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Belghalia E, Ouabane M, El Bahi S, Rehman HM, Sbai A, Lakhlifi T, Bouachrine M. In silico research on new sulfonamide derivatives as BRD4 inhibitors targeting acute myeloid leukemia using various computational techniques including 3D-QSAR, HQSAR, molecular docking, ADME/Tox, and molecular dynamics. J Biomol Struct Dyn 2024; 42:9201-9219. [PMID: 37656159 DOI: 10.1080/07391102.2023.2250460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/15/2023] [Indexed: 09/02/2023]
Abstract
Acute myeloid leukemia, a serious condition affecting stem cells, drives uncontrollable myeloblast proliferation, leading to accumulation. Extensive research seeks rapid, effective chemotherapeutics. A potential option is a BRD4 inhibitor, known for suppressing cell proliferation. Sulfonamide derivatives probed essential structural elements for potent BRD4 inhibitors. To achieve this goal, we employed 3D-QSAR molecular modeling techniques, including CoMFA, CoMSIA, and HQSAR models, along with molecular docking and molecular dynamics simulations. The validation of the 2D/3D QSAR models, both internally and externally, underscores their robustness and reliability. The contour plots derived from CoMFA, CoMSIA, and HQSAR analyses played a pivotal role in shaping the design of effective BRD4 inhibitors. Importantly, our findings highlight the advantageous impact of incorporating bulkier substituents on the pyridinone ring and hydrophobic/electrostatic substituents on the methoxy-substituted phenyl ring, enhancing interactions with the BRD4 target. The interaction mode of the new compounds with the BRD4 receptor (PDB ID: 4BJX) was investigated using molecular docking simulations, revealing favorable binding energies, supported by the formation of hydrogen and hydrophobic bonds with key protein residues. Moreover, these novel inhibitors exhibited good oral bioavailability and demonstrated non-toxic properties based on ADMET analysis. Furthermore, the newly designed compounds along with the most active one from series 58, underwent a molecular dynamics simulation to analyze their behavior. The simulation provided additional evidence to support the molecular docking results, confirming the sustained stability of the analyzed molecules over the trajectory. This outcome could serve as a valuable reference for designing and developing novel and effective BRD4 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Etibaria Belghalia
- Molecular chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Mohamed Ouabane
- Molecular chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
- Chemistry- Biologie Applied to the Environment URL CNRT 13, Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Salma El Bahi
- Molecular chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | | | - Abdelouahid Sbai
- Molecular chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Tahar Lakhlifi
- Molecular chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Mohammed Bouachrine
- Higher School of Technology - Khenifra (EST-Khenifra), University of Sultan My Slimane, Beni Mellal, Morocco
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Soufi H, Moussaoui M, Baammi S, Baassi M, Salah M, Daoud R, El Allali A, Belghiti ME, Moutaabbid M, Belaaouad S. Multi-combined QSAR, molecular docking, molecular dynamics simulation, and ADMET of Flavonoid derivatives as potent cholinesterase inhibitors. J Biomol Struct Dyn 2024; 42:6027-6041. [PMID: 37485860 DOI: 10.1080/07391102.2023.2238314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 06/21/2023] [Indexed: 07/25/2023]
Abstract
In searching for a new and efficient therapeutic agent against Alzheimer's disease, a Quantitative structure-activity relationship (QSAR) was derived for 45 Flavonoid derivatives recently synthesized and evaluated as cholinesterase inhibitors. The multiple linear regression method (MLR) was adopted to develop an adequate mathematical model that describes the relationship between a variety of molecular descriptors of the studied compounds and their biological activities (cholinesterase inhibitors). Golbraikh and Tropsha criteria were applied to verify the validity of the built model. The built MLR model was statistically reliable, robust, and predictive (R2 = 0.801, Q2cv = 0.876, R2test = 0.824). Dreiding energy and Molar Refractivity were the major factors that govern the Anti-cholinesterase activity. These results were further exploited to design a new series of Flavonoid derivatives with higher Anti-cholinesterase activities than the existing ones. Thereafter, molecular docking and molecular dynamic studies were performed to predict the binding types of the designed compounds and to investigate their stability at the active site of the Butyrylcholinestérase BuChE protein. The negative and low binding affinity calculated for all designed compounds shows that designed compound 1 has a favorable affinity for the 4TPK. Moreover, molecular dynamics simulation studies confirmed the stability of designed compound 1 in the active pocket of 4TPK over 100 ns. Finally, the ADMET analysis was incorporated to analyze the pharmacokinetics and toxicity parameters. The designed compounds were found to meet the ADMET descriptor criteria at an acceptable level having respectable intestinal permeability and water solubility and can reach the intended destinations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hatim Soufi
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Benguerir, Morocco
| | - Mohamed Moussaoui
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Benguerir, Morocco
| | - Soukayna Baammi
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Mouna Baassi
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Benguerir, Morocco
| | - Mohammed Salah
