtual identification of novel PPARα/γ dual agonists by scaffold hopping of saroglitazar. J Biomol Struct Dyn 2017; 36:3496-3512. [DOI: 10.1080/07391102.2017.1392363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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
| | - Zhi Jing
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xin 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
| | - Ya-Ya Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Shu-Qing Wang
- 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
| | - Jian-Wen Liu
- State Key Laboratory of Bioreactor Engineering & Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 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
|
32
|
Liu X, Jing Z, Jia WQ, Wang SQ, Ma Y, Xu WR, Liu JW, Cheng XC. Identification of novel PPARα/γ dual agonists by virtual screening, ADMET prediction and molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:2988-3002. [DOI: 10.1080/07391102.2017.1373706] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Xin Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Zhi Jing
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Wen-Qing Jia
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Shu-Qing Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Wei-Ren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, China
| | - Jian-Wen Liu
- State Key Laboratory of Bioreactor Engineering & Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| |
Collapse
|
33
|
Design, sythesis and evaluation of a series of 3- or 4-alkoxy substituted phenoxy derivatives as PPARs agonists. Oncotarget 2017; 8:20766-20783. [PMID: 28186999 PMCID: PMC5400543 DOI: 10.18632/oncotarget.15198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 01/25/2017] [Indexed: 11/25/2022] Open
Abstract
Peroxisome proliferators-activated receptors (PPARα, γ and δ) are potentially effective targets for Type 2 diabetes mellitus therapy. The severe effects of known glitazones and the successfully approved agents (saroglitazar and lobeglitazone) motivated us to study novelly potent PPARs drugs with improved safety profile. In this work, we received 15 carboxylic acids based on the combination principle to integrate the polar head of bezafibrate with the hydrophobic tail of pioglitazone. Another 12 tetrazoles based on the bioisosterism principle were obtained accordingly. Furthermore, in vitro PPARs transactivation assays on these 3- or 4-alkoxy substituted phenoxy derivatives afforded six compounds. Interactions and binding stability from the docking analysis and 20 ns molecular dynamic simulations confirmed the representative compounds to be suitable and plausible for PPARs pockets. The above-mentioned results demonstrated that the compounds may be used as reference for further optimization for enhanced PPARs activities and wide safety range.
Collapse
|
34
|
Ganesan A, Coote ML, Barakat K. Molecular dynamics-driven drug discovery: leaping forward with confidence. Drug Discov Today 2017; 22:249-269. [DOI: 10.1016/j.drudis.2016.11.001] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/22/2016] [Accepted: 11/01/2016] [Indexed: 12/11/2022]
|
35
|
Yadava U, Yadav VK, Yadav RK. Novel anti-tubulin agents from plant and marine origins: insight from a molecular modeling and dynamics study. RSC Adv 2017. [DOI: 10.1039/c7ra00370f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The screening of a variety of botanical species and marine organisms provided satisfactory novel tubulin binding agents (TBAs).
Collapse
Affiliation(s)
- Umesh Yadava
- Department of Physics
- Deen Dayal Upadhyaya Gorakhpur University
- Gorakhpur 273009
- India
| | - Vivek Kumar Yadav
- Institute for Computational Molecular Science
- Temple University
- Philadelphia
- USA
| | | |
Collapse
|
36
|
Zhang J, Liu X, Wang SQ, Liu GY, Xu WR, Cheng XC, Wang RL. Identification of dual ligands targeting angiotensin II type 1 receptor and peroxisome proliferator-activated receptor-γ by core hopping of telmisartan. J Biomol Struct Dyn 2016; 35:2665-2680. [PMID: 27602589 DOI: 10.1080/07391102.2016.1227726] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
It has been reported previously that some angiotensin II receptor blockers not only antagonize angiotensin II type 1 receptor (AT1R), but also exert stimulation in peroxisome proliferator-activated receptor γ (PPARγ) partial activation, among which telmisartan displays the best. Telmisartan has been tested as a bifunctional ligand with antihypertensive and hypoglycemic activity. Aiming at more potent leads with selective AT1R antagonism and PPARγ partial agonism, the three parts of telmisartan including the distal benzimidazole ring, the biphenyl moiety, and the carboxylic acid group experienced modification by core hopping method in our study. The central benzimidazole ring, however, remained intact considering its great affinity toward AT1R and PPARγ. We utilized computational techniques for the sake of details on the binding interactions and conformational stability. Standard precision docking analysis and absorption, distribution, metabolism, excretion, and toxicity prediction received 10 molecules with higher Glide scores, similar interactions, and improved pharmacokinetic profiles compared to telmisartan. Comp#91 with highest scores for AT1R (-11.92 kcal/mol) and PPARγ (-13.88 kcal/mol) exhibited excellent binding modes and pharmacokinetic parameters. Molecular dynamics trajectories on best docking pose of comp#91 confirmed the docking results and verified the conformational stability with both receptors throughout the course of 20-ns simulations. Thus, comp#91 could be identified as a promising lead in the development of dual AT1R antagonist and PPARγ partial agonist against hypertension and type 2 diabetes.
Collapse
Affiliation(s)
- Jun Zhang
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin 300070 , China
| | - Xin Liu
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin 300070 , China
| | - Shu-Qing Wang
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin 300070 , China
| | - Gui-You Liu
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin 300070 , China
| | - Wei-Ren Xu
- b Tianjin Key Laboratory of Molecular Design and Drug Discovery , Tianjin Institute of Pharmaceutical Research , Tianjin 300193 , China
| | - Xian-Chao Cheng
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin 300070 , China
| | - Run-Ling Wang
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin 300070 , China
| |
Collapse
|