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Nour H, Daoui O, Abchir O, ElKhattabi S, Belaidi S, Chtita S. Combined computational approaches for developing new anti-Alzheimer drug candidates: 3D-QSAR, molecular docking and molecular dynamics studies of liquiritigenin derivatives. Heliyon 2022; 8:e11991. [PMID: 36544815 PMCID: PMC9761610 DOI: 10.1016/j.heliyon.2022.e11991] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022] Open
Abstract
Butyrylcholinesterase is an acetylcholine-degrading enzyme involved in the memorization process, which is becoming an interesting target for the symptomatic treatment of Alzheimer's disease. In the present investigation, the structure-activity relationship of a set of Liquiritigenin derivatives recently revealed to be Butyrylcholinesterase inhibitors was studied basing on comparative field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMISA). As a result, performant models with high predictive capability have been developed (CoMFA model: R2 = 0.91, Q2 = 0.62, R2 pred = 0.85; CoMISA model: R2 = 0.92, Q2 = 0.59, R2 pred = 0.83) and implemented to design new Liquiritigenin derivatives with improved activity. Besides, the affinity of the designed derivatives towards the active site of Butyrylcholinesterase, was confirmed by molecular docking and molecular dynamics studies. Moreover, they exhibited good pharmacokinetics properties. Accordingly, the outcomes of the present investigations can provide important direction for the development of new anti-Alzheimer's drug candidates.
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Daoui O, Nour H, Abchir O, Elkhattabi S, Bakhouch M, Chtita S. A computer-aided drug design approach to explore novel type II inhibitors of c-Met receptor tyrosine kinase for cancer therapy: QSAR, molecular docking, ADMET and molecular dynamics simulations. J Biomol Struct Dyn 2023; 41:7768-7785. [PMID: 36120976 DOI: 10.1080/07391102.2022.2124456] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 09/09/2022] [Indexed: 10/14/2022]
Abstract
Small molecules such as 4-phenoxypyridine derivatives have remarkable inhibitory activity against c-Met enzymatic activity and proliferation of cancer cell lines. Since there is a relationship between structure and biological activity of these molecules, these little compounds may have great potential for clinical pharmaceutical use against various types of cancer caused by c-Met activity. The purpose of this study was to remodel the structures of 4-phenoxypyridine derivatives to achieve strong inhibitory activity against c-Met and provide favorable pharmacokinetic properties for drug design and discovery. Therefore, this paper describes the structure-activity relationship and the rationalization of appropriate pharmacophore sites to improve the biological activity of the investigated molecules, based on bioinformatics techniques represented by a computer-aided drug design approach. Accordingly, robust and reliable 3D-QSAR models were developed based on CoMFA and CoMSIA techniques. As a result, 46 lead molecules were designed and their biological and pharmacokinetic activities were predicted in silico. Screening filters by 3D-QSAR, Molecular Docking, drug-like and ADME-Tox identified the computer-designed compounds P54 and P55 as the best candidates to achieve high inhibition of c-Met enzymatic activity compared to the synthesized template compound T14. Finally, through molecular dynamics simulations, the structural properties and dynamics of c-Met free and complex (PDB code: 3LQ8) in the presence of 4-phenoxypyridine-derived compounds in an aqueous environment are discussed. Overall, the rectosynthesis of the designed drug inhibitors (P54 and P55) and their in vitro and in vivo bioactivity evaluation may be attractive for design and discovery of novel drug effective to inhibit c-Met enzymatic activity.Communicated by Ramaswamy H. Sarma.
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Basri R, Ullah S, Khan A, Mali SN, Abchir O, Chtita S, El-Gokha A, Taslimi P, Binsaleh AY, El-Kott AF, Al-Harrasi A, Shafiq Z. Synthesis, biological evaluation and molecular modelling of 3-Formyl-6-isopropylchromone derived thiosemicarbazones as α-glucosidase inhibitors. Bioorg Chem 2023; 139:106739. [PMID: 37478545 DOI: 10.1016/j.bioorg.2023.106739] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/11/2023] [Accepted: 07/15/2023] [Indexed: 07/23/2023]
Abstract
Type-2 Diabetes Mellitus (T2DM) is one of the most common metabolic disorders in the world and over the past three decades its incidence has increased drastically. α-Glucosidase inhibitors are used to control the hyperglycemic affect of T2DM. Herein, we report the synthesis, α-glucosidase inhibition, structure activity relationship, pharmacokinetics and docking analysis of various novel chromone based thiosemicarbazones 3(a-r). The derivatives displayed potent activity against α-glucosidase with IC50 in range of 0.11 ± 0.01-79.37 ± 0.71 µM. Among all the synthesized compounds, 3a (IC50 = 0.17 ± 0.026 µM), 3 g (IC50 = 0.11 ± 0.01 µM), 3n (IC50 = 0.55 ± 0.02 µM), and 3p (IC50 = 0.43 ± 0.025 µM) displayed higher inhibitory activity as compared to the standard, acarbose. Moreover, we have developed a statistically significant 2D-QSAR model (R2tr:0.9693; F: 50.4647 and Q2LOO:0.9190), which can be used in future to further design potent thiosemicarbazones as inhibitors of α-glucosidase.