- Team of Chemoinformatics Research and Spectroscopy and Quantum Chemistry, Department of Chemistry, Faculty of Science, University Chouaib Doukkali, El Jadida, Morocco
| | - Rachid Daoud
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Achraf El Allali
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
| | - M E Belghiti
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Benguerir, Morocco
- Laboratory of Nernest Technology, Sherbrook, QC, Canada
| | - Mohammed Moutaabbid
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Benguerir, Morocco
| | - Said Belaaouad
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Benguerir, Morocco
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Moussaoui M, Baammi S, Soufi H, Baassi M, El Allali A, Belghiti ME, Daoud R, Belaaouad S. QSAR, ADMET, molecular docking, and dynamics studies of 1,2,4-triazine-3(2H)-one derivatives as tubulin inhibitors for breast cancer therapy. Sci Rep 2024; 14:16418. [PMID: 39013949 PMCID: PMC11252338 DOI: 10.1038/s41598-024-66877-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 07/04/2024] [Indexed: 07/18/2024] Open
Abstract
Breast cancer remains a leading cause of cancer-related deaths among women globally, necessitating the development of more effective therapeutic agents with minimal side effects. This study explores novel 1,2,4-triazine-3(2H)-one derivatives as potential inhibitors of Tubulin, a pivotal protein in cancer cell division, highlighting a targeted approach in cancer therapy. Using an integrated computational approach, we combined quantitative structure-activity relationship (QSAR) modeling, ADMET profiling, molecular docking, and molecular dynamics simulations to evaluate and predict the efficacy and stability of these compounds. Our QSAR models, developed through rigorous statistical analysis, revealed that descriptors such as absolute electronegativity and water solubility significantly influence inhibitory activity, achieving a predictive accuracy (R2) of 0.849. Molecular docking studies identified compounds with high binding affinities, particularly Pred28, which exhibited the best docking score of - 9.6 kcal/mol. Molecular dynamics simulations conducted over 100 ns provided further insights into the stability of these interactions. Pred28 demonstrated notable stability, with the lowest root mean square deviation (RMSD) of 0.29 nm and root mean square fluctuation (RMSF) values indicative of a tightly bound conformation to Tubulin. The novelty of this work lies in its methodological rigor and the integration of multiple advanced computational techniques to pinpoint compounds with promising therapeutic potential. Our findings advance the current understanding of Tubulin inhibitors and open avenues for the synthesis and experimental validation of these compounds, aiming to offer new solutions for breast cancer treatment.
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Affiliation(s)
- Mohamed Moussaoui
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco.
| | - Soukayna Baammi
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Hatim Soufi
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco
| | - Mouna Baassi
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco
| | - Achraf El Allali
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - M E Belghiti
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco
- Laboratory of Nernest Technology, 163 Willington Street, Sherbrook, QC, J1H5C7, Canada
| | - Rachid Daoud
- Chemical and Biochemical Sciences-Green Processing Engineering, Mohammed VI Polytechnic University, Ben Guerir, Morocco.
| | - Said Belaaouad
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco
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Sadeghi M, Miroliaei M, Ghanadian M. Drug repurposing for diabetes mellitus: In silico and in vitro investigation of DrugBank database for α-glucosidase inhibitors. Int J Biol Macromol 2024; 270:132164. [PMID: 38729474 DOI: 10.1016/j.ijbiomac.2024.132164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/19/2024] [Accepted: 05/05/2024] [Indexed: 05/12/2024]
Abstract
The process of developing novel compounds/drugs is arduous, time-intensive, and financially burdensome, characterized by a notably low success rate and relatively high attrition rates. To alleviate these challenges, compound/drug repositioning strategies are employed to predict potential therapeutic effects for DrugBank-approved compounds across various diseases. In this study, we devised a computational and enzyme inhibitory mechanistic approach to identify promising compounds from the pool of DrugBank-approved substances targeting Diabetes Mellitus (DM). Molecular docking analyses were employed to validate the binding interaction patterns and conformations of the screened compounds within the active site of α-glucosidase. Notably, Asp352 and Glu277 participated in interactions within the α-glucosidase-ligand complexes, mediated by conventional hydrogen bonding and van der Waals forces, respectively. The stability of the docked complexes (α-glucosidase-compounds) was scrutinized through Molecular Dynamics (MD) simulations. Subsequent in vitro analyses assessed the therapeutic potential of the repositioned compounds against α-glucosidase. Kinetic studies revealed that "Forodesine" exhibited a lower IC50 (0.24 ± 0.04 mM) compared to the control, and its inhibitory pattern corresponds to that of competitive inhibitors. In-depth in silico secondary structure content analysis detailed the interactions between Forodesine and α-glucosidase, unveiling significant alterations in enzyme conformation upon binding, impacting its catalytic activity. Overall, our findings underscore the potential of Forodesine as a promising candidate for DM treatment through α-glucosidase inhibition. Further validation through in vitro and in vivo studies is imperative to confirm the therapeutic benefits of Forodesine in conformational diseases such as DM.
