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Iqbal D, Alsaweed M, Jamal QMS, Asad MR, Rizvi SMD, Rizvi MR, Albadrani HM, Hamed M, Jahan S, Alyenbaawi H. Pharmacophore-Based Screening, Molecular Docking, and Dynamic Simulation of Fungal Metabolites as Inhibitors of Multi-Targets in Neurodegenerative Disorders. Biomolecules 2023; 13:1613. [PMID: 38002295 PMCID: PMC10669353 DOI: 10.3390/biom13111613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Neurodegenerative disorders, such as Alzheimer's disease (AD), negatively affect the economic and psychological system. For AD, there is still a lack of disease-altering treatments and promising cures due to its complex pathophysiology. In this study, we computationally screened the natural database of fungal metabolites against three known therapeutic target proteins of AD. Initially, a pharmacophore-based, drug-likeness category was employed for screening, and it filtered the 14 (A-N) best hits out of 17,544 fungal metabolites. The 14 best hits were docked individually against GSK-3β, the NMDA receptor, and BACE-1 to investigate the potential of finding a multitarget inhibitor. We found that compounds B, F, and L were immuno-toxic, whereas E, H, I, and J had a higher LD50 dose (5000 mg/kg). Among the examined metabolites, the Bisacremine-C (compound I) was found to be the most active molecule against GSK-3β (ΔG: -8.7 ± 0.2 Kcal/mol, Ki: 2.4 × 106 M-1), NMDA (ΔG: -9.5 ± 0.1 Kcal/mol, Ki: 9.2 × 106 M-1), and BACE-1 (ΔG: -9.1 ± 0.2 Kcal/mol, Ki: 4.7 × 106 M-1). It showed a 25-fold higher affinity with GSK-3β, 6.3-fold higher affinity with NMDA, and 9.04-fold higher affinity with BACE-1 than their native ligands, respectively. Molecular dynamic simulation parameters, such as RMSD, RMSF, Rg, and SASA, all confirmed that the overall structures of the targeted enzymes did not change significantly after binding with Bisacremine-C, and the ligand remained inside the binding cavity in a stable conformation for most of the simulation time. The most significant hydrophobic contacts for the GSK-3β-Bisacremine-C complex are with ILE62, VAL70, ALA83, and LEU188, whereas GLN185 is significant for H-bonds. In terms of hydrophobic contacts, TYR184 and PHE246 are the most important, while SER180 is vital for H-bonds in NMDA-Bisacremine-C. THR232 is the most crucial for H-bonds in BACE-1-Bisacremine-C and ILE110-produced hydrophobic contacts. This study laid a foundation for further experimental validation and clinical trials regarding the biopotency of Bisacremine-C.
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Affiliation(s)
- Danish Iqbal
- Department of Health Information Management, College of Applied Medical Sciences, Buraydah Private Colleges, Buraydah 51418, Saudi Arabia
| | - Mohammed Alsaweed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (M.A.); (S.J.)
| | - Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia;
| | - Mohammad Rehan Asad
- Department of Basic Medical Science, College of Medicine, Majmaah University, Al Majmaah 11952, Saudi Arabia;
| | - Syed Mohd Danish Rizvi
- Department of Pharmaceutics, College of Pharmacy, University of Ha’il, Ha’il 81442, Saudi Arabia;
| | - Moattar Raza Rizvi
- School of Allied Health Sciences, Manav Rachna International Institute of Research & Studies (MRIIRS), Faridabad 121001, India;
| | - Hind Muteb Albadrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia;
| | - Munerah Hamed
- Department of Pathology, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Sadaf Jahan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (M.A.); (S.J.)
| | - Hadeel Alyenbaawi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (M.A.); (S.J.)