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Abchir O, Yamari I, Nour H, Daoui O, Elkhattabi S, Errougui A, Chtita S. Structure‐Based Virtual Screening, ADMET analysis, and Molecular Dynamics Simulation of Moroccan Natural Compounds as Candidates α‐Amylase Inhibitors. ChemistrySelect 2023; 8. [DOI: 10.1002/slct.202301092] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/19/2023] [Indexed: 01/04/2025]
Abstract
AbstractCurrent treatments for diabetes mellitus are ineffective, as evidenced by the rise in diabetes cases. This has forced researchers to develop novel chemicals as drugs to block the enzyme alpha‐amylase as the severe way to treat diabetes disease. Many previous studies were done to determine the biological activity of a set of molecules isolated from medicinal plants. Morocco is renowned for the abundance of plants it has and for the traditional medical uses of these plants, which drives us to employ our cultural heritage and the variety of our nation‘s natural resources in the therapeutic area. In the current study, extensive research was conducted to compile a group of phytoconstituents derived from Moroccan plants and used in conventional Moroccan medicine to treat local illnesses. To assess the stability of the generated complexes, molecular docking of the investigated compounds was carried out in the active site of 4 distinct alpha‐amylase proteins. The remaining compounds with a high negative binding affinity were then subjected to the ADMET analysis to determine their pharmacological characteristics. The findings showed that two drugs have strong binding affinity for the target proteins and may be used orally as potential alpha‐amylase inhibitors. The results of molecular dynamics analysis and MMGBSA calculation were used to validate the optimal stability of created complexes (L97 with studied proteins 1HNY, 1OSE, 1UA7 and 1BAG).
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Abchir O, Khedraoui M, Nour H, Yamari I, Errougui A, Samadi A, Chtita S. Integrative Approach for Designing Novel Triazole Derivatives as α-Glucosidase Inhibitors: QSAR, Molecular Docking, ADMET, and Molecular Dynamics Investigations. Pharmaceuticals (Basel) 2024; 17:261. [PMID: 38399476 PMCID: PMC10892212 DOI: 10.3390/ph17020261] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/11/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
In response to the increasing prevalence of diabetes mellitus and the limitations associated with the current treatments, there is a growing need to develop novel medications for this disease. This study is focused on creating new compounds that exhibit a strong inhibition of alpha-glucosidase, which is a pivotal enzyme in diabetes control. A set of 33 triazole derivatives underwent an extensive QSAR analysis, aiming to identify the key factors influencing their inhibitory activity against α-glucosidase. Using the multiple linear regression (MLR) model, seven promising compounds were designed as potential drugs. Molecular docking and dynamics simulations were employed to shed light on the mode of interaction between the ligands and the target, and the stability of the obtained complexes. Furthermore, the pharmacokinetic properties of the designed compounds were assessed to predict their behavior in the human body. The binding free energy was also calculated using MMGBSA method and revealed favorable thermodynamic properties. The results highlighted three novel compounds with high biological activity, strong binding affinity to the target enzyme, and suitability for oral administration. These results offer interesting prospects for the development of effective and well-tolerated medications against diabetes mellitus.
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Yamari I, Abchir O, Mali SN, Errougui A, Talbi M, Kouali ME, Chtita S. The anti-SARS-CoV-2 activity of novel 9, 10-dihydrophenanthrene derivatives: an insight into molecular docking, ADMET analysis, and molecular dynamics simulation. SCIENTIFIC AFRICAN 2023; 21:e01754. [PMID: 37332393 PMCID: PMC10260260 DOI: 10.1016/j.sciaf.2023.e01754] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/31/2023] [Accepted: 06/08/2023] [Indexed: 06/20/2023] Open
Abstract
Originating in Wuhan, the COVID-19 pandemic wave has had a profound impact on the global healthcare system. In this study, we used a 2D QSAR technique, ADMET analysis, molecular docking, and dynamic simulations to sort and evaluate the performance of thirty-nine bioactive analogues of 9,10-dihydrophenanthrene. The primary goal of the study is to use computational approaches to create a greater variety of structural references for the creation of more potent SARS-CoV-2 3Clpro inhibitors. This strategy is to speed up the process of finding active chemicals. Molecular descriptors were calculated using 'PaDEL' and 'ChemDes' software, and then redundant and non-significant descriptors were eliminated by a module in 'QSARINS ver. 2.2.2'. Subsequently, two statistically robust QSAR models were developed by applying multiple linear regression (MLR) methods. The correlation coefficients obtained by the two models are 0.89 and 0.82, respectively. These models were then subjected to internal and external validation tests, Y-randomization, and applicability domain analysis. The best model developed is applied to designate new molecules with good inhibitory activity values against severe acute respiratory syndrome coronavirus 2 (SARS CoV-2). We also examined various pharmacokinetic properties using ADMET analysis. Then, through molecular docking simulations, we used the crystal structure of the main protease of SARS-CoV-2 (3CLpro/Mpro) in a complex with the covalent inhibitor "Narlaprevir" (PDB ID: 7JYC). We also supported our molecular docking predictions with an extended molecular dynamics simulation of a docked ligand-protein complex. We hope that the results obtained in this study can be used as good anti-SARS-CoV-2 inhibitors.