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Affiliation(s)
- Morteza Sadeghi
- Faculty of Biological Science and Technology, Department of Cell and Molecular Biology & Microbiology, University of Isfahan, Isfahan, Iran.
| | - Mehran Miroliaei
- Faculty of Biological Science and Technology, Department of Cell and Molecular Biology & Microbiology, University of Isfahan, Isfahan, Iran.
| | - Mustafa Ghanadian
- Department of Pharmacognosy, Isfahan Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
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Elbouhi M, Ouabane M, Tabti K, Badaoui H, Abdessadak O, El Alaouy MA, Elkamel K, Lakhlifi T, Sbai A, Ajana MA, Bouachrine M. Computational evaluation of 1,2,3-triazole-based VEGFR-2 inhibitors: anti-angiogenesis potential and pharmacokinetic assessment. J Biomol Struct Dyn 2024:1-11. [PMID: 38193897 DOI: 10.1080/07391102.2023.2301686] [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: 04/01/2023] [Accepted: 11/20/2023] [Indexed: 01/10/2024]
Abstract
The vascular endothelial growth factor (VEGF) and its cell surface receptor, as well as the human VEGFR-2 domain kinase, are some of the signaling pathways that have received the most attention in this field. This study aimed to identify novel molecules as VEGFR-2 inhibitors using 3D-QSAR modeling based on 1,2,3-triazole. Docking studies and dynamic simulations were performed to analyze novel interactions with the inhibitors and validate the molecular docking, dynamic simulations, and ADMET analyses. The optimized CoMSIA/SEH model showed good statistical results, and molecular docking and molecular dynamics simulations demonstrated stability of M3 ligand with the receptor and provided insight into ligand-receptor interactions. The newly developed compounds performed well in ADMET evaluations and showed promising results using Lipinski's rule of five, suggesting that the molecule M3 could be a useful anti-angiogenesis agent. In conclusion, this study provides insights into the structure-activity relationship of VEGFR-2 inhibitors and identifies M3 as a potential new anti-angiogenesis drug. The methodology used in this study can be applied to other similar drug targets to discover new and potent inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mhamed Elbouhi
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Mohamed Ouabane
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Kamal Tabti
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Hassan Badaoui
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Oumayma Abdessadak
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Moulay Ahfid El Alaouy
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Khalid Elkamel
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Abdelouahid Sbai
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Mohammed Aziz Ajana
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
- Higher School of Technology (EST Khenifra), Sultan Moulay Slimane University, Beni-Mellal, Morocco
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Baammi S, El Allali A, Daoud R. Unleashing Nature's potential: a computational approach to discovering novel VEGFR-2 inhibitors from African natural compound using virtual screening, ADMET analysis, molecular dynamics, and MMPBSA calculations. Front Mol Biosci 2023; 10:1227643. [PMID: 37800126 PMCID: PMC10548200 DOI: 10.3389/fmolb.2023.1227643] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/07/2023] [Indexed: 10/07/2023] Open
Abstract
One of the characteristic features of cancer is angiogenesis, the process by which new, aberrant blood vessels are formed from pre-existing blood vessels. The process of angiogenesis begins when VEGF binds to its receptor, the VEGF receptor (VEGFR). The formation of new blood vessels provides nutrients that can promote the growth of cancer cells. When it comes to new blood vessel formation, VEGFR2 is a critical player. Therefore, inhibiting VEGFR2 is an effective way to target angiogenesis in cancer treatment. The aim of our research was to find new VEGFR-2 inhibitors by performing a virtual screening of 13313 from African natural compounds using different in silico techniques. Using molecular docking calculations and ADMET properties, we identified four compounds that exhibited a binding affinity ranging from -11.0 kcal/mol to -11.5 Kcal/mol when bound to VEGFR-2. These four compounds were further analyzed with 100 ns simulations to determine their stability and binding energy using the MM-PBSA method. After comparing the compounds with Regorafenib, a drug approved for anti-angiogenesis treatment, it was found that all the candidates (EANPDB 252, NANPDB 4577, and NANPDB 4580), with the exception of EANPDB 76, could target VEGFR-2 similarly effectively to Regorafenib. Therefore, we recommend three of these agents for anti-angiogenesis treatment because they are likely to deactivate VEGFR-2 and thus inhibit angiogenesis. However, it should be noted that the safety and suitability of these agents for clinical use needs further investigation, as the computer-assisted study did not include in vitro or in vivo experiments.
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Affiliation(s)
- Soukayna Baammi
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Rachid Daoud
- Chemical and Biochemical Sciences-Green Processing Engineering, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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Tabti K, Abdessadak O, Sbai A, Maghat H, Bouachrine M, Lakhlifi T. Design and development of novel spiro-oxindoles as potent antiproliferative agents using quantitative structure activity based Monte Carlo method, docking molecular, molecular dynamics, free energy calculations, and pharmacokinetics /toxicity studies. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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