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Hamidian M, Salehi A, Naghiha R, Movahhedi Dehnavi M, Mohammadi H, Nejad Mirfathi M, Mojarab-Mahboubkar M, Azizi R. Biological activity of essential oils from Ferulago angulata and Ferula assa-foetida against food-related microorganisms (antimicrobial) and Ephestia kuehniella as a storage pest (insecticidal); an in vitro and in silico study. Fitoterapia 2024; 175:105937. [PMID: 38565381 DOI: 10.1016/j.fitote.2024.105937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/20/2024] [Accepted: 03/30/2024] [Indexed: 04/04/2024]
Abstract
Misuse of synthetic pesticides and antimicrobials in agriculture and the food industry has resulted in food contamination, promoting resistant pests and pathogen strains and hazards for humanity and the environment. Therefore, ever-increasing concern about synthetic chemicals has stimulated interest in eco-friendly compounds. Ferulago angulata (Schltdl.) Boiss. and Ferula assa-foetida L., as medicinal species with restricted natural distribution and unknown biological potential, aimed at investigation of their essential oil (EO) biological properties, were subjected. Z-β-Ocimene and Z-1-Propenyl-sec-butyl disulfide molecules were identified as the major composition of the essential oil of the fruits of F. angulata and F. assa-foetida, respectively. In vitro antimicrobial activity and membrane destruction investigation by scanning electron microscopy imaging illustrated that F. angulata EO had potent antibacterial activity. Besides, the EOs of both plants exhibited significant anti-yeast activity against Candida albicans. In relation to insecticidal activity, both EOs indicated appropriate potential against Ephestia kuehniella; however, the F. assa-foetida EO had more toxicity on the studied pest. Among several insecticidal-related targets, acetylcholinesterase was identified as the main target of EO based on the molecular docking approach. Hence, in line with in vitro results, in silico evaluation determined that F. assa-foetida has a higher potential for inhibiting acetylcholinesterase and, consequently, better insecticide properties. Overall, in addition to the antioxidant properties of both EO, F. angulata EO could serve as an effective prevention against microbial spoilage and foodborne pathogens, and F. assa-foetida EO holds promise as a multi-purpose and natural biocide for yeast contamination and pest management particularly against E. kuehniella.
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Affiliation(s)
- Mohammad Hamidian
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Yasouj University, Iran
| | - Amin Salehi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Yasouj University, Iran.
| | - Reza Naghiha
- Department of Animal Sciences, Faculty of Agriculture, Yasouj University, Yasouj, Iran; Department of Pathobiology, Faculty of Veterinary Medicine Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | | | | | | | | | - Roya Azizi
- Department of Plant Protection, College of Agricultural Sciences, University of Guilan, Rasht, Iran
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Touati I, Abdalla M, Ali NH, AlRuwaili R, Alruwaili M, Britel MR, Maurady A. Constituents of Stachys plants as potential dual inhibitors of AChE and NMDAR for the treatment of Alzheimer's disease: a molecular docking and dynamic simulation study. J Biomol Struct Dyn 2024; 42:2586-2602. [PMID: 37325873 DOI: 10.1080/07391102.2023.2217925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/17/2023] [Indexed: 06/17/2023]
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative condition characterized by progressive cognitive impairment. While the formation of β-amyloid plaques and neurofibrillary tangles are the hallmarks features of AD, the downstream consequence of these byproducts is the disruption of the cholinergic and glutamatergic neural systems. Growing evidence for the existence of interplay between AChE and NMDARs has opened up new venues for the discovery of novel ligands endowed with anticholinesterase and NMDAR-blocking activity. Plants belonging to the stachys genus have been extensively explored for having a broad range of therapeutic applications and have been used traditionally for millennia, to treat various CNS-related disorders, which makes them the ideal source of novel therapeutics. The present study was designed to identify natural dual-target inhibitors for AChE and NMDAR deriving from stachys genus for their potential use in AD. Using molecular docking, drug-likeness-profiling, MD simulation and MMGBSA calculations, an in-house database of