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Arzine A, Abchir O, Chalkha M, Chebbac K, Rhazi Y, Barghady N, Yamari I, El Moussaoui A, Nakkabi A, Akhazzane M, Bakhouch M, Chtita S, El Yazidi M. Design, synthesis, In-vitro, In-silico and DFT studies of novel functionalized isoxazoles as antibacterial and antioxidant agents. Comput Biol Chem 2024; 108:107993. [PMID: 38071761 DOI: 10.1016/j.compbiolchem.2023.107993] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 01/22/2024]
Abstract
A series of new isoxazolederivatives incorporating the sulfonate ester function has been synthesized from 2-benzylidenebenzofuran-3(2 H)-one, known as aurone. The synthesis of the target compounds was carried out following an efficient methodology that allows access to the desired products in a reproducible way and with good yield. The structures of the synthesized compounds were established using NMR (1H and 13C) spectroscopy and mass spectrometry. A theoretical study was performed to optimize the geometrical structures and to calculate the structural and electronic parameters of the synthesized compounds. The calculations were also carried out to understand the influence and the effect of substitutions on the chemical reactivity of the studied compounds. The synthesized isoxazoles were screened for their antioxidant and antibacterial activities. The findings demonstrate that the studied compounds exhibit good to moderate antibacterial activity against the tested bacteria (Staphylococcus aureus, Bacillus subtilis, and Escherichia coli). Moreover, a number of the tested isoxazole derivatives exhibit high effectiveness against DPPH free radicals. Besides that, molecular docking studies were carried out to predict binding affinity and identify the most likely binding interactions between the active molecules and the target microorganisms' proteins. A 100 ns molecular dynamics study was then conducted to examine the dynamic behavior and stability of the highly potent isoxazole 4e in complex with the target bacterial proteins. Finally, the ADMET analyses suggest that all the synthesized isoxazoles have good pharmacokinetic profiles and non-toxicity and non-carcinogenicity in biological systems.
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Nour H, Abchir O, Belaidi S, Qais FA, Chtita S, Belaaouad S. 2D‐QSAR and molecular docking studies of carbamate derivatives to discover novel potent anti‐butyrylcholinesterase agents for Alzheimer's disease treatment. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Abchir O, Nour H, Daoui O, Yamari I, ElKhattabi S, El Kouali M, Talbi M, Errougui A, Chtita S. Structure-based virtual screening, ADMET analysis, and molecular dynamics simulation of Moroccan natural compounds as candidates for the SARS-CoV-2 inhibitors. Nat Prod Res 2024; 38:4347-4354. [PMID: 37966948 DOI: 10.1080/14786419.2023.2281002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 10/26/2023] [Accepted: 11/03/2023] [Indexed: 11/17/2023]
Abstract
The lack of treatments and vaccines effective against SARS-CoV-2 has forced us to explore natural compounds that could potentially inhibit this virus. Additionally, Morocco is renowned for its rich plant diversity and traditional medicinal uses, which inspires us to leverage our cultural heritage and the abundance of natural resources in our country for therapeutic purposes. In this study, an extensive investigation was conducted to gather a collection of phytoconstituents extracted from Moroccan plants, aiming to evaluate their ability to inhibit the proliferation of the SARS-CoV-2 virus. Molecular docking of the studied compounds was performed at the active sites of the main protease (6lu7) and spike (6m0j) proteins to assess their binding affinity to these target proteins. Compounds exhibiting high affinity to the proteins underwent further evaluation based on Lipinski's rule and ADME-Tox analysis to gain insights into their oral bioavailability and safety. The results revealed that the two compounds demonstrated strong binding affinity to the target proteins, making them potential candidates for oral antiviral drugs against SARS-CoV-2. The molecular dynamics results from this computational analysis supported the overall stability of the resulting complex.
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Bouhadi M, Abchir O, Yamari I, El Hamsas El Youbi A, Azgaoui A, Chtita S, El Hajjouji H, El Kouali M, Talbi M, Fougrach H. Genotoxic effects and mitosis aberrations of chromium (VI) on root cells of Vicia faba and its molecular docking analysis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108361. [PMID: 38237423 DOI: 10.1016/j.plaphy.2024.108361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 01/01/2024] [Accepted: 01/10/2024] [Indexed: 03/16/2024]
Abstract
Like other heavy metals, Cr (VI) is a powerful carcinogen and mutagen agent. Its toxic effects on plants are well considered. In order to elucidate its adverse effects, the present work aims to study the mitosis aberrations of Cr (VI) on the Vicia faba root-cells and its molecular docking analysis to understand the genotoxicity mechanisms. In-vivo, Vicia faba plants were exposed to 50 and 100 μM Cr (VI) for 48 h. In-silico, molecular docking and molecular dynamics simulation were used to study the interactions between dichromate and tubulin tyrosine ligase T2R-TTL (PDBID: 5XIW) with reference to Colchicine (microtubule inhibitor). According to our results, Cr (VI) affects growth and cell division and also induces many mitosis aberrations such as chromosome sticking, anaphase/telophase bridges, lagging chromosomes and fragmentation during all phases of mitosis. On the one hand, Cr (VI) reduces mitotic index and promotes micronuclei induction. The in-silico results showed that dichromate establishes very strong bonds at the binding site of the tubulin tyrosine ligase T2R-TTL, with a binding affinity of -5.17 Kcal/Mol and an inhibition constant of 163.59 μM. These interactions are similar to those of colchicine with this protein, so dichromate could be a very potent inhibitor of this protein's activity. TTL plays a fundamental role in the tyrosination/detyrosination of tubulin, which is crucial to the regulation of the microtubule cytoskeleton. Its inhibition leads to the appearance of many morphogenic abnormalities such as mitosis aberrations. In conclusion, our data confirm the highest genotoxicity effects of Cr (VI) on Vicia faba root-cells.