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Varma M, Ugale V, Shaukat J, Hollmann M, Shete P, Shravage B, Tayade S, Kumbhar A, Butcher R, Jani V, Sonavane U, Joshi R, Lokwani D, Kulkarni P. Novel alkyl-substituted 4-methoxy benzaldehyde thiosemicarbazones: Multi-target directed ligands for the treatment of Alzheimer's disease. Eur J Pharmacol 2023; 957:176028. [PMID: 37657740 DOI: 10.1016/j.ejphar.2023.176028] [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: 01/28/2023] [Revised: 08/14/2023] [Accepted: 08/25/2023] [Indexed: 09/03/2023]
Abstract
Alzheimer's disease (AD) is a devastating neurodegenerative disorder affecting mental ability and interrupts neurocognitive functions. Treating multifactorial conditions of AD with a single-target-directed drug is highly difficult. Thus, a multi-target-directed ligand (MTDL) development strategy has been developed as a promising approach for the treatment of AD. Herein, we have synthesized two novel thiosemicarbazones as MTDLs and reported their bioactivities against diverse neuropathological events involved in AD. In vitro studies revealed that both compounds exhibited promising anticholinesterase activity (AChE, IC50 = 15.98 μM, MZET and IC50 = 30.23 μM, MZMT), well supported by a detailed computational study. Both analogs have shown good thermodynamic behaviour and stability through interactions with characteristic amino acid residues throughout simulation of 100 ns against acetylcholinesterase enzyme. In an electrophysiology assay, these analogs have shown a characteristic inhibitory response against the GluN1-1a + GluN2B subunit of N-methyl-D-aspartate receptors. Pre-treatment of BV-2 microglial cells with MZET effectively decreased nitrite production compared to nitrite produced by lipopolysaccharide-treated cells alone. Further, the effect of MZMT and MZET on autophagy regulation was determined using stably transfected SH-SY5Y neuroblastoma cells. MZET significantly enhanced the autophagy flux in neuroblastoma cells. A significant decrease in copper-catalysed oxidation of amyloid-β in presence of synthesized thiosemicarbazones was also observed. Collectively, our findings indicated that these analogs have potential as effective anti-AD candidates and can be used as a prototype to develop more safer multi-targeted anti-AD drugs.
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Affiliation(s)
- Mokshada Varma
- Bioprospecting Group, Agharkar Research Institute, Savitribai Phule Pune University, G. G. Agharkar Road, Pune, Maharashtra, 411004, India
| | - Vinod Ugale
- Bioprospecting Group, Agharkar Research Institute, Savitribai Phule Pune University, G. G. Agharkar Road, Pune, Maharashtra, 411004, India; Department of Biochemistry I - Receptor Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany; Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, 425405, India.
| | - Javeria Shaukat
- Department of Biochemistry I - Receptor Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Michael Hollmann
- Department of Biochemistry I - Receptor Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Padmaja Shete
- Bioprospecting Group, Agharkar Research Institute, Savitribai Phule Pune University, G. G. Agharkar Road, Pune, Maharashtra, 411004, India
| | - Bhupendra Shravage
- Developmental Biology Group, Agharkar Research Institute, Savitribai Phule Pune University, Pune, Maharashtra, 411004, India
| | - Sakharam Tayade
- Department of Chemistry, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
| | - Avinash Kumbhar
- Department of Chemistry, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
| | - Ray Butcher
- Department of Chemistry, Howard University, Washington, DC, 20059, USA
| | - Vinod Jani
- HPC Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
| | - Uddhavesh Sonavane
- HPC Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
| | - Rajendra Joshi
- HPC Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
| | - Deepak Lokwani
- Rajashri Shahu College of Pharmacy, Buldana, Maharashtra, India
| | - Prasad Kulkarni
- Bioprospecting Group, Agharkar Research Institute, Savitribai Phule Pune University, G. G. Agharkar Road, Pune, Maharashtra, 411004, India.
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Malathi V, Sharon N, Padmaja P, Lokwani D, Khadse S, Chaudhari P, Shirkhedkar AA, Reddy PN, Ugale VG. Design, synthesis, and pharmacological evaluation of [1, 3] dioxolo-chromeno[2,3-b]pyridines as anti-seizure agents. Mol Divers 2023; 27:1809-1827. [PMID: 36214960 DOI: 10.1007/s11030-022-10538-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/29/2022] [Indexed: 10/17/2022]
Abstract
An efficient one-pot three-component reaction for the synthesis of [1,3]dioxolo[4',5':6,7]chromeno[2,3-b]pyridines 4(a-i) has been developed. Synthesis was achieved by reacting sesamol (1), aromatic aldehydes 2(a-i), and 2-aminopropene-1,1,3-tricarbonitrile (3) in the presence of triethylamine at 100 °C under neat reaction condition. Simple operational procedure, broad substrate scope, column chromatography free separations, and high yield of products make it an efficient and largely acceptable synthetic strategy. Synthesized compounds 4(a-i) were further screened for preliminary anticonvulsant activity using MES and scPTZ tests. These analogs were also checked for neurotoxicity and hepatotoxicity. Selected active compounds have been then screened quantitatively to determine ED50 and TD50 values. Analog 4h was found effective in both preclinical seizure models with significant therapeutic/toxicity profile (4h: ED50 = 34.7 mg/kg, MES test; ED50 = 37.9 mg/kg, scPTZ test; TD50 = 308.7 mg/kg). Molecular dynamic simulation for 100 ns of compound 4h-complexed with GABAA receptor revealed good thermodynamic behavior and fairly stable interactions (4h, Docking score = - 10.94). In conclusion, effective synthetic strategy, significant anticonvulsant activity with good toxicity profile and detailed molecular modeling studies led us to anticipate the emergence of these analogs as valid leads for the development of future effective neurotherapeutic agents.