biomolecules pertaining to the stachys genus was shortlisted based on their binding affinity, overall stability and critical ADMET parameters. Pre- and post-MD analysis revealed that Isoorientin effectively binds to AChE and NMDAR with various vital interactions, exhibits a stable behavior with minor fluctuations relative to two clinical drugs used as positive control, and displays strong and consistent interactions that lasted for the majority of the simulation. Findings from this study have elucidated the rationale behind the traditional use of Stachys plants for the treatment of AD and could provide new impetus for the development of novel dual-target therapeutics for AD treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Iman Touati
- Laboratory of Innovative Technologies, National School of Applied Sciences of Tangier, Abdelmalek Essaadi University, Tetouan, Morocco
| | - Mohnad Abdalla
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Naif H Ali
- Department of Internal Medicine, Medical College, Najran University, Najran, Saudi Arabia
| | - Raed AlRuwaili
- Department of Internal Medicine, College of Medicine, Jouf University, Sakaka, Saudi Arabia
| | - Mubarak Alruwaili
- Department of Internal Medicine, College of Medicine, Jouf University, Sakaka, Saudi Arabia
| | - Mohammed Reda Britel
- Laboratory of Innovative Technologies, National School of Applied Sciences of Tangier, Abdelmalek Essaadi University, Tetouan, Morocco
| | - Amal Maurady
- Laboratory of Innovative Technologies, National School of Applied Sciences of Tangier, Abdelmalek Essaadi University, Tetouan, Morocco
- Faculty of Sciences and Techniques of Tangier, Abdelmalek Essaadi University, Tetouan, Morocco
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Srivastava S, Sharma S, Deep S, Khare SK. Screening of Multitarget-Directed Natural Compounds as Drug Candidates for Alzheimer's Disease Using In Silico Techniques: Their Extraction and In Vitro Validation. ACS Omega 2023; 8:38118-38129. [PMID: 37867692 PMCID: PMC10586450 DOI: 10.1021/acsomega.3c04261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/18/2023] [Indexed: 10/24/2023]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder that impairs neurocognitive function. Acetylcholinesterase (AChE) and β-site APP cleaving enzyme 1 (BACE1) are the two main proteins implicated in AD. Indeed, the major available commercial drugs (donepezil, rivastigmine, and galantamine) against Alzheimer's are AChE inhibitors. However, none of these drugs are known to reverse or reduce the pathophysiological condition of the disease since there are multiple contributing factors to AD. Therefore, there is a need to develop a multitarget-directed ligand approach for its treatment. In the present study, plant bioactive compounds were screened for their AChE and BACE1 inhibition potential by conducting molecular docking studies. Considering their docking score and pharmacokinetic properties, limonin, peimisine, serratanine B, and withanolide A were selected as the lead compounds. Molecular dynamics simulations of these protein-ligand complexes confirmed the conformational and energetically stabilized enzyme-inhibitor complexes. The inhibition potential of the lead compounds was validated by in vitro enzyme assay. Withanolide A inhibited AChE (IC50 value of 107 μM) and showed mixed-type inhibition. At this concentration, it inhibited BACE1 activity by 57.10% and was stated as most effective. Both the compounds, as well as their crude extracts, were found to have no cytotoxic effect on the SH-SY5Y cell line.
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Affiliation(s)
- Sukriti Srivastava
- Enzyme
and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shilpa Sharma
- Biophysical
Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shashank Deep
- Biophysical
Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Sunil Kumar Khare
- Enzyme
and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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Almalki SG, Alqurashi YE, Alturaiki W, Almawash S, Khan A, Ahmad P, Iqbal D. Antioxidant, LC-MS Analysis, and Cholinesterase Inhibitory Potentials of Phoenix dactylifera Cultivar Khudari: An In Vitro Enzyme Kinetics and In Silico Study. Biomolecules 2023; 13:1474. [PMID: 37892156 PMCID: PMC10605097 DOI: 10.3390/biom13101474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