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Nour H, Abchir O, Belaidi S, Chtita S. Research of new acetylcholinesterase inhibitors based on QSAR and molecular docking studies of benzene-based carbamate derivatives. Struct Chem 2022. [DOI: 10.1007/s11224-022-01966-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Mohamed AS, Elmi A, Spina R, Kordofani MAY, Laurain-Mattar D, Nour H, Abchir O, Chtita S. In vitro and in silico analysis for elucidation of antioxidant potential of Djiboutian Avicennia Marina (Forsk.) Vierh. phytochemicals. J Biomol Struct Dyn 2024; 42:3410-3425. [PMID: 37194334 DOI: 10.1080/07391102.2023.2213338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/06/2023] [Indexed: 05/18/2023]
Abstract
The present work aims to study the phytochemical composition, the antioxidant capacity of the crude extracts, and the fraction of extract giving the best antioxidant activity of Avicennia marina. The leaves contain high TFC compared to other parts of the plant, whereas fruits have the highest amount of TPC. Fat-soluble pigments are strongly present in the leaves of Avicennia marina i.e. β-carotene, lycopene, chlorophyll a, and chlorophyll b. The crude methanolic flower extracts showed strong DPPH and ABTS radical scavenging activity with IC50 values of 0.30 and 0.33 mg/mL respectively compared to the leaf and stem methanolic extracts for the DPPH and ABTS models with a value IC50 greater than 1 mg/mL. The crude fruit extract shows good activity with the ABTS model, unlike the DPPH model whose IC50 values are 0.95 and 0.38 mg/mL, respectively. Fractionation improved the antioxidant effect of crude flower extract. The ethyl acetate fraction exhibits the best antioxidant activity for both DPPH and ABTS methods with IC50 values of 0.125 and 0.16 mg/mL. The HR-LCMS/MS led to the identification of 13 compounds: 6 flavonoids and 7 iridoid glycoside compounds in the different parts of the plant. A bioinformatics study was performed to evaluate the antioxidant activity of the three major Iridoid glycosides towards the target protein Catalase compound II through free binding energy. Out of these three iridoid glycosides, compound C10 does not represent any toxicity, unlike C8 and C9 which showed an irritancy effect. Furthermore, molecular dynamics shows good stability of the C10-2CAG complex. HighlightsExtraction and fractionation of different part (leaf, stem, flower and fruit) of Avicennia marina.Botanical description and phytochemical analysis of crude extract methanolic. Investigation by HR-LCMS characterization of polyphenols and iridoid glycosides.Evaluation the antioxidant activity of crudes extracts methanolics by two methods in vitro DPPH and ABTS.Antioxidant activity of the fraction of the crude flower extracts presenting the best biological response.Evaluate the contribution of three major compounds 2'-Cinnamoylmussaenosidic acid, 10-O-[E-Cinnamoyl]-geniposidic acid and 10-O-[(E)-p-Coumaroyl]-geniposidic acid in the ethyl acetate fraction on the antioxidant activity through docking and dynamic molecular.Communicated by Ramaswamy H. Sarma.
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Yamari I, Bouamri LE, Abchir O, Bouachrine M, Kouali ME, Samadi A, Chtita S. Integrated Exploration of Pyranocoumarin Derivatives as Synergistic Inhibitors of Dual-target for Mpro and PLpro Proteins of SARS-CoV-2 through Molecular Docking, ADMET Analysis, and Molecular Dynamics Simulation. Curr Med Chem 2024; 31:CMC-EPUB-143583. [PMID: 39364869 DOI: 10.2174/0109298673331781240829094334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 07/28/2024] [Accepted: 07/31/2024] [Indexed: 10/05/2024]
Abstract
AIMS This study aimed to explore the potential of natural anticoagulant compounds as synergistic inhibitors of the main protease (Mpro) and papain-like protease (PLpro) of SARS-CoV-2 and find effective therapies against SARS-CoV-2 by investigating the inhibitory effects of natural anticoagulant compounds on key viral proteases. OBJECTIVE The objectives of this study were to conduct rigorous virtual screening and molecular docking analyses to evaluate the binding affinities and interactions of selected anticoagulant compounds with Mpro and PLpro, to assess the pharmacokinetic and pharmacodynamic profiles of the compounds to determine their viability for therapeutic use, and to employ molecular dynamics simulations to understand the stability of the identified compounds over time. METHODS In this study, a curated collection of natural anticoagulant compounds was conducted. Virtual screening and molecular docking analyses were performed to assess binding affinities and interactions with Mpro and PLpro. Furthermore, pharmacokinetic and pharmacodynamic analyses were carried out to evaluate absorption, distribution, metabolism, and excretion profiles. Molecular dynamics simulations were performed to elucidate compound stability. RESULTS Natural compounds exhibiting significant inhibitory activity against Mpro and PLpro were identified. A dual-target approach was established as a promising strategy for attenuating viral replication and addressing coagulopathic complications associated with SARS-CoV-2 infection. CONCLUSION The study lays a solid foundation for experimental validation and optimization of identified compounds, potentially leading to the development of precise treatments for SARS-CoV-2.
