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Article ; Online: Probing the molecular mechanisms of α-synuclein inhibitors unveils promising natural candidates through machine-learning QSAR, pharmacophore modeling, and molecular dynamics simulations.

Boulaamane, Yassir / Jangid, Kailash / Britel, Mohammed Reda / Maurady, Amal

2023

Abstract: Parkinson's disease is characterized by a multifactorial nature that is linked to different pathways. Among them, the abnormal deposition and accumulation of α-synuclein fibrils is considered a neuropathological hallmark of Parkinson's disease. Several ... ...

Abstract	Parkinson's disease is characterized by a multifactorial nature that is linked to different pathways. Among them, the abnormal deposition and accumulation of α-synuclein fibrils is considered a neuropathological hallmark of Parkinson's disease. Several synthetic and natural compounds have been tested for their potency to inhibit the aggregation of α-synuclein. However, the molecular mechanisms responsible for the potency of these drugs to further rationalize their development and optimization are yet to be determined. To enhance our understanding of the structural requirements necessary for modulating the aggregation of α-synuclein fibrils, we retrieved a large dataset of α-synuclein inhibitors with their reported potency from the ChEMBL database to explore their chemical space and to generate QSAR models for predicting new bioactive compounds. The best performing QSAR model was applied to the LOTUS natural products database to screen for potential α-synuclein inhibitors followed by a pharmacophore design using the representative compounds sampled from each cluster in the ChEMBL dataset. Five natural products were retained after molecular docking studies displaying a binding affinity of - 6.0 kcal/mol or lower. ADMET analysis revealed satisfactory properties and predicted that all the compounds can cross the blood-brain barrier and reach their target. Finally, molecular dynamics simulations demonstrated the superior stability of LTS0078917 compared to the clinical candidate, Anle138b. We found that LTS0078917 shows promise in stabilizing the α-synuclein monomer by specifically binding to its hairpin-like coil within the N-terminal region. Our dynamic analysis of the inhibitor-monomer complex revealed a tendency towards a more compact conformation, potentially reducing the likelihood of adopting an elongated structure that favors the formation and aggregation of pathological oligomers. These findings offer valuable insights for the development of novel α-synuclein inhibitors derived from natural sources.
Language	English
Publishing date	2023-07-18
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-023-10691-x
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Article ; Online: In silico

Boulaamane, Yassir / Ibrahim, Mahmoud A A / Britel, Mohammed Reda / Maurady, Amal

Journal of integrative bioinformatics

2022 Volume 19, Issue 4

Abstract: Parkinson's disease is considered the second most frequent neurodegenerative disease. It is described by the loss of dopaminergic neurons in the mid-brain. For many decades, L-DOPA has been considered as the gold standard for treating Parkinson's disease ...

Abstract	Parkinson's disease is considered the second most frequent neurodegenerative disease. It is described by the loss of dopaminergic neurons in the mid-brain. For many decades, L-DOPA has been considered as the gold standard for treating Parkinson's disease motor symptoms, however, due to the decrease of efficacy, in the long run, there is an urgent need for novel antiparkinsonian drugs. Caffeine derivatives have been reported several times for their neuroprotective properties and dual blockade of monoamine oxidase (MAO) and adenosine A
MeSH term(s)	Humans ; Caffeine/pharmacology ; Caffeine/therapeutic use ; Parkinson Disease/drug therapy ; Monoamine Oxidase Inhibitors/pharmacology ; Monoamine Oxidase Inhibitors/therapeutic use ; Monoamine Oxidase Inhibitors/chemistry ; Neurodegenerative Diseases/drug therapy ; Adenosine A2 Receptor Antagonists/pharmacology ; Adenosine A2 Receptor Antagonists/therapeutic use ; Adenosine A2 Receptor Antagonists/chemistry ; Monoamine Oxidase/therapeutic use
Chemical Substances	Caffeine (3G6A5W338E) ; Monoamine Oxidase Inhibitors ; Adenosine A2 Receptor Antagonists ; Monoamine Oxidase (EC 1.4.3.4)
Language	English
Publishing date	2022-09-19
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2147212-9
ISSN	1613-4516 ; 1613-4516
ISSN (online)	1613-4516
ISSN	1613-4516
DOI	10.1515/jib-2021-0027
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Article ; Online: Chemical library design, QSAR modeling and molecular dynamics simulations of naturally occurring coumarins as dual inhibitors of MAO-B and AChE.