We evaluated the therapeutic potentials of Khudari fruit pulp, a functional food and cultivar of Phoenix dactylifera, against neurological disorders. Our results demonstrate a good amount of phytochemicals (total phenolic content: 17.77 ± 8.21 µg GA/mg extract) with a high antioxidant potential of aqueous extract (DPPH assay IC50 = 235.84 ± 11.65 µg/mL) and FRAP value: 331.81 ± 4.56 µmol. Furthermore, the aqueous extract showed the marked inhibition of cell-free acetylcholinesterase (electric eel) with an IC50 value of 48.25 ± 2.04 µg/mL, and an enzyme inhibition kinetics study revealed that it exhibits mixed inhibition. Thereafter, we listed the 18 best-matched phytochemical compounds present in aqueous extract through LC/MS analysis. The computational study revealed that five out of eighteen predicted compounds can cross the BBB and exert considerable aqueous solubility. where 2-{5-[(1E)-3-methylbuta-1,3-dien-1-yl]-1H-indol-3-yl}ethanol (MDIE) indicates an acceptable LD50. value. A molecular docking study exhibited that the compounds occupied the key residues of acetylcholinesterase with ΔG range between -6.91 and -9.49 kcal/mol, where MDIE has ∆G: -8.67 kcal/mol, which was better than that of tacrine, ∆G: -8.25 kcal/mol. Molecular dynamics analyses of 100 ns supported the stability of the protein-ligand complexes analyzed through RMSD, RMSF, Rg, and SASA parameters. TRP_84 and GLY_442 are the most critical hydrophobic contacts for the complex, although GLU_199 is important for H-bonds. Prime/MM-GBSA showed that the protein-ligand complex formed a stable confirmation. These findings suggest that the aqueous extract of Khudari fruit pulp has significant antioxidant and acetylcholinesterase inhibition potentials, and its compound, MDIE, forms stably with confirmation with the target protein, though this fruit of Khudari dates can be a better functional food for the treatment of Alzheimer's disease. Further investigations are needed to fully understand the therapeutic role of this plant-based compound via in vivo study.
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Affiliation(s)
- Sami G. Almalki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia;
| | - Yaser E. Alqurashi
- Department of Biology, College of Science Al-Zulfi, Majmaah University, Al-Majmaah 11952, Saudi Arabia;
| | - Wael Alturaiki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia;
| | - Saud Almawash
- Department of Pharmaceutical Sciences, College of Pharmacy, Shaqra University, Shaqra 11961, Saudi Arabia;
| | - Amir Khan
- Oral Medicine and Allied Dental Sciences Department, Faculty of Dentistry, Taif University, Taif 11099, Saudi Arabia;
| | - Parvej Ahmad
- IIRC-5 Clinical Biochemistry and Natural Product Research Laboratory, Integral University, Lucknow 226026, India;
| | - Danish Iqbal
- Department of Health Information Management, College of Applied Medical Sciences, Buraydah Private Colleges, Buraydah 51418, Saudi Arabia
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ahmad S, Alrouji M, Alhajlah S, Alomeir O, Pandey RP, Ashraf MS, Ahmad S, Khan S. Secondary Metabolite Profiling, Antioxidant, Antidiabetic and Neuroprotective Activity of Cestrum nocturnum (Night Scented-Jasmine): Use of In Vitro and In Silico Approach in Determining the Potential Bioactive Compound. Plants (Basel) 2023; 12:1206. [PMID: 36986895 PMCID: PMC10051713 DOI: 10.3390/plants12061206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/05/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
This study aims to describe the therapeutic potential of C. nocturnum leaf extracts against diabetes and neurological disorders via the targeting of α-amylase and acetylcholinesterase (AChE) activities, followed by computational molecular docking studies to establish a strong rationale behind the α-amylase and AChE inhibitory potential of C. nocturnum leaves-derived secondary metabolites. In our study, the antioxidant activity of the sequentially extracted C. nocturnum leaves extract was also investigated, in which the methanolic fraction exhibited the strongest antioxidant potential against DPPH (IC50 39.12 ± 0.53 µg/mL) and ABTS (IC50 20.94 ± 0.82 µg/mL) radicals. This extract strongly inhibited the α-amylase (IC50188.77 ± 1.67 µg/mL) and AChE (IC50 239.44 ± 0.93 µg/mL) in a non-competitive and competitive manner, respectively. Furthermore, in silico analysis of compounds identified in the methanolic extract of the leaves of C. nocturnum using GC-MS revealed high-affinity binding of these compounds with the catalytic sites of α-amylase and AChE, with binding energy ranging from -3.10 to -6.23 kcal/mol and from -3.32 to -8.76 kcal/mol, respectively. Conclusively, the antioxidant, antidiabetic, and anti-Alzheimer activity of this extract might be driven by the synergistic effect of these bioactive phytoconstituents.