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Rossafi B, Abchir O, El Kouali M, Chtita S. Advancements in Computational Approaches for Antidiabetic Drug Discovery: A Review. Curr Top Med Chem 2024:CTMC-EPUB-142370. [PMID: 39162267 DOI: 10.2174/0115680266311132240807065631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 06/13/2024] [Accepted: 07/10/2024] [Indexed: 08/21/2024]
Abstract
Diabetes mellitus (DM) manifests as a complex and chronic metabolic disorder, posing a significant threat to global public health and contributing substantially to mortality rates. It is characterized by elevated blood glucose levels or hyperglycemia and requires effective preventive and therapeutic strategies. One promising approach involves targeting the inhibition of α- glucosidase and α-amylase, key enzymes responsible for carbohydrate hydrolysis. Inhibiting these enzymes proves beneficial in reducing postprandial glucose levels and mitigating postprandial hyperglycemia. However, existing antidiabetic medications are associated with undesirable side effects, highlighting the need to develop new molecules with increased efficacy and reduced side effects. Traditional methods for designing such molecules are often lengthy and costly. To address this, computer-based molecular modeling tools offer a promising approach to evaluate the antidiabetic activities of chemical compounds. This review aims to compile information on chemical compounds assessed for their anti-diabetic activities through molecular modeling, with a particular focus on the period from 2020 to 2023.
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Fattouche M, Belaidi S, Abchir O, Al-Shaar W, Younes K, Al-Mogren MM, Chtita S, Soualmia F, Hochlaf M. ANN-QSAR, Molecular Docking, ADMET Predictions, and Molecular Dynamics Studies of Isothiazole Derivatives to Design New and Selective Inhibitors of HCV Polymerase NS5B. Pharmaceuticals (Basel) 2024; 17:1712. [PMID: 39770554 PMCID: PMC11678770 DOI: 10.3390/ph17121712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2024] [Revised: 12/05/2024] [Accepted: 12/11/2024] [Indexed: 01/11/2025] Open
Abstract
Background/Objectives: RNA polymerase (NS5B), serves as a crucial target for pharmaceutical interventions aimed at combating the hepatitis C virus (HCV), which poses significant health challenges worldwide. The present research endeavors to explore and implement a variety of advanced molecular modeling techniques that aim to create and identify innovative and highly effective inhibitors that specifically target the RNA polymerase enzyme. Methods: In this study, a QSAR investigation was carried out on a set of thirty-eight isothiazole derivatives targeting NS5B inhibition and thus hepatitis C virus (HCV) treatment. The research methodology made use of various statistical techniques including multiple linear regression (MLR) and artificial neural networks (ANNs) to develop satisfactory models in terms of internal and external validation parameters, indicating their reliability in predicting the activity of new inhibitors. Accordingly, a series of potent NS5B inhibitors is designed, and their inhibitory potential is confirmed through molecular docking simulations. Results: These simulations showed that the interactions between these inhibitors and the active site 221 binding pocket of the NS5B protein are hydrophobic and hydrogen bond interactions, as well as carbon-hydrogen bonds and electrostatic interactions. Additionally, these newly formulated compounds displayed favorable ADMET characteristics, with molecular dynamics investigations revealing a stable energetic state and dynamic equilibrium. Conclusions: Our work highlights the importance of NS5B inhibition for the treatment of HCV.
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Tighadouini S, Yamari I, Roby O, Y A Alzahrani A, Abchir O, Nait Irahal I, Saddik R, Ferbinteanu M, Chtita S. Synthesis, X-Ray Structure, Characterization, Antifungal Activity, DFT, and Molecular Simulation of a Novel Pyrazole Carboxylic Acid. Curr Top Med Chem 2025; 25:CTMC-EPUB-145989. [PMID: 39844551 DOI: 10.2174/0115680266348692241211111312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 11/01/2024] [Accepted: 11/12/2024] [Indexed: 01/24/2025]
Abstract
BACKGROUND The search for new antifungal agents is critical due to the rising resistance of fungal pathogens to existing treatments. This study focuses on the synthesis and evaluation of a novel compound, 1-benzyl-5-methyl-1H-pyrazole-3-carboxylic acid (compound L1), as a potential antifungal agent. METHODS Compound L1 was synthesized and characterized using a range of analytical techniques, including 1H^1H1H NMR, 13C^{13}C13C NMR, FT-IR, GC-MS, and X-ray single crystal diffraction (XRD). The antifungal activity of the compound was assessed in vitro, and its molecular structure was studied using Density Functional Theory (DFT). Molecular docking and dynamics simulations were conducted to evaluate the interaction of the compound with sterol 14-alpha demethylase (CYP51) from Candida albicans. ADME/Tox evaluations were also performed to assess the drug-like properties of compound L1. RESULTS Compound L1 exhibited moderate antifungal activity with an IC50 value of 34.25 μg/mL. DFT studies confirmed the highly stable molecular structure of the compound. Molecular docking and dynamics simulations demonstrated that compound L1 had a higher affinity and stability when forming complexes with the crystal structure of CYP51, particularly in interaction with the tetrazole- based antifungal drug candidate VT1161 (PDB ID: 5TZ1). ADME/Tox evaluations indicated favorable drug-like properties for compound L1. CONCLUSION The results suggest that compound L1 is a promising antifungal candidate, showing greater potential than fluconazole in the conducted evaluations. Further studies are warranted to explore its full therapeutic potential.