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Affiliation(s)
- Visarapu Malathi
- Department of Chemistry, School of Science, Gitam Deemed to be University, Hyderabad, TS, India
| | - Nissi Sharon
- Department of Chemistry, School of Science, Gitam Deemed to be University, Hyderabad, TS, India
| | - Pannala Padmaja
- Centre for Semio Chemicals, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - Deepak Lokwani
- Rajarshi Shahu College of Pharmacy, Buldana, Maharashtra, India
| | - Saurabh Khadse
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, 425405, India
| | - Prashant Chaudhari
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, 425405, India
| | - Atul A Shirkhedkar
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, 425405, India
| | | | - Vinod G Ugale
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, 425405, India.
- Bioprospecting Group, Agharkar Research Institute, Savitribai Phule Pune University, G. G. Agarkar Road, Pune, Maharashtra, 411004, India.
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Iqbal D, Rehman MT, Alajmi MF, Alsaweed M, Jamal QMS, Alasiry SM, Albaker AB, Hamed M, Kamal M, Albadrani HM. Multitargeted Virtual Screening and Molecular Simulation of Natural Product-like Compounds against GSK3β, NMDA-Receptor, and BACE-1 for the Management of Alzheimer's Disease. Pharmaceuticals (Basel) 2023; 16:ph16040622. [PMID: 37111379 PMCID: PMC10143309 DOI: 10.3390/ph16040622] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/18/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
The complexity of Alzheimer's disease (AD) and several side effects of currently available medication inclined us to search for a novel natural cure by targeting multiple key regulatory proteins. We initially virtually screened the natural product-like compounds against GSK3β, NMDA receptor, and BACE-1 and thereafter validated the best hit through molecular dynamics simulation (MDS). The results demonstrated that out of 2029 compounds, only 51 compounds exhibited better binding interactions than native ligands, with all three protein targets (NMDA, GSK3β, and BACE) considered multitarget inhibitors. Among them, F1094-0201 is the most potent inhibitor against multiple targets with binding energy -11.7, -10.6, and -12 kcal/mol, respectively. ADME-T analysis results showed that F1094-0201 was found to be suitable for CNS drug-likeness in addition to their other drug-likeness properties. The MDS results of RMSD, RMSF, Rg, SASA, SSE and residue interactions indicated the formation of a strong and stable association in the complex of ligands (F1094-0201) and proteins. These findings confirm the F1094-0201's ability to remain inside target proteins' binding pockets while forming a stable complex of protein-ligand. The free energies (MM/GBSA) of BACE-F1094-0201, GSK3β-F1094-0201, and NMDA-F1094-0201 complex formation were -73.78 ± 4.31 kcal mol-1, -72.77 ± 3.43 kcal mol-1, and -52.51 ± 2.85 kcal mol-1, respectively. Amongst the target proteins, F1094-0201 have a more stable association with BACE, followed by NMDA and GSK3β. These attributes of F1094-0201 indicate it as a possible option for the management of pathophysiological pathways associated with AD.
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Affiliation(s)
- Danish Iqbal
- Department of Health Information Management, College of Applied Medical Sciences, Buraydah Private Colleges, Buraydah 51418, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohamed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammed Alsaweed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia
| | - Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Sharifa M Alasiry
- Critical Care Nursing, Department of Nursing, College of Applied Medical Sciences, Majmaah University, Al-Majmaah 15341, Saudi Arabia
| | - Awatif B Albaker
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Munerah Hamed
- Department of Pathology, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mehnaz Kamal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Hind Muteb Albadrani
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia
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Ajala A, Uzairu A, Shallangwa GA, Abechi SE. QSAR, simulation techniques, and ADMET/pharmacokinetics assessment of a set of compounds that target MAO-B as anti-Alzheimer agent. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2023. [DOI: 10.1186/s43094-022-00452-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Abstract
Background
Alzheimer’s disease (AD), the most common cause of dementia in the elderly, is a progressive neurodegenerative disorder that gradually affects cognitive function and eventually causes death. Most approved drugs can only treat the disease alleviating the disease symptoms; therefore, there is a need to develop drugs that can treat this illness holistically. The medical community is searching for new drugs and new drug targets to cure this disease. In this study, QSAR, molecular docking evaluation, and ADMET/pharmacokinetics assessment were used as modeling methods to identify the compounds with outstanding physicochemical properties.
