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Boutalaka M, El Bahi S, Alaqarbeh M, El Alaouy MA, Koubi Y, Khatabi KE, Maghat H, Bouachrine M, Lakhlifi T. Computational investigation of imidazo[2,1-b]oxazole derivatives as potential mutant BRAF kinase inhibitors: 3D-QSAR, molecular docking, molecular dynamics simulation, and ADMETox studies. J Biomol Struct Dyn 2024; 42:5268-5287. [PMID: 37424193 DOI: 10.1080/07391102.2023.2233629] [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: 03/01/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023]
Abstract
BRAF inhibitors are known to be an effective therapeutic target for treating melanoma and other types of cancer. Using 3D-QSAR, molecular docking, and MD simulations, this study evaluated various imidazo[2,1-b]oxazole derivatives that function as mutant BRAF kinase inhibitors. Comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) were used to create the 3D-QSAR models. CoMSIA/SEHA model has solid predictive power across several models (Q2 = 0.578; R2 = 0.828; R2pred = 0.74) and is the best model according to the numerous field models generated. The created model's predictive power was evaluated through external validation using a test set. CoMSIA/SEHA contour maps collect information that can be used to identify critical regions with solid anticancer activity. We developed four inhibitors with high predicted activity due to these observations. ADMET prediction was used to assess the toxicity of the proposed imidazo[2,1-b]oxazole compounds. The predictive molecules (T1-T4) demonstrated good ADMET properties, excluding the toxic active compounds 11r from the database. Molecular docking was also used to determine the patterns and modes of interactions between imidazo[2,1-b]oxazole ligands and receptors, which revealed that the proposed imidazo[2,1-b]oxazole scaffold was stable in the receptor's active site (PDB code: 4G9C). The suggested compounds (T1-T4) were subjected to molecular dynamics simulations lasting 100 ns to determine their binding free energies. The results showed that T2 had a more favorable binding free energy (-149.552 kJ/mol) than T1 (-112.556 kJ/mol), T3 (-115.503 kJ/mol), and T4 (-102.553 kJ/mol). The results suggest that the imidazo[2,1-b]oxazole compounds investigated in this study have potential as inhibitors of BRAF kinase and could be further developed as anticancer drugs. Highlights22 imidazo[2,1-b]oxazole compounds were subjected to research on three-dimensional quantitative conformational relationships.Using contour maps from 3D-QSAR models as a guide was used to figure out the areas and strategies for structural optimization.Combined molecular docking, molecular dynamics simulations, and binding free energy calculations to verify the inhibitor activity of the proposed 22 imidazo[2,1-b]oxazole compounds.Four potential B-RAF Kinase inhibitors were discovered, providing theoretical clues for developing a highly anticancer agent.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Meryem Boutalaka
- Department of Chemistry, Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University of Moulay Ismail, Meknes, Morocco
| | - Salma El Bahi
- Department of Chemistry, Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University of Moulay Ismail, Meknes, Morocco
| | | | - Moulay Ahfid El Alaouy
- Department of Chemistry, Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University of Moulay Ismail, Meknes, Morocco
| | - Yassine Koubi
- Department of Chemistry, Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University of Moulay Ismail, Meknes, Morocco
| | - Khalil El Khatabi
- Department of Chemistry, Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University of Moulay Ismail, Meknes, Morocco
| | - Hamid Maghat
- Department of Chemistry, Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University of Moulay Ismail, Meknes, Morocco
| | - Mohammed Bouachrine
- Department of Chemistry, Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University of Moulay Ismail, Meknes, Morocco
- EST Khenifra, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - Tahar Lakhlifi
- Department of Chemistry, Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University of Moulay Ismail, Meknes, Morocco
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Zhang Y, Chen L, Wang Z, Zhu Y, Jiang H, Xu J, Xiong F. Design of novel DABO derivatives as HIV-1 RT inhibitors using molecular docking, molecular dynamics simulations and ADMET properties. J Biomol Struct Dyn 2024; 42:4196-4213. [PMID: 37272892 DOI: 10.1080/07391102.2023.2219331] [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: 02/07/2023] [Accepted: 05/23/2023] [Indexed: 06/06/2023]
Abstract
HIV-1 reverse transcriptase is an important target for developing effective anti-HIV-1 inhibitors. Different types of small molecules have been designed based on this target, showing different levels of inhibitory activity against various types of HIV-1 strains. The relationship between structure and activity of DABO derivatives was investigated by means of 3D-QSAR molecular model, molecular docking, molecular dynamics and ADMET properties. The statistical results of molecular models show that the CoMFA and CoMSIA models have good internal stability (CoMFA: q2 = 0.623, r2 = 0.946; CoMSIA: q2 = 0.668, r2 = 0.983) and external prediction ability (CoMFA: rpred2 = 0.961; CoMSIA: rpred2 = 0.961). In addition, molecular docking has explored the mechanism of action between small molecules and receptor proteins, and the results show that hydrogen bonding between amino acid Lys101 and small molecules can improve the affinity of ligands to receptor binding. A total of 12 novel molecules were designed and their activities were predicted based on the 3D-QSAR model and molecular docking results. The results showed that the designed molecules had higher predictive activity. Subsequently, 100 ns MD simulation and binding free energy verified the stability of molecular docking results. Finally, the pharmacokinetic properties of the novel designed molecule were verified by using ADMET to predict its properties. These results can provide reference for the design and development of novel and effective HIV-1 RT inhibitors, and provide new ideas for the design of subsequent drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yanjun Zhang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Lu Chen