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Affiliation(s)
- Saheem Ahmad
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 2440, Saudi Arabia
| | - Mohammed Alrouji
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Shaqra 11961, Saudi Arabia
| | - Sharif Alhajlah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Shaqra 11961, Saudi Arabia
| | - Othman Alomeir
- Department of Pharmacy Practice, College of Pharmacy, Shaqra University, Shaqra 11961, Saudi Arabia
| | | | - Mohammad Saquib Ashraf
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Riyadh ELM University, Riyadh 12734, Saudi Arabia
| | - Shafeeque Ahmad
- Department of Biochemistry, Noida International Institute of Medical Sciences, Noida International University, Gautam Budh Nagar 203 201, India
| | - Saif Khan
- Department of Basic Dental and Medical Sciences, College of Dentistry, University of Hail, Hail 2440, Saudi Arabia
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Setlur AS, K C, Pandey S, Sarkar M, Niranjan V. Comprehensive Molecular Interaction Studies to Construe the Repellent/Kill Activity of Geraniol During Binding Event Against Aedes aegypti Proteins. Mol Biotechnol 2022; 65:726-740. [PMID: 36169809 DOI: 10.1007/s12033-022-00560-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/06/2022] [Indexed: 11/27/2022]
Abstract
Aedes aegypti is an etiological agent for dengue, chikungunya, zika, and yellow fever viruses. With the advent of the use of natural alternatives as repellents, their precise mode of action during the event of binding is still unclear. Geraniol is one such bioactive natural that has been previously shown to have some insecticide properties. Thus, the present study aimed to understand the mechanism of the binding event of geraniol with the whole proteome of A. aegypti. Twenty protein target categories were shortlisted for the mosquito, wherein the proteins were downloaded with respect to the reference proteome. Conserved domain analysis was performed for the same using the CDD search tool to find the proteins that have common domains. 309 proteins were modeled using RaptorX standalone tool, and validated using Ramachandran plots from SAVES v6.0 from ProCheck. These modeled and validated proteins were then docked against geraniol, using POAP software, for understanding the binding energies. The top 3 best-docked complexes were then analyzed for their stabilities and event of binding via 100 ns simulation studies using DESMOND's Maestro environment. The docking results showed that the geraniol-voltage-gated sodium channel had the best energy of - 7.1 kcal/mol, followed by geraniol-glutathione-S-transferase (- 6.8 kcal/mol) and geraniol-alpha esterase (- 6.8 kcal/mol). The simulations for these 3 complexes revealed that several residues of the proteins interacted well with geraniol at a molecular level, and all three docked complexes were found to be stable when simulated (RMSD: 16-18 Å, 3.6-4.8 Å, 4.8-5.6 Å, respectively). Thus, the present study provides insights into the mechanism of the binding event of geraniol with the major A. aegypti targets, thereby, assisting the use of geraniol as a natural repellent.
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Affiliation(s)
- Anagha S Setlur
- Department of Biotechnology, RV College of Engineering, Bangalore, 560059, India
| | - Chandrashekar K
- Department of Biotechnology, RV College of Engineering, Bangalore, 560059, India
| | - Shruti Pandey
- Research and Development, Reckitt Benckiser India Pvt. Ltd., Gurgaon, Haryana, 122001, India
| | - Manas Sarkar
- Research and Development, Reckitt Benckiser India Pvt. Ltd., Gurgaon, Haryana, 122001, India
| | - Vidya Niranjan
- Department of Biotechnology, RV College of Engineering, Bangalore, 560059, India.