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Abchir O, Yamari I, Shtaiwi AM, Nour H, Kouali ME, Talbi M, Errougui A, Chtita S. Insights into the inhibitory potential of novel hydrazinyl thiazole-linked indenoquinoxaline against alpha-amylase: a comprehensive QSAR, pharmacokinetic, and molecular modeling study. J Biomol Struct Dyn 2024:1-18. [PMID: 38305802 DOI: 10.1080/07391102.2024.2310778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/20/2024] [Indexed: 02/03/2024]
Abstract
The rising prevalence of diabetes necessitates the development of novel drugs, especially given the side effects associated with current medications like Acarbose and Voglibose. A series of 36 Hydrazinyl thiazole-linked indenoquinoxaline derivatives with notable activity against alpha-amylase were studied. To create a molecular model predicting alpha-amylase activity, a QSAR study was performed on these compounds. Molecular descriptors were calculated using Chem3D and Gaussian software and then correlated with their IC50 biological activities to form a dataset. This model data was refined using PCA and modeled with MLR. The model's performance was statistically verified (R2 =0.800; R adj 2 = 0.767; R cv 2 = 0.651) and its applicability domain was defined. It was predicted to possess high predictive power (R test 2 = 0.872). Based on this, new compounds were proposed, and their activities were predicted using the developed model. Additionally, their binding ability to the biological target was studied through molecular docking and dynamics. Their pharmacokinetics were also evaluated using ADMET predictions. Two designed compounds named AE and AB emerged as particularly promising, displaying properties that suggest substantial therapeutic potential and they can form stable complexes into the binding pocket of alpha-amylase enzyme.
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Khedraoui M, Abchir O, Nour H, Yamari I, Errougui A, Samadi A, Chtita S. An In Silico Study Based on QSAR and Molecular Docking and Molecular Dynamics Simulation for the Discovery of Novel Potent Inhibitor against AChE. Pharmaceuticals (Basel) 2024; 17:830. [PMID: 39065681 PMCID: PMC11280381 DOI: 10.3390/ph17070830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/09/2024] [Accepted: 06/17/2024] [Indexed: 07/28/2024] Open
Abstract
Acetylcholinesterase (AChE) is one of the main drug targets for treating Alzheimer's disease. This current study relies on multiple molecular modeling approaches to develop new potent inhibitors of AChE. We explored a 2D QSAR study using the statistical method of multiple linear regression based on a set of substituted 5-phenyl-1,3,4-oxadiazole and N-benzylpiperidine analogs, which were recently synthesized and proved their inhibitory activities against acetylcholinesterase (AChE). The molecular descriptors, polar surface area, dipole moment, and molecular weight are the key structural properties governing AChE inhibition activity. The MLR model was selected based on its statistical parameters: R2 = 0.701, R2test = 0.76, Q2CV = 0.638, and RMSE = 0.336, demonstrating its predictive reliability. Randomization tests, VIF tests, and applicability domain tests were adopted to verify the model's robustness. As a result, 11 new molecules were designed with higher anti-Alzheimer's activities than the model molecule. We demonstrated their improved pharmacokinetic properties through an in silico ADMET study. A molecular docking study was conducted to explore their AChE inhibition mechanisms and binding affinities in the active site. The binding scores of compounds M1, M2, and M6 were (-12.6 kcal/mol), (-13 kcal/mol), and (-12.4 kcal/mol), respectively, which are higher than the standard inhibitor Donepezil with a binding score of (-10.8 kcal/mol). Molecular dynamics simulations over 100 ns were used to validate the molecular docking results, indicating that compounds M1 and M2 remain stable in the active site, confirming their potential as promising anti-AChE inhibitors.
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Nour H, Abchir O, Mounadi N, Samadi A, Salah B, Chtita S. Exploration of natural products for the development of promising cholinesterase inhibitors in Alzheimer's disease treatment. Heliyon 2025; 11:e42479. [PMID: 40034281 PMCID: PMC11874547 DOI: 10.1016/j.heliyon.2025.e42479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 01/25/2025] [Accepted: 02/04/2025] [Indexed: 03/05/2025] Open
Abstract
Cholinesterase enzymes (BuChE and AChE) are privileged biological targets for the symptomatic treatment of Alzheimer's disease. Indeed, inhibition of cholinesterase enzymes has been proven to improve the neurotransmission mechanisms in Alzheimer's disease patients. In this investigation, we attempt to highlight new cholinesterase inhibitors from natural products. For this purpose, secondary metabolites (299 phytoconstituents) of twenty-eight Medicinal plants were virtually screened using molecular docking, pharmacokinetic and toxicological analysis. Ten phytoconstituents (L82, L86, L92, L121, L148, L187, L211, L221, L228) exhibited their high binding affinity with BuChE, and five phytoconstituents, namely L119, L147, L149, L192 and L193, exhibited their strong binding ability with AChE. Subsequently, these phytoconstituents were evaluated for their ADMET properties. As result, L221 is predicted to be highly bioavailable and readily absorbed by the human intestinal tract without significant toxicity concerns, making it suitable for oral administration. Crucially, it can penetrate the blood-brain barrier (BBB), allowing it to effectively reach the central nervous system. Molecular dynamics simulations and MM-PBSA analysis revealed that the best-screened phytoconstituent form thermodynamically favorable and stable complex with the BuChE binding site. The conducted investigations highlighted promising outcomes that can orient towards the rational development of effective Cholinesterase inhibitors.