Boulaamane, Yassir / Kandpal, Pallavi / Chandra, Anshuman / Britel, Mohammed Reda / Maurady, Amal

Journal of biomolecular structure & dynamics

2023 Volume 42, Issue 4, Page(s) 1629–1646

Abstract: Coumarins are a highly privileged scaffold in medicinal chemistry. It is present in many natural products and is reported to display various pharmacological properties. A large plethora of compounds based on the coumarin ring system have been synthesized ...

Abstract	Coumarins are a highly privileged scaffold in medicinal chemistry. It is present in many natural products and is reported to display various pharmacological properties. A large plethora of compounds based on the coumarin ring system have been synthesized and were found to possess biological activities such as anticonvulsant, antiviral, anti-inflammatory, antibacterial, antioxidant as well as neuroprotective properties. Despite the wide activity spectrum of coumarins, its naturally occurring derivatives are yet to be investigated in detail. In the current study, a chemical library was created to assemble all chemical information related to naturally occurring coumarins from the literature. Additionally, a multi-stage virtual screening combining QSAR modeling, molecular docking, and ADMET prediction was conducted against monoamine oxidase B and acetylcholinesterase, two relevant targets known for their neuroprotective properties and 'disease-modifying' potential in Parkinson's and Alzheimer's disease. Our findings revealed ten coumarin derivatives that may act as dual-target drugs against MAO-B and AChE. Two coumarin candidates were selected from the molecular docking study: CDB0738 and CDB0046 displayed favorable interactions for both proteins as well as suitable ADMET profiles. The stability of the selected coumarins was assessed through 100 ns molecular dynamics simulations which revealed promising stability through key molecular interactions for CDB0738 to act as dual inhibitor of MAO-B and AChE. However, experimental studies are necessary to evaluate the bioactivity of the proposed candidate. The current results may generate an increasing interest in bioprospecting naturally occurring coumarins as potential candidates against relevant macromolecular targets by encouraging virtual screening studies against our chemical library.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Monoamine Oxidase/chemistry ; Molecular Dynamics Simulation ; Monoamine Oxidase Inhibitors/pharmacology ; Monoamine Oxidase Inhibitors/chemistry ; Monoamine Oxidase Inhibitors/metabolism ; Molecular Docking Simulation ; Acetylcholinesterase/chemistry ; Cholinesterase Inhibitors/pharmacology ; Cholinesterase Inhibitors/chemistry ; Quantitative Structure-Activity Relationship ; Coumarins/pharmacology ; Coumarins/chemistry ; Structure-Activity Relationship
Chemical Substances	Monoamine Oxidase (EC 1.4.3.4) ; Monoamine Oxidase Inhibitors ; Acetylcholinesterase (EC 3.1.1.7) ; Cholinesterase Inhibitors ; Coumarins
Language	English
Publishing date	2023-05-18
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2209650
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Article ; Online: Effect of temperature and different pre-treatments on seed germination of Stachys mouretii Batt. & Pit

El Ismaili, Soumaya / Maurady, Amal / Lachkar, Mohammed / Britel, Mohammed Reda / Homrani-Bakali, Abdelmonaim

Journal of Applied Research on Medicinal and Aromatic Plants. 2022 Oct. 10, p.100438-

2022 , Page(s) 100438–

Abstract: Stachys mouretii Batt. & Pit. is an endemic species of Morocco, it is considered as rare and threatened species. In order to conserve and valorize this species, our study aims to determine the optimal germination conditions of S. mouretii. Seeds ... ...