Results
The 37 MAO-B compounds were screened using the aforementioned methods and yielded a model with the following molecular properties: AATS1v, AATS3v, GATS4m, and GATS6e. Good statistical values were R2train = 0.69, R2adj = 0.63, R2pred = 0.57, LOF = 0.23, and RMSE = 0.38. The model was validated using an evaluation set that confirmed its robustness. The molecular docking was also utilized using crystal structure of human monoamine oxidase B in complex with chlorophenylchromone-carboxamide with ID code of 6FW0, and three compounds were identified with outstanding high binding affinity (13 = − 30.51 kcal mol−1, 31 = − 31.85 kcal mol−1, and 33 = − 33.70 kcal mol−1), and better than the Eldepryl (referenced) drug (− 11.40 kcal mol−1).
Conclusions
These three compounds (13, 31, and 33) were analyzed for ADMET/pharmacokinetics evaluation and found worthy of further analysis as promising drug candidates to cure AD and could also serve as a template to design several monoamine oxidase B inhibitors in the future to cure AD.
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Padmaja P, Reddy PN, Reddy BS, Tiwari AK, Ugale VG, Komati A, Sridhar B. Design, synthesis, in vitro α-glucosidase inhibitory, antioxidant activity and molecular docking studies of novel pyridine linked imidazo[1,2-a]pyridine derivatives. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Computational identification of 2,4-disubstituted amino-pyrimidines as L858R/T790M-EGFR double mutant inhibitors using pharmacophore mapping, molecular docking, binding free energy calculation, DFT study and molecular dynamic simulation. In Silico Pharmacol 2021; 9:54. [PMID: 34631361 DOI: 10.1007/s40203-021-00113-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/24/2021] [Indexed: 10/20/2022] Open
Abstract
Pharmacophore modelling studies have been performed for a series of 2,4-disubstituted-pyrimidines derivatives as EGFR L858R/T790M tyrosine kinase inhibitors. The high scoring AARR.15 hypothesis was selected as the best pharmacophore model with the highest survival score of 3.436 having two hydrogen bond acceptors and two aromatic ring features. Pharmacophore-based virtual screening followed by structure-based yielded the six molecules (ZINC17013227, ZINC17013215, ZINC9573324, ZINC9573445, ZINC24023331 and ZINC17013503) from the ZINC database with significant in silico predicted activity and strong binding affinity towords the EGFR L858R/T790M tyrosine kinase. In silico toxicity and cytochrome profiling indicates that all the 06 virtually screened compounds were substrate/inhibitors of the CYP-3A4 metabolizing enzyme and were non-carcinogenic and devoid of Ames mutagenesis. Density functional theory (DFT) and molecular dynamic (MD) simulation further validated the obtained hits. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-021-00113-x.