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Guerguer FZ, Rossafi B, Abchir O, Raouf YS, Albalushi DB, Samadi A, Chtita S. Potential Azo-8-hydroxyquinoline derivatives as multi-target lead candidates for Alzheimer's disease: An in-depth in silico study of monoamine oxidase and cholinesterase inhibitors. PLoS One 2025; 20:e0317261. [PMID: 39883631 PMCID: PMC11781659 DOI: 10.1371/journal.pone.0317261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Accepted: 12/25/2024] [Indexed: 02/01/2025] Open
Abstract
Cognitive dysfunction in Alzheimer's disease results from a complex interplay of various pathological processes, including the dysregulation of key enzymes such as acetylcholinesterase (AChE), butyrylcholinesterase (BuChE), and monoamine oxidase B (MAO-B). This study proposes and designs a series of novel molecules derived from 8-hydroxyquinoline (Azo-8HQ) as potential multi-target lead candidates for treating AD. An exhaustive in silico analysis was conducted, encompassing docking studies, ADMET analysis, density functional theory (DFT) studies, molecular dynamics simulations, and subsequent MM-GBSA calculations to examine the pharmacological potential of these molecules with the specific targets of interest. Out of the 63 Azo-8HQ derivatives analysed, two molecules, 14c and 17c, demonstrated strong affinities for AChE, BuChE, and MAO-B, along with favourable pharmacokinetic profiles and electronic properties. Molecular dynamics simulations confirmed the stability of these molecules within the active sites of the targets, and MM-GBSA calculations revealed low binding energies, indicating robust interactions. These findings identify molecules 14c and 17c as promising multi-target candidates for the treatment of AD, based on an in-depth computational study aimed at minimizing drug development costs and time. Future work will include the synthesis of these molecules followed by in-depth in vitro and in vivo testing to validate their potential therapeutic efficacy.
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Yamari I, Abchir O, Khedraoui M, Errougui A, Talbi M, Samadi A, Kouali MHE, Chtita S. Targeting Fructosamine Oxidase (Amadoriase II) in Aspergillus fumigatus: Comprehensive Virtual Screening, ADMET Analysis, and Molecular Dynamics Simulation of Triazole Derivatives. Curr Med Chem 2024:CMC-EPUB-142985. [PMID: 39279120 DOI: 10.2174/0109298673321782240829082610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 07/26/2024] [Accepted: 07/26/2024] [Indexed: 09/18/2024]
Abstract
INTRODUCTION Aspergillus fumigatus, a significant fungal pathogen, poses a threat to human health, especially in immunocompromised individuals. Addressing the need for novel antifungal strategies, this study employs virtual screening to identify potential inhibitors of Fructosamine oxidase, also known as Amadoriase II, a crucial enzyme in A. fumigatus (PDB ID: 3DJE). METHOD Virtual screening of 81,197 triazole derivatives was subjected to computational analysis, aiming to pinpoint molecules with high binding affinity to the active site of Fructosamine oxidase. Subsequently, an in-depth ADMET analysis assessed the pharmacokinetic properties of lead compounds, ensuring their viability for further development. Molecular dynamics simulations were performed to evaluate the stability of top-ranked compounds over time. RESULTS The results unveil a subset of triazole derivatives displaying promising interactions, suggesting their potential as inhibitors for further investigation. CONCLUSION This approach contributes to the development of targeted antifungal agents, offering a rational starting point for experimental validation and drug development against Aspergillus fumigatus infections.
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Bouribab A, Karim EM, Khedraoui M, Abchir O, Errougui A, Raouf YS, Samadi A, Chtita S. Exploring Moroccan Medicinal Plants for Anticancer Therapy Development Through In Silico Studies. Pharmaceuticals (Basel) 2024; 17:1528. [PMID: 39598438 PMCID: PMC11597486 DOI: 10.3390/ph17111528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Revised: 10/31/2024] [Accepted: 11/07/2024] [Indexed: 11/29/2024] Open
Abstract
BACKGROUND Angiogenesis is a crucial process in the growth and proliferation of cancer, enabling tumor growth through the formation of new vasculature and the supply of nutrients and oxygen to growing malignant cells. This disease-promoting process can be targeted through the inhibition of tyrosine kinase enzymes. OBJECTIVES The objective of this study is to evaluate the anticancer potential of various Moroccan plants from different regions. While these plants have a rich history of traditional medicinal use, they have not been extensively investigated as anticancer therapies. METHODS This study employed a multifaceted approach to evaluate the anticancer potential of various Moroccan plants. Receptor-ligand docking and virtual screening were used to assess the binding affinity of phytocompounds to the EGFR and VEGFR2 receptors. Additionally, predictive pharmacokinetic analyses were conducted to evaluate the ADMET properties of the selected compounds, followed by molecular dynamics simulations to analyze the stability of the receptor-ligand complexes. RESULTS In our research, we identified three notable active compounds-catechin, 4-O-glucoside ferulic acid, and 3-glucoside resveratrol-in the Moroccan plant Ajuga iva L. These findings suggest that Ajuga iva L. may possess significant potential for cancer inhibition. CONCLUSIONS This research highlights the potential of the Moroccan plant Ajuga iva L. as a source of active compounds with significant anticancer properties. Further investigation is essential to validate these findings and explore new therapeutic avenues based on these traditional resources.