Abstract	Stachys mouretii Batt. & Pit. is an endemic species of Morocco, it is considered as rare and threatened species. In order to conserve and valorize this species, our study aims to determine the optimal germination conditions of S. mouretii. Seeds collected from natural plant populations were subjected to six alternating temperatures (10/0 °C, 15/5 °C, 20/10 °C, 25/10 °C, 35/20 °C and 40/25 °C, with a 14/10h. light/dark photoperiod) and nine pre-treatments: pre- soaked seeds in cold distilled water for 24 and 48h and gibberellic acid (GA₃) (250 and 500mg/l), prechilling during 15 and 25 days, manual scarification, manual scarification combined with pre-soaking in cold water for 24h and finally the combination of GA3 (500mg/l) and prechilling at 4 °C during 15 days. The results showed that alternating temperature had a significant effect on the germination parameters. The highest germination percentage (66.5%) was obtained at 25/10 °C, while germination was not observed at 10/0 °C. The temperature regime of 35/20 °C has been the best, combining higher capacity and speed germination as indicated by the germination index (GI=6.0%/day). Our study demonstrated that pre-soaking in 500mg/l GA₃ was significantly the best pre-treatment for seed germination by improving germination capacity to 91.5% and reducing the germination time as indicated by the mean germination time (MGT) which was 5.6 days versus 12.9 days for the control. The median germination time (T₅₀) was 4.4 days for GA₃-500 mg/l versus 11.3 days for control. These findings are useful for the choice of suitable pre-treatment that can contribute to improve germination of S. mouretii seeds.
Keywords	Stachys ; applied research ; cold ; gibberellic acid ; indigenous species ; presoaking ; seed germination ; seeds ; temperature ; threatened species ; water ; Morocco ; Stachys mouretii ; Germination ; Endemic ; Preservation
Language	English
Dates of publication	2022-1010
Publishing place	Elsevier GmbH
Document type	Article ; Online
Note	Pre-press version
ZDB-ID	2763238-6
ISSN	2214-7861
ISSN	2214-7861
DOI	10.1016/j.jarmap.2022.100438
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Molecular docking study and molecular dynamic simulation of human cyclooxygenase-2 (COX-2) with selected eutypoids.

Taidi, Loubna / Maurady, Amal / Britel, Mohammed Reda

Journal of biomolecular structure & dynamics

2020 Volume 40, Issue 3, Page(s) 1189–1204

Abstract: Inflammation is a key factor linked to almost all chronic and degenerative diseases implicit with certain levels of pain. In studies, over the past few years, it has been discovered that prostaglandins are the main cause of this inflammation and ... ...

Abstract	Inflammation is a key factor linked to almost all chronic and degenerative diseases implicit with certain levels of pain. In studies, over the past few years, it has been discovered that prostaglandins are the main cause of this inflammation and therefore could be blocked. Although no steroidal medications can be effective, natural compounds may offer a safer and often an effective alternative treatment for pain relief, especially for long-term use. Hence to find out natural anti-inflammatory compounds, we have highlighted five important butenolides that are eutypoid A, B, C, D and E with structure similar to that of rofecoxib, by ADMET and druglikeness analysis, followed by molecular docking with human COX-2 enzyme. Molecular docking studies revealed the importance of hydrophobic and hydrophilic amino acid residues for the stability of the ligands and that eutypoids C and E are the best candidates for the synthetic drugs with binding energy of -10.39 kcal/mol and -9.87 kcal/mol, respectively. The resulting complexes were then subject to 50 ns molecular dynamics (MD) simulation studies with the GROMACS package to analyze the stability of docked protein-ligand complexes and to assess the fluctuation and conformational changes during protein-ligand interaction. From the RMSD, RMSF, number of hydrogen bonds, SASA, PCA and MM/PBSA binding free energy analysis, we have found that out of five selected compounds eutypoid E showed good binding free energy of -174.45 kJ/mol, which is also good in other structural analyses. This compound displayed excellent pharmacological and structural properties to be drug candidates.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Cyclooxygenase 2/chemistry ; Cyclooxygenase 2 Inhibitors/chemistry ; Humans ; Hydrogen Bonding ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation
Chemical Substances	Cyclooxygenase 2 Inhibitors ; Ligands ; Cyclooxygenase 2 (EC 1.14.99.1) ; PTGS2 protein, human (EC 1.14.99.1)
Language	English
Publishing date	2020-09-29
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1823884
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Article ; Online: Structural exploration of selected C6 and C7-substituted coumarin isomers as selective MAO-B inhibitors.