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Zhonghua Wang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, P. R. China
| | - Yiren Zhu
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Huifang Jiang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Jie Xu
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Fei Xiong
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
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Shallangwa GA, Mahmud AW, Uzairu A, Ibrahim MT. 2,4-disubstituted 6-fluoroquinolines as potent antiplasmodial agents: QSAR, homology modeling, molecular docking and ADMET studies. J Taibah Univ Med Sci 2024; 19:233-247. [PMID: 38179257 PMCID: PMC10762476 DOI: 10.1016/j.jtumed.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/29/2023] [Accepted: 11/09/2023] [Indexed: 01/06/2024] Open
Abstract
Objective This work was designed to study 2,4-disubstituted 6-fluoroquinolines as antiplasmodial agents by using in silico techniques, to aid in the design of novel analogs with high potency against malaria and high inhibition of Plasmodium falciparum translation elongation factor 2 (PfeEF2), a novel drug target. Methods Quantitative structure-activity relationships (QSAR) of 2,4-disubstituted 6-fluoroquinolines were studied with the genetic function approximation technique in Material Studio software. The 3D structure of PfeEF2 was modeled in the SWISS-MODEL workspace through homology modeling. A molecular docking study of the modeled PfeEF2 and 2,4-disubstituted 6-fluoroquinolines was conducted with Autodock Vina in Pyrx software. Furthermore, the in silico pharmacokinetic properties of selected compounds were investigated. Results A robust, reliable and predictive QSAR model was developed that related the chemical structures of 2,4-disubstituted 6-fluoroquinolines to their antiplasmodium activities. The model had an internal squared correlation coefficient R2 of 0.921, adjusted squared correlation coefficient R2adj of 0.878, leave-one-out cross-validation coefficient Q2cv of 0.801 and predictive squared correlation coefficient R2pred of 0.901. The antiplasmodium activity of 6-fluoroquinolines was found to depend on the n5Ring, GGI9, TDB7u, TDB8u and RDF75i physicochemical properties: n5Ring, TDB8u and RDF75i were positively associated, whereas GGI9 and TDB7u were negatively associated, with the antiplasmodium activity of the compounds. Stable complexes formed between the compounds and modeled PfeEF2, with binding affinity ranging from -8.200 to -10.700 kcal/mol. Compounds 5, 11, 16, 22 and 24 had better binding affinities than quinoline-4-carboxamide (DDD107498), as well as good pharmacokinetic properties, and therefore may be better inhibitors of this novel target. Conclusion QSAR and docking studies provided insight into designing novel 2,4-disubstituted 6-fluoroquinolines with high antiplasmodial activity and good structural properties for inhibiting a novel antimalarial drug target.
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Affiliation(s)
| | - Aliyu W. Mahmud
- Department of Applied Chemistry, Kaduna Polytechnic, P.M.B 2021, Kaduna, Nigeria
| | - Adamu Uzairu
- Chemistry Department, Ahmadu Bello University, Zaria, Nigeria
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Bhawna, Kumar S, Kumar P, Kumar A. Correlation intensity index-index of ideality of correlation: A hyphenated target function for furtherance of MAO-B inhibitory activity assessment. Comput Biol Chem 2024; 108:107975. [PMID: 37950961 DOI: 10.1016/j.compbiolchem.2023.107975] [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: 08/20/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/13/2023]
Abstract
Monoamine oxidases are the enzymes involved in the management of brain homeostasis through oxidative deamination of monoamines such as neurotransmitters, tyramine etc. The excessive production of monoamine oxidase-B specifically results in numerous neurodegenerative disorders like Alzheimer's and Parkinson's diseases. Inhibitors of monoamine oxidase-B are applied in the management of these disorders. Here in this article we have developed robust hybrid descriptor based QSAR models related to 123 monoamine oxidase-B inhibitors through CORAL software by means of Monte Carlo optimization method. Three target functions were applied to prepare QSAR models and three splits were made for each target function. The most reliable, robust and better predictive QSAR models were developed with TF3 (correlation intensity index -index of ideality of correlation). Correlation intensity index showed positive effect on QSAR models. The structural features obtained from the QSAR modeling were incorporated in newly designed molecules and exhibited positive effect on their endpoint. Significant binding interactions were represented by these molecules in docking studies. Molecule B5 displayed prominent pIC50 (8.3) and binding affinity (-11.5 kcal mol-1) towards monoamine oxidase-B.
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Affiliation(s)
- Bhawna
- Department of Pharmaceutical Sciences,Guru Jambheshwar University of Science and Technology, Hisar, Haryana 125001, India
| | - Sunil Kumar
- Department of Pharmaceutical Sciences,Guru Jambheshwar University of Science and Technology, Hisar, Haryana 125001, India
| | - Parvin Kumar
- Department of Chemistry, Kurukshetra University, Kurukshetra, India
| | - Ashwani Kumar
- Department of Pharmaceutical Sciences,Guru Jambheshwar University of Science and Technology, Hisar, Haryana 125001, India.