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Quan J, Ma C, Wang Y, Hu B, Zhang D, Zhang Z, Wang J, Cheng M. Repurposing of cefpodoxime proxetil as potent neuroprotective agent through computational prediction and in vitro validation. J Biomol Struct Dyn 2021; 39:3975-3985. [PMID: 32448083 DOI: 10.1080/07391102.2020.1772884] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 05/18/2020] [Indexed: 01/17/2023]
Abstract
In recent reports, NR2B-NMDA receptor antagonists showed more research value because of its strong targeting ability and less side effects potential. In 2016, EVT-101 was reported to bind in an almost entirely new binding region of this target. Whether strikingly different binding modes can improve targeting and reduce side effects is worth studying. In our preliminary work, we explored the binding patterns of ifenprodil and EVT-101, found the key amino acids and summarized the pharmacophores, hoping to find such antagonists that target the two binding modes simultaneously. In this study, we developed a scalable virtual screening workflow in the FDA-approved drugs library to identify novel NR2B-NMDAR antagonists based on the combination of two pharmacophores. Cefpodoxime proxetil (5) was identified as the hit compound, and it was found for the first time that 5 might have neuroprotective activity as a NR2B-NMDAR antagonist. This result interested us to make further study, the ligand-receptor interactions modeled by molecular docking studies showed that the compound could perfectly merge both the pharmacophore characteristics of ifenprodil and EVT-101 at the binding cavity between the ATDs of GluN1 and GluN2B. The accuracy of molecular docking results and binding stability of ligand-receptor complexes were validated through 100 ns molecular dynamics simulation and binding free energy calculation. Afterwards, MTT assay (49.8%±0.1%, 5 μM) on NMDA injured SH-SY5Y cells and evidence of the effect on attenuating Ca2+ influx induced by NMDA were applied to validate the computational results, further investigation showed that 5 could suppress the NR2B upregulation induced by NMDA. [Formula: see text] Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jishun Quan
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Chao Ma
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Ying Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Baichun Hu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Dongping Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Zhuo Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
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Belal A. 3D-Pharmacophore Modeling, Molecular Docking, and Virtual Screening for Discovery of Novel CDK4/6 Selective Inhibitors. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021330013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Ugale V, Dhote A, Narwade R, Khadse S, Reddy PN, Shirkhedkar A. GluN2B/N-methyl-D-aspartate Receptor Antagonists: Advances in Design, Synthesis, and Pharmacological Evaluation Studies. CNS & NEUROLOGICAL DISORDERS-DRUG TARGETS 2021; 20:822-862. [PMID: 33687902 DOI: 10.2174/1871527320666210309141627] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/13/2020] [Accepted: 01/11/2021] [Indexed: 11/22/2022]
Abstract
Selective GluN2B/N-methyl-D-aspartate receptor (NMDAR) antagonists have exposed their clinical effectiveness in a cluster of neurodegenerative diseases, such as epilepsy, Alzheimer's disease, Parkinson's disease, pain, and depression. Hence, GluN2B/NMDARs are considered to be a prospective target for the management of neurodegenerative diseases. Here, we have discussed the current results and significance of subunit selective GluN2B/NMDAR antagonists to pave the way for the establishment of new, safe, and economical drug candidates in the near future. By using summarized data of selective GluN2B/NMDAR antagonists, medicinal chemists are certainly a step closer to the goal of improving the therapeutic and side effect profile of selective antagonists. Outlined summary of designing strategies, synthetic schemes, and pharmacological evaluation studies reinvigorate efforts to identify, modify, and synthesize novel GluN2B/NMDAR antagonists for treating neurodegenerative diseases.
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Affiliation(s)
- Vinod Ugale
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dist: Dhule (MS) 425405, India
| | - Ashish Dhote
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dist: Dhule (MS) 425405, India
| | - Rushikesh Narwade
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dist: Dhule (MS) 425405, India
| | - Saurabh Khadse
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dist: Dhule (MS) 425405, India
| | - P Narayana Reddy
- Department of Chemistry, Gitam School of Technology, Gitam University, Hyderabad (T.S), India
| | - Atul Shirkhedkar
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dist: Dhule (MS) 425405, India
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11
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Molecular docking utilising the OliveNet™ library reveals novel phenolic compounds which may potentially target key proteins associated with major depressive disorder. Comput Biol Chem 2020; 86:107234. [PMID: 32220809 DOI: 10.1016/j.compbiolchem.2020.107234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/31/2020] [Accepted: 02/10/2020] [Indexed: 11/21/2022]
Abstract
The antidepressant medications that are currently prescribed to patients suffering from major depressive disorder (MDD) have limitations and as a result, there is an urgent need to increase the options that are available. A number of studies have found that natural polyphenols have neuroprotective properties and there is evidence to suggest that they modulate neurotransmitter systems. There are more than 200 phenolic compounds that have been identified in Olea europaea, many of which have not yet been investigated for their potential biological effects. In this study, in silico methods were used to screen the phenolic library from the OliveNet™ database and identify novel lead compounds for proteins implicated in the pathophysiology of MDD. The molecular docking results revealed that the monoamine oxidase enzyme isoforms (MAO-A/MAO-B) had binding specificities for certain phenolic subclasses. The lead ligands that were identified from these subclasses were positioned near the flavin adenine dinucleotide (FAD) cofactor, interacting in a similar manner as known inhibitors. In addition to the MAO enzymes, several phenolic compounds were docked to neurotransmitter transporters and postsynaptic receptors, as well as proteins involved in neuroinflammation, oxidative stress and the endocannabinoid system. Based on the binding affinity, position, orientation and interactions of the lead phenolic compounds identified in this study, it is predicted that they may have antidepressant properties. The results should be validated further using molecular dynamics (MD) simulations, as well as in vivo and in vitro techniques.