Boulaamane, Yassir / Ahmad, Iqrar / Patel, Harun / Das, Niloy / Britel, Mohammed Reda / Maurady, Amal

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 6, Page(s) 2326–2340

Abstract: Monoamine Oxidase B is considered a successful target for developing antiparkinsonian drugs. Due to the side effects of current MAO-B inhibitors, there's an urgent need for novel potent and highly selective MAO-B inhibitors. A recent study has shown that ...

Abstract	Monoamine Oxidase B is considered a successful target for developing antiparkinsonian drugs. Due to the side effects of current MAO-B inhibitors, there's an urgent need for novel potent and highly selective MAO-B inhibitors. A recent study has shown that coumarins tend to be more selective towards MAO-B than MAO-A when connected to a hex-5-ynyloxy chain at position 6 in contrast to their C7-isomers. The present study describes the mode of interaction of the C6 and C7-substituted coumarin isomers characterized by their difference in selectivity towards MAO-B through molecular docking and molecular dynamics simulations in an effort to elucidate the structural components and molecular interactions that may be responsible for MAO-B selectivity. Three isomeric coumarin pairs connected to ether chain at position 6 or 7 were taken from the literature and modelled according to their IUPAC nomenclature. Molecular docking study revealed one π- π stacking interaction with Tyr-326 in common between the selective coumarin C6-isomers. Resulting complexes of one isomeric coumarin pair that displayed the highest selectivity shift towards MAO-B were subject to 100 ns molecular dynamics simulations study to analyze the stability of the docked complexes. Molecular dynamics revealed that the C7-isomer is relatively stable in both MAO isoforms through the simulation duration, whereas the C6-isomer deemed unstable for MAO-A which may be due to the bulky Phe-208 residue in MAO-A. Our results might be applied for further development and optimization of coumarin derivatives into a successful drug against Parkinson's disease.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Monoamine Oxidase Inhibitors/pharmacology ; Monoamine Oxidase Inhibitors/chemistry ; Molecular Docking Simulation ; Structure-Activity Relationship ; Monoamine Oxidase/chemistry ; Coumarins/pharmacology ; Coumarins/chemistry ; Molecular Dynamics Simulation
Chemical Substances	Monoamine Oxidase Inhibitors ; coumarin (A4VZ22K1WT) ; Monoamine Oxidase (EC 1.4.3.4) ; Coumarins
Language	English
Publishing date	2022-02-15
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2033643
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Article ; Online: Exploring natural products as multi-target-directed drugs for Parkinson's disease: an

Boulaamane, Yassir / Touati, Iman / Goyal, Nainee / Chandra, Anshuman / Kori, Lokesh / Ibrahim, Mahmoud A A / Britel, Mohammed Reda / Maurady, Amal

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–18

Abstract: Parkinson's disease is a neurodegenerative disorder characterized by the progressive loss of dopaminergic neurons in the midbrain. Current treatments provide limited symptomatic relief without halting disease progression. A multi-targeting approach has ... ...

Abstract	Parkinson's disease is a neurodegenerative disorder characterized by the progressive loss of dopaminergic neurons in the midbrain. Current treatments provide limited symptomatic relief without halting disease progression. A multi-targeting approach has shown potential benefits in treating neurodegenerative diseases. In this study, we employed
Language	English
Publishing date	2023-09-27
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2260879
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Article ; Online: Identification of novel dual acting ligands targeting the adenosine A2A and serotonin 5-HT1A receptors.