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Khare N, Maheshwari SK, Rizvi SMD, Albadrani HM, Alsagaby SA, Alturaiki W, Iqbal D, Zia Q, Villa C, Jha SK, Jha NK, Jha AK. Homology Modelling, Molecular Docking and Molecular Dynamics Simulation Studies of CALMH1 against Secondary Metabolites of Bauhinia variegata to Treat Alzheimer's Disease. Brain Sci 2022; 12:brainsci12060770. [PMID: 35741655 PMCID: PMC9220886 DOI: 10.3390/brainsci12060770] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/05/2022] [Accepted: 05/31/2022] [Indexed: 02/06/2023] Open
Abstract
Calcium homeostasis modulator 1 (CALHM1) is a protein responsible for causing Alzheimer’s disease. In the absence of an experimentally designed protein molecule, homology modelling was performed. Through homology modelling, different CALHM1 models were generated and validated through Rampage. To carry out further in silico studies, through molecular docking and molecular dynamics simulation experiments, various flavonoids and alkaloids from Bauhinia variegata were utilised as inhibitors to target the protein (CALHM1). The sequence of CALHM1 was retrieved from UniProt and the secondary structure prediction of CALHM1 was done through CFSSP, GOR4, and SOPMA methods. The structure was identified through LOMETS, MUSTER, and MODELLER and finally, the structures were validated through Rampage. Bauhinia variegata plant was used to check the interaction of alkaloids and flavonoids against CALHM1. The protein and protein–ligand complex were also validated through molecular dynamics simulations studies. The model generated through MODELLER software with 6VAM A was used because this model predicted the best results in the Ramachandran plot. Further molecular docking was performed, quercetin was found to be the most appropriate candidate for the protein molecule with the minimum binding energy of −12.45 kcal/mol and their ADME properties were analysed through Molsoft and Molinspiration. Molecular dynamics simulations showed that CALHM1 and CALHM1–quercetin complex became stable at 2500 ps. It may be seen through the study that quercetin may act as a good inhibitor for treatment. With the help of an in silico study, it was easier to analyse the 3D structure of the protein, which may be scrutinized for the best-predicted model. Quercetin may work as a good inhibitor for treating Alzheimer’s disease, according to in silico research using molecular docking and molecular dynamics simulations, and future in vitro and in vivo analysis may confirm its effectiveness.
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Affiliation(s)
- Noopur Khare
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki 225003, Uttar Pradesh, India; (N.K.); (S.K.M.)
- Department of Biotechnology, Dr. A.P.J. Abdul Kalam Technical University, Lucknow 226021, Uttar Pradesh, India
| | - Sanjiv Kumar Maheshwari
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki 225003, Uttar Pradesh, India; (N.K.); (S.K.M.)
| | - Syed Mohd Danish Rizvi
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 2240, Saudi Arabia;
| | - Hind Muteb Albadrani
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (H.M.A.); (S.A.A.); (W.A.); (Q.Z.)
| | - Suliman A. Alsagaby
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (H.M.A.); (S.A.A.); (W.A.); (Q.Z.)
| | - Wael Alturaiki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (H.M.A.); (S.A.A.); (W.A.); (Q.Z.)
| | - Danish Iqbal
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (H.M.A.); (S.A.A.); (W.A.); (Q.Z.)
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 15341, Saudi Arabia
- Correspondence: (D.I.); (A.K.J.)
| | - Qamar Zia
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (H.M.A.); (S.A.A.); (W.A.); (Q.Z.)
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 15341, Saudi Arabia
| | - Chiara Villa
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy;
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida 201310, Uttar Pradesh, India; (S.K.J.); (N.K.J.)
- Department of Biotechnology, School of Applied & Life Sciences (SALS), Uttaranchal University, Dehradun 248007, Uttarakhand, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali 140413, Punjab, India
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida 201310, Uttar Pradesh, India; (S.K.J.); (N.K.J.)
- Department of Biotechnology, School of Applied & Life Sciences (SALS), Uttaranchal University, Dehradun 248007, Uttarakhand, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali 140413, Punjab, India
| | - Abhimanyu Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida 201310, Uttar Pradesh, India; (S.K.J.); (N.K.J.)
- Correspondence: (D.I.); (A.K.J.)
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Zeng W, Wang Z, Xiao Y, Teng K, Cao Z, Cai H, Liu Y, Yin H, Cao P, Tao J. Insights into the Interactions Between Root Phenotypic Traits and the Rhizosphere Bacterial Community. Curr Microbiol 2022; 79:176. [PMID: 35488936 DOI: 10.1007/s00284-022-02870-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 04/08/2022] [Indexed: 11/03/2022]
Abstract
The root phenotypic traits have been considered as important factors in shaping the rhizosphere microbiome and regulating plant growth. However, the relationships between root phenotypic traits and the rhizosphere bacterial community remain unclear. We investigated two fields with different developing tobacco roots by a long-term positioning test in Hengshi. The well-developed root system (WDR) showed much more superiority in root phenotypic traits, including total root length, total projection area, surface area, and root tip number, than the underdeveloped root system. The specific root traits in WDR provided more ecological niches for the rhizosphere microorganisms, contributing to a more diverse microbial community and a more complex microbial network. The total root length and root tip number were the key factors shaping bacterial communities in the rhizosphere. In turn, the phyla Acidobacteria and Bacteroidetes might play vital roles in modifying root development and promoting plant growth according to their positive correlation with root phenotypic traits. Linking root phenotypic traits to the microbiome may enhance our understanding of rhizospheric interactions and their roles in developing rhizosphere ecosystems.