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Blaikie L, Kay G, Kong Thoo Lin P. Current and emerging therapeutic targets of alzheimer's disease for the design of multi-target directed ligands. MEDCHEMCOMM 2019; 10:2052-2072. [PMID: 32206241 PMCID: PMC7069509 DOI: 10.1039/c9md00337a] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/14/2019] [Indexed: 12/22/2022]
Abstract
Alzheimer's disease (AD) is the most prevalent neurodegenerative disease, and a major cause of death worldwide. The number of people suffering from this debilitating disorder is rising at an unprecedented rate, with a subsequent surge in healthcare costs. Only four drugs are clinically available for the treatment of AD symptoms, but they are not disease-modifying. Consequently, there is an urgent need for a cure. Although the cause of this debilitating condition remains poorly understood, it is believed that several factors may be involved in combination - including, health and lifestyle, environmental, and genetic factors. In recent years, a number of hallmarks of the disease have also been discovered, and it is believed that these factors may play an important role in the development of AD. Amyloid aggregation is one such factor which has been highly investigated, in addition to cholinesterase enzymes and tau aggregation. In the last decade, multi-target drugs have been increasingly investigated for their application to AD treatment. By combining two or more pharmacophores in a single compound, it is possible to synthesise a drug which can target several factors that are involved in AD development. This is a particularly attractive approach as it would avoid the use of combination therapies. As a result, it could reduce the burden on carers and families, and decrease healthcare and social care costs. Many active pharmacophores have been employed for the development of hybrid drugs, due to their abilities to inhibit the factors currently widely recognised to be involved in AD. These compounds have demonstrated promising results; however, research is still required to optimise the pharmacological profiles of the drugs, in addition to their potencies. Meanwhile, extensive research is continuously being performed into other potential targets for the treatment of AD. Based on the results obtained thus far, it is likely that multi-target compounds will continue to be increasingly studied in the future as potential treatments for AD.
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Affiliation(s)
- Laura Blaikie
- School of Pharmacy and Life Sciences , Robert Gordon University , Aberdeen , Scotland , UK .
| | - Graeme Kay
- School of Pharmacy and Life Sciences , Robert Gordon University , Aberdeen , Scotland , UK .
| | - Paul Kong Thoo Lin
- School of Pharmacy and Life Sciences , Robert Gordon University , Aberdeen , Scotland , UK .
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Structure based virtual screening of novel noncompetitive antagonist of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor. J Biotechnol 2019; 295:9-18. [PMID: 30831124 DOI: 10.1016/j.jbiotec.2019.01.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/13/2018] [Accepted: 01/19/2019] [Indexed: 11/24/2022]
Abstract
The α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) subtype ionotropic glutamate receptors are attractive antiepileptic targets responsible for mediating the majority of excitatory neurotransmission and plasticity. The noncompetitive antagonists obtain more and more attention as drug candidates for treatment of the neurological diseases involving excessive activity of AMPARs, due to they regulate AMPA receptors (AMPARs) activity independently of endogenous glutamate levels unlike the competitive antagonists. Development of novel AMPAR noncompetitive antagonists, which are safer and more efficacious than competitive antagonists, is highly under demand. Here, we present the discovery of novel antagonists against AMPAR through Structure-Based Virtual Screening (SBVS). Three compounds were successfully distinguished by several different filtering strategies, namely STOCK6S-10902, STOCK1N-49134 and STOCK5S-68665. The interaction mode of these compounds was further explored through molecular dynamics simulation, binding free energy calculation and the binding free energy decomposition. It is demonstrated that some residues within the binding pocket, which have been proved their importance in antagonist binding and gating, form strong hydrogen bond interactions with these three molecules. In particular, H-bond interactions with high occupancies between Ser516, Ser788 and STOCK6S-10902 and Ser516, Asn791 and STOCK1N-49134 were observed. The three hit compounds with new scaffolds and the detailed binding modes could potentially serve as a starting point for further optimization and development.