Touati, Iman / Abdalla, Mohnad / Boulaamane, Yassir / Al-Hoshani, Nawal / Alouffi, Abdulaziz / Britel, Mohammed Reda / Maurady, Amal

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–16

Abstract: GPCRs are a family of transmembrane receptors that are profoundly linked to various neurological disorders, among which is Parkinson's disease (PD). PD is the second most ubiquitous neurological disorder after Alzheimer's disease, characterized by the ... ...

Abstract	GPCRs are a family of transmembrane receptors that are profoundly linked to various neurological disorders, among which is Parkinson's disease (PD). PD is the second most ubiquitous neurological disorder after Alzheimer's disease, characterized by the depletion of dopamine in the central nervous system due to the impairment of dopaminergic neurons, leading to involuntary movements or dyskinesia. The current standard of care for PD is Levodopa, a dopamine precursor, yet the chronic use of this agent can exacerbate motor symptoms. Recent studies have investigated the effects of combining A2AR antagonist and 5-HT1A agonist on dyskinesia and motor complications in animal models of PD. It has been proved that the drug combination has significantly improved involuntary movements while maintaining motor activity, highlighting as a result new lines of therapy for PD treatments, through the regulation of both receptors. Using a combination of ligand-based pharmacophore modelling, virtual screening, and molecular dynamics simulation, this study intends on identifying potential dual-target compounds from IBScreen. Results showed that the selected models displayed good enrichment metrics with a near perfect receiver operator characteristic (ROC) and Area under the accumulation curve (AUAC) values, signifying that the models are both specific and sensitive. Molecular docking and ADMET analysis revealed that STOCK2N-00171 could be potentially active against A2AR and 5-HT1A. Post-MD analysis confirmed that the ligand exhibits a stable behavior throughout the simulation while maintaining crucial interactions. These results imply that STOCK2N-00171 can serve as a blueprint for the design of novel and effective dual-acting ligands targeting A2AR and 5-HT1A.Communicated by Ramaswamy H. Sarma.
Language	English
Publishing date	2023-10-18
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2270753
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Article ; Online: 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.

Touati, Iman / Abdalla, Mohnad / Ali, Naif H / AlRuwaili, Raed / Alruwaili, Mubarak / Britel, Mohammed Reda / Maurady, Amal

Journal of biomolecular structure & dynamics

2023 Volume 42, Issue 5, Page(s) 2586–2602

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 ... ...

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.
MeSH term(s)	Humans ; Acetylcholinesterase/chemistry ; Alzheimer Disease/drug therapy ; Cholinesterase Inhibitors/pharmacology ; Cholinesterase Inhibitors/chemistry ; Computer Simulation ; Molecular Docking Simulation ; Stachys/chemistry ; Receptors, N-Methyl-D-Aspartate/antagonists & inhibitors
Chemical Substances	Acetylcholinesterase (EC 3.1.1.7) ; Cholinesterase Inhibitors ; Receptors, N-Methyl-D-Aspartate
Language	English
Publishing date	2023-06-16
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2217925
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Article: Dynamics of the Gut Bacteriome During a Laboratory Adaptation Process of the Mediterranean Fruit Fly,

Bel Mokhtar, Naima / Catalá-Oltra, Marta / Stathopoulou, Panagiota / Asimakis, Elias / Remmal, Imane / Remmas, Nikolaos / Maurady, Amal / Britel, Mohammed Reda / García de Oteyza, Jaime / Tsiamis, George / Dembilio, Óscar

Frontiers in microbiology

2022 Volume 13, Page(s) 919760

Abstract: Laboratory adaptation process used in sterile insect technique (SIT) programs can exert a significant impact on the insect-gut microbiome relationship, which may negatively impact the quality and performance of the fly. In the present study, changes in ... ...

Abstract	Laboratory adaptation process used in sterile insect technique (SIT) programs can exert a significant impact on the insect-gut microbiome relationship, which may negatively impact the quality and performance of the fly. In the present study, changes in the gut microbiota that occur through laboratory adaptation of two
Language	English
Publishing date	2022-07-01
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2022.919760
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