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Iqbal D, Rizvi SMD, Rehman MT, Khan MS, Bin Dukhyil A, AlAjmi MF, Alshehri BM, Banawas S, Zia Q, Alsaweed M, Madkhali Y, Alsagaby SA, Alturaiki W. Soyasapogenol-B as a Potential Multitarget Therapeutic Agent for Neurodegenerative Disorders: Molecular Docking and Dynamics Study. Entropy (Basel) 2022; 24:e24050593. [PMID: 35626478 PMCID: PMC9141571 DOI: 10.3390/e24050593] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/12/2022] [Accepted: 04/20/2022] [Indexed: 01/27/2023]
Abstract
Neurodegenerative disorders involve various pathophysiological pathways, and finding a solution for these issues is still an uphill task for the scientific community. In the present study, a combination of molecular docking and dynamics approaches was applied to target different pathways leading to neurodegenerative disorders such as Alzheimer’s disease. Initially, abrineurin natural inducers were screened using physicochemical properties and toxicity assessment. Out of five screened compounds, a pentacyclic triterpenoid, i.e., Soyasapogenol B appeared to be the most promising after molecular docking and simulation analysis. Soyasapogenol B showed low TPSA (60.69), high absorption (82.6%), no Lipinski rule violation, and no toxicity. Docking interaction analysis revealed that Soyasapogenol B bound effectively to all of the targeted proteins (AChE, BuChE MAO-A, MAO-B, GSK3β, and NMDA), in contrast to other screened abrineurin natural inducers and inhibitors. Importantly, Soyasapogenol B bound to active site residues of the targeted proteins in a similar pattern to the native ligand inhibitor. Further, 100 ns molecular dynamics simulations analysis showed that Soyasapogenol B formed stable complexes against all of the targeted proteins. RMSD analysis showed that the Soyasapogenol B–protein complex exhibited average RMSD values of 1.94 Å, 2.11 Å, 5.07 Å, 2.56 Å, 3.83 Å and 4.07 Å. Furthermore, the RMSF analysis and secondary structure analysis also indicated the stability of the Soyasapogenol B–protein complexes.
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Affiliation(s)
- Danish Iqbal
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (A.B.D.); (B.M.A.); (S.B.); (Q.Z.); (M.A.); (Y.M.); (S.A.A.); (W.A.)
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 15341, Saudi Arabia
- Correspondence: (D.I.); (S.M.D.R.)
| | - Syed Mohd Danish Rizvi
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia
- Correspondence: (D.I.); (S.M.D.R.)
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.T.R.); (M.F.A.)
| | - M. Salman Khan
- Clinical Biochemistry & Natural Product Research Laboratory, Department of Biosciences, Integral University, Lucknow 226026, U.P., India;
| | - Abdulaziz Bin Dukhyil
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (A.B.D.); (B.M.A.); (S.B.); (Q.Z.); (M.A.); (Y.M.); (S.A.A.); (W.A.)
| | - Mohamed F. AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.T.R.); (M.F.A.)
| | - Bader Mohammed Alshehri
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (A.B.D.); (B.M.A.); (S.B.); (Q.Z.); (M.A.); (Y.M.); (S.A.A.); (W.A.)
| | - Saeed Banawas
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (A.B.D.); (B.M.A.); (S.B.); (Q.Z.); (M.A.); (Y.M.); (S.A.A.); (W.A.)
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 15341, Saudi Arabia
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Qamar Zia
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (A.B.D.); (B.M.A.); (S.B.); (Q.Z.); (M.A.); (Y.M.); (S.A.A.); (W.A.)
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 15341, Saudi Arabia
| | - Mohammed Alsaweed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (A.B.D.); (B.M.A.); (S.B.); (Q.Z.); (M.A.); (Y.M.); (S.A.A.); (W.A.)
| | - Yahya Madkhali
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (A.B.D.); (B.M.A.); (S.B.); (Q.Z.); (M.A.); (Y.M.); (S.A.A.); (W.A.)
| | - Suliman A. Alsagaby
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (A.B.D.); (B.M.A.); (S.B.); (Q.Z.); (M.A.); (Y.M.); (S.A.A.); (W.A.)
| | - Wael Alturaiki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (A.B.D.); (B.M.A.); (S.B.); (Q.Z.); (M.A.); (Y.M.); (S.A.A.); (W.A.)