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Zhang YM, Yu DX, Yin BS, Li XR, Li LN, Li YN, Wang YX, Chen Y, Liu WH, Gao L. Xylazine Regulates the Release of Glycine and Aspartic Acid in Rat Brain. J Vet Res 2018; 62:121-128. [PMID: 29978137 PMCID: PMC5957471 DOI: 10.1515/jvetres-2018-0017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/14/2018] [Indexed: 11/15/2022] Open
Abstract
Introduction Xylazine, a type of α2-adrenoceptors, is a commonly used drug in veterinary medicine. Xylazine-induced changes in the content of amino acid neurotransmitters - glycine (Gly) and aspartic acid (Asp), in different brain regions and neurons were studied. Material and Methods Wistar rats were administered 50 mg/kg or 70 mg/kg of xylazine by intraperitoneal injection. In addition, in vitro experiments were conducted, in which neurons were treated with 15 μg/mL, 25 μg/mL, 35μg/mL, and 45 μg/mL of xylazine. Test methods were based on the enzyme-linked immunosorbent assays (ELISA). Results During anaesthesia, Asp levels in each brain area were significantly lower compared to the control group. Except for the cerebrum, levels of Gly in other brain areas were significantly increased during the anaesthesia period. In vitro, xylazine-related neuron secretion of Gly increased significantly compared to the control group at 60 min and 90 min. Moreover, xylazine caused a significant decrease in the levels of Asp secreted by neurons at 20 min, but gradually returned to the level of the control group. Conclusion The data showed that during anaesthesia the overall levels of Asp decreased and overall levels of Gly increased. In addition, the inhibitory effect of xylazine on Asp and the promotion of Gly were dose-dependent. Our data showed that different effects of xylazine on excitatory and inhibitory neurotransmitters provided a theoretical basis for the mechanism of xylazine activity in clinical anaesthesia.
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Affiliation(s)
- Yi-Ming Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150000, China
| | - Dong-Xu Yu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150000, China
| | - Bai-Shuang Yin
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150000, China
| | - Xin-Ran Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150000, China
| | - Li-Na Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150000, China
| | - Ya-Nan Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150000, China
| | - Yu-Xin Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150000, China
| | - Yu Chen
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150000, China
| | - Wen-Han Liu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150000, China
| | - Li Gao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150000, China
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Abstract
Abstract
Introduction
Xylazine, a type of α2-adrenoceptors, is a commonly used drug in veterinary medicine. Xylazine-induced changes in the content of amino acid neurotransmitters – glycine (Gly) and aspartic acid (Asp), in different brain regions and neurons were studied.
Material and Methods
Wistar rats were administered 50 mg/kg or 70 mg/kg of xylazine by intraperitoneal injection. In addition, in vitro experiments were conducted, in which neurons were treated with 15 μg/mL, 25 μg/mL, 35μg/mL, and 45 μg/mL of xylazine. Test methods were based on the enzyme-linked immunosorbent assays (ELISA).
Results
During anaesthesia, Asp levels in each brain area were significantly lower compared to the control group. Except for the cerebrum, levels of Gly in other brain areas were significantly increased during the anaesthesia period. In vitro, xylazine-related neuron secretion of Gly increased significantly compared to the control group at 60 min and 90 min. Moreover, xylazine caused a significant decrease in the levels of Asp secreted by neurons at 20 min, but gradually returned to the level of the control group.
Conclusion
The data showed that during anaesthesia the overall levels of Asp decreased and overall levels of Gly increased. In addition, the inhibitory effect of xylazine on Asp and the promotion of Gly were dose-dependent. Our data showed that different effects of xylazine on excitatory and inhibitory neurotransmitters provided a theoretical basis for the mechanism of xylazine activity in clinical anaesthesia.