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Abchir O, Khedraoui M, Yamari I, Nour H, Errougui A, Samadi A, Chtita S. Exploration of alpha-glucosidase inhibitors: A comprehensive in silico approach targeting a large set of triazole derivatives. PLoS One 2024; 19:e0308308. [PMID: 39241083 PMCID: PMC11379377 DOI: 10.1371/journal.pone.0308308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 07/19/2024] [Indexed: 09/08/2024] Open
Abstract
BACKGROUND The increasing prevalence of diabetes and the side effects associated with current medications necessitate the development of novel candidate drugs targeting alpha-glucosidase as a potential treatment option. METHODS This study employed computer-aided drug design techniques to identify potential alpha-glucosidase inhibitors from the PubChem database. Molecular docking was used to evaluate 81,197 compounds, narrowing the set for further analysis and providing insights into ligand-target interactions. An ADMET study assessed the pharmacokinetic properties of these compounds, including absorption, distribution, metabolism, excretion, and toxicity. Molecular dynamics simulations validated the docking results. RESULTS 9 compounds were identified as potential candidate drugs based on their ability to form stable complexes with alpha-glucosidase and their favorable pharmacokinetic profiles, three of these compounds were subjected to the molecular dynamics, which showed stability throughout the entire 100 ns simulation. CONCLUSION These findings suggest promising new alpha-glucosidase inhibitors for diabetes treatment. Further validation through in vitro and in vivo studies is recommended to confirm their efficacy and safety.
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Yamari I, Abchir O, Nour H, Khedraoui M, Rossafi B, Errougui A, Talbi M, Samadi A, Kouali MHE, Chtita S. Unveiling Moroccan Nature's Arsenal: A Computational Molecular Docking, Density Functional Theory, and Molecular Dynamics Study of Natural Compounds against Drug-Resistant Fungal Infections. Pharmaceuticals (Basel) 2024; 17:886. [PMID: 39065737 PMCID: PMC11279552 DOI: 10.3390/ph17070886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/28/2024] Open
Abstract
Candida albicans and Aspergillus fumigatus are recognized as significant fungal pathogens, responsible for various human infections. The rapid emergence of drug-resistant strains among these fungi requires the identification and development of innovative antifungal therapies. We undertook a comprehensive screening of 297 naturally occurring compounds to address this challenge. Using computational docking techniques, we systematically analyzed the binding affinity of each compound to key proteins from Candida albicans (PDB ID: 1EAG) and Aspergillus fumigatus (PDB ID: 3DJE). This rigorous in silico examination aimed to unveil compounds that could potentially inhibit the activity of these fungal infections. This was followed by an ADMET analysis of the top-ranked compound, providing valuable insights into the pharmacokinetic properties and potential toxicological profiles. To further validate our findings, the molecular reactivity and stability were computed using the DFT calculation and molecular dynamics simulation, providing a deeper understanding of the stability and behavior of the top-ranking compounds in a biological environment. The outcomes of our study identified a subset of natural compounds that, based on our analysis, demonstrate notable potential as antifungal candidates. With further experimental validation, these compounds could pave the way for new therapeutic strategies against drug-resistant fungal pathogens.
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Islam M, Hossain A, Yamari I, Abchir O, Chtita S, Ali F, Kawsar SMA. Synthesis, Antimicrobial, Molecular Docking Against Bacterial and Fungal Proteins and In Silico Studies of Glucopyranoside Derivatives as Potent Antimicrobial Agents. Chem Biodivers 2024; 21:e202400932. [PMID: 38949892 DOI: 10.1002/cbdv.202400932] [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: 04/19/2024] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/03/2024]
Abstract
Carbohydrate derivatives play a crucial roles in biochemical and medicinal research, especially in the fields of chemistry and biochemistry. From this perspective, the present study was designed to explore the synthesis of methyl α-D-glucopyranoside derivatives (1-8), focusing on their efficacy against bacterial and fungal inhibition. The structure of the synthesized compounds was ascertained using FTIR, 1H-NMR, 13C-NMR, mass and elemental analyses. Antimicrobial screening revealed strong antifungal properties, with compound 7 exhibiting minimum inhibitory concentrations (MICs) ranging from 16-32 μg/L and minimum bactericidal concentrations (MBCs) ranging from 64-128 μg/L. Incorporating decanoyl acyl groups at C-2 and C-3 of (7) significantly improved the efficacy against bacteria and fungi. Structure-activity relationship (SAR) analysis indicated that adding nonanoyl and decanoyl groups to the ribose moiety enhanced potency against both bacterial and fungal strains. Computational methods, including molecular docking, density functional theory (DFT), Petra, Osiris, Molinspiration (POM) evaluation, and molecular dynamics (MD) simulations, were used to assess the efficacy of these derivatives. Compounds 6 and 7, which presented nonanoyl and decanoyl substituents, demonstrated greater efficacy. In addition, DFT studies identified compound 8 as possessing ideal electronic properties. Molecular docking revealed that compound 8 exhibits exceptional binding affinities to bacterial proteins, conferring potent antibacterial and antifungal activities. In addition, pharmacokinetic optimization via POM analysis highlighted compounds 1 and 2 as promising bioavailable drugs with minimal toxicity. Molecular dynamics simulations confirmed the stability of the 2-S. aureus complex, revealing the therapeutic potential of compounds 2 and 8. Future experiments are required to validate their efficacy for pharmaceutical development. The integration of in vitro and in silico methods, including DFT anchoring dynamics and molecular dynamics simulations, provides a solid framework for the advancement of effective anti-infective drugs.
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