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12
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Bijani S, Iqbal D, Mirza S, Jain V, Jahan S, Alsaweed M, Madkhali Y, Alsagaby SA, Banawas S, Algarni A, Alrumaihi F, Rawal RM, Alturaiki W, Shah A. Green Synthesis and Anticancer Potential of 1,4-Dihydropyridines-Based Triazole Derivatives: In Silico and In Vitro Study. Life (Basel) 2022; 12:life12040519. [PMID: 35455010 PMCID: PMC9029820 DOI: 10.3390/life12040519] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 11/16/2022] Open
Abstract
A library of 1,4-dihydropyridine-based 1,2,3-triazol derivatives has been designed, synthesized, and evaluated their cytotoxic potential on colorectal adenocarcinoma (Caco-2) cell lines. All compounds were characterized and identified based on their 1H and 13C NMR (Nuclear Magnetic Resonance) spectroscopic data. Furthermore, molecular docking of best anticancer hits with target proteins (protein kinase CK2α, tankyrase1, and tankyrase2) has been performed. Our results implicated that most of these compounds have significant antiproliferative activity with IC50 values between 0.63 ± 0.05 and 5.68 ± 0.14 µM. Moreover, the mechanism of action of most active compounds 13ab′ and 13ad′ suggested that they induce cell death through apoptosis in the late apoptotic phase as well as dead phase, and they could promote cell cycle arrest at the G2/M phase. Furthermore, the molecular docking study illustrated that 13ad′ possesses better binding interaction with the catalytic residues of target proteins involved in cell proliferation and antiapoptotic pathways. Based on our in vitro and in silico study, 13ad′ was found to be a highly effective anti-cancerous compound. The present data indicate that dihydropyridine-linked 1,2,3-triazole conjugates can be generated as potent anticancer agents.
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Affiliation(s)
- Sabera Bijani
- Department of Chemistry, Marwadi University, Rajkot 360005, Gujarat, India; (S.B.); (V.J.)
- Center of Excellence, National Facility for Drug Discovery Complex, Department of Chemistry, Saurashtra University, Rajkot 360005, Gujarat, India
| | - Danish Iqbal
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia; (S.J.); (M.A.); (Y.M.); (S.A.A.); (S.B.); (W.A.)
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 15341, Saudi Arabia
- Correspondence: (D.I.); (A.S.)
| | - Sheefa Mirza
- Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa;
| | - Vicky Jain
- Department of Chemistry, Marwadi University, Rajkot 360005, Gujarat, India; (S.B.); (V.J.)
- Center of Excellence, National Facility for Drug Discovery Complex, Department of Chemistry, Saurashtra University, Rajkot 360005, Gujarat, India
| | - Sadaf Jahan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia; (S.J.); (M.A.); (Y.M.); (S.A.A.); (S.B.); (W.A.)
| | - Mohammed Alsaweed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia; (S.J.); (M.A.); (Y.M.); (S.A.A.); (S.B.); (W.A.)
| | - Yahya Madkhali
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia; (S.J.); (M.A.); (Y.M.); (S.A.A.); (S.B.); (W.A.)
| | - Suliman A. Alsagaby
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia; (S.J.); (M.A.); (Y.M.); (S.A.A.); (S.B.); (W.A.)
| | - Saeed Banawas
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia; (S.J.); (M.A.); (Y.M.); (S.A.A.); (S.B.); (W.A.)
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 15341, Saudi Arabia
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Abdulrahman Algarni
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Northern Border University, Arar 91431, Saudi Arabia;
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51425, Saudi Arabia;
| | - Rakesh M. Rawal
- Department of Life Sciences, Gujarat University, Ahmedabad 380009, Gujarat, India;
| | - Wael Alturaiki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia; (S.J.); (M.A.); (Y.M.); (S.A.A.); (S.B.); (W.A.)
| | - Anamik Shah
- Center of Excellence, National Facility for Drug Discovery Complex, Department of Chemistry, Saurashtra University, Rajkot 360005, Gujarat, India
- B/H Forensic Laboratory, Saurashtra University Karmachari Cooperative Society, Rajkot 360005, Gujarat, India
- Correspondence: (D.I.); (A.S.)
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