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Exploration of structural and physicochemical properties of small molecules to inhibit NMDA functionality. Struct Chem 2018. [DOI: 10.1007/s11224-018-1103-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Iqbal S, Anantha Krishnan D, Gunasekaran K. Identification of potential PKC inhibitors through pharmacophore designing, 3D-QSAR and molecular dynamics simulations targeting Alzheimer’s disease. J Biomol Struct Dyn 2017; 36:4029-4044. [DOI: 10.1080/07391102.2017.1406824] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Saleem Iqbal
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu, India
| | - Dhanabalan Anantha Krishnan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu, India
- Bioinformatics Infrastructure Facility, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu, India
| | - Krishnasamy Gunasekaran
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu, India
- Bioinformatics Infrastructure Facility, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu, India
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Development of Pharmacophore Model for Indeno[1,2-b]indoles as Human Protein Kinase CK2 Inhibitors and Database Mining. Pharmaceuticals (Basel) 2017; 10:ph10010008. [PMID: 28075359 PMCID: PMC5374412 DOI: 10.3390/ph10010008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 12/16/2022] Open
Abstract
Protein kinase CK2, initially designated as casein kinase 2, is an ubiquitously expressed serine/threonine kinase. This enzyme, implicated in many cellular processes, is highly expressed and active in many tumor cells. A large number of compounds has been developed as inhibitors comprising different backbones. Beside others, structures with an indeno[1,2-b]indole scaffold turned out to be potent new leads. With the aim of developing new inhibitors of human protein kinase CK2, we report here on the generation of common feature pharmacophore model to further explain the binding requirements for human CK2 inhibitors. Nine common chemical features of indeno[1,2-b]indole-type CK2 inhibitors were determined using MOE software (Chemical Computing Group, Montreal, Canada). This pharmacophore model was used for database mining with the aim to identify novel scaffolds for developing new potent and selective CK2 inhibitors. Using this strategy several structures were selected by searching inside the ZINC compound database. One of the selected compounds was bikaverin (6,11-dihydroxy-3,8-dimethoxy-1-methylbenzo[b]xanthene-7,10,12-trione), a natural compound which is produced by several kinds of fungi. This compound was tested on human recombinant CK2 and turned out to be an active inhibitor with an IC50 value of 1.24 µM.
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Ugale VG, Bari SB. Structural Exploration of Quinazolin-4(3H)-ones as Anticonvulsants: Rational Design, Synthesis, Pharmacological Evaluation, and Molecular Docking Studies. Arch Pharm (Weinheim) 2016; 349:864-880. [DOI: 10.1002/ardp.201600218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/12/2016] [Accepted: 09/14/2016] [Indexed: 01/24/2023]
Affiliation(s)
- Vinod G. Ugale
- Department of Pharmaceutical Chemistry; R. C. Patel Institute of Pharmaceutical Education and Research; Shirpur (Dhule) Maharashtra India
| | - Sanjay B. Bari
- Department of Pharmaceutical Chemistry; H. R. Patel Institute of Pharmaceutical Education and Research; Shirpur (Dhule) Maharashtra India
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Vyas VK, Qureshi G, Ghate M, Patel H, Dalai S. Identification of novel PfDHODH inhibitors as antimalarial agents via pharmacophore-based virtual screening followed by molecular docking and in vivo antimalarial activity. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2016; 27:427-440. [PMID: 27310104 DOI: 10.1080/1062936x.2016.1189959] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 05/11/2016] [Indexed: 06/06/2023]
Abstract
Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) catalyses the fourth reaction of de novo pyrimidine biosynthesis in parasites, and represents an important target for the treatment of malaria. In this study, we describe pharmacophore-based virtual screening combined with docking study and biological evaluation as a rational strategy for identification of novel hits as antimalarial agents. Pharmacophore models were established from known PfDHODH inhibitors using the GALAHAD module with IC50 values ranging from 0.033 μM to 142 μM. The best pharmacophore model consisted of three hydrogen bond acceptor, one hydrogen bond donor and one hydrophobic features. The pharmacophore models were validated through receiver operating characteristic and Günere-Henry scoring methods. The best pharmacophore model as a 3D search query was searched against the IBS database. Several compounds with different structures (scaffolds) were retrieved as hit molecules. Among these compounds, those with a QFIT value of more than 81 were docked in the PfDHODH enzyme to further explore the binding modes of these compounds. In silico pharmacokinetic and toxicities were predicted for the best docked molecules. Finally, the identified hits were evaluated in vivo for their antimalarial activity in a parasite inhibition assay. The hits reported here showed good potential to become novel antimalarial agents.
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Affiliation(s)
- V K Vyas
- a Department of Pharmaceutical Chemistry , Institute of Pharmacy, Nirma University , Ahmedabad , India
| | - G Qureshi
- a Department of Pharmaceutical Chemistry , Institute of Pharmacy, Nirma University , Ahmedabad , India
| | - M Ghate
- a Department of Pharmaceutical Chemistry , Institute of Pharmacy, Nirma University , Ahmedabad , India
| | - H Patel
- b Institute of Science, Nirma University , Ahmedabad , India
| | - S Dalai
- b Institute of Science, Nirma University , Ahmedabad , India
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