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Haloui R, Mkhayar K, Daoui O, El Khattabi K, El Abbouchi A, Chtita S, Elkhattabi S. Design of new small molecules derived from indolin-2-one as potent TRKs inhibitors using a computer-aided drug design approach. J Biomol Struct Dyn 2024:1-18. [PMID: 38217880 DOI: 10.1080/07391102.2024.2302944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/02/2024] [Indexed: 01/15/2024]
Abstract
Tropomyosin receptor kinase (TRKs) enzymes are responsible for cancers associated with the neurotrophic tyrosine kinase receptor gene fusion and are identified as effective targets for anticancer drug discovery. A series of small-molecule indolin-2-one derivatives showed remarkable biological activity against TRKs enzymatic activity. These small molecules could have an excellent profile for pharmaceutical application in the treatment of cancers caused by TRKs activity. The aim of this study is to modify the structure of these molecules to obtain new molecules with improved TRK inhibitory activity and pharmacokinetic properties favorable to the design of new drugs. Based on these series, we carried out a 3D-QSAR study. As a result, robust and reliable CoMFA and CoMSIA models are developed and applied to the design of 11 new molecules. These new molecules have a biological activity superior to the most active molecule in the starting series. The eleven designed molecules are screened using drug-likeness, ADMET proprieties, molecular docking, and MM-GBSA filters. The results of this screening identified the T1, T3, and T4 molecules as the best candidates for strong inhibition of TRKs enzymatic activity. In addition, molecular dynamics simulations are performed for TRK free and complexed with ligands T1, T3, and T4 to evaluate the stability of ligand-protein complexes over the simulation time. On the other hand, we proposed experimental synthesis routes for these newly designed molecules. Finally, the designed molecules T1, T2, and T3 have great potential to become reliable candidates for the conception of new drug inhibitors of TRKs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rachid Haloui
- Laboratory of Engineering, Systems, and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, Fez, Morocco
| | - Khaoula Mkhayar
- Laboratory of Engineering, Systems, and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, Fez, Morocco
| | - Ossama Daoui
- Laboratory of Engineering, Systems, and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, Fez, Morocco
| | - Kaouakeb El Khattabi
- Department of Fundamental Sciences, Faculty of Medicine Dentistry, Mohammed V University of Rabat, Rabat, Morocco
| | - Abdelmoula El Abbouchi
- Euromed Research Center, Euromed Faculty of Pharmacy, Euromed University of Fes (UEMF), Fez, Morocco
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Souad Elkhattabi
- Laboratory of Engineering, Systems, and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, Fez, Morocco
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Krishnan K A, Valavi SG, Joy A. Identification of Novel EGFR Inhibitors for the Targeted Therapy of Colorectal Cancer Using Pharmacophore Modelling, Docking, Molecular Dynamic Simulation and Biological Activity Prediction. Anticancer Agents Med Chem 2024; 24:263-279. [PMID: 38173208 DOI: 10.2174/0118715206275566231206094645] [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: 08/04/2023] [Revised: 10/30/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Colorectal cancer (CRC) is considered the second deadliest cancer in the world. One of the reasons for the occurrence of this cancer is the deregulation of the Epidermal Growth Factor Receptor (EGFR), which plays a critical role in regulating cell division, persistence, differentiation, and migration. The overexpression of the EGFR protein leads to its dysregulation and causes CRC. OBJECTIVES Hence, this work aims to identify and validate novel EGFR inhibitors for the treatment of colorectal cancer employing various computer aided techniques such as pharmacophore modeling, docking, molecular dynamic simulation and Quantitative Structure-Activity Relationship (QSAR) analysis. METHODS In this work, a shared-featured ligand-based pharmacophore model was generated using the known inhibitors of EGFR. The best model was validated and screened against ZincPharmer and Maybridge databases, and 143 hits were obtained. Pharmacokinetic and toxicological properties of these hits were studied, and the acceptable ligands were docked against EGFR. The best five protein-ligand complexes with binding energy less than -5 kcal/mol were selected. The molecular dynamic simulation studies of these complexes were conducted for 100 nanoseconds (ns), and the results were analyzed. The biological activity of this ligand was calculated using QSAR analysis. RESULTS The best complex with Root Mean Square Deviation (RMSD) 3.429 Å and Radius of Gyration (RoG) 20.181 Å was selected. The Root Mean Square Fluctuations (RMSF) results were also found to be satisfactory. The biological activity of this ligand was found to be 1.38 μM. CONCLUSION This work hereby proposes the ligand 2-((1,6-dimethyl-4-oxo-1,4-dihydropyridin-3-yl)oxy)-N- (1H-indol-4-yl)acetamide as a potential EGFR inhibitor for the treatment of colorectal cancer. The wet lab analysis must be conducted, however, to confirm this hypothesis.
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Affiliation(s)
- Amrutha Krishnan K
- Department of Applied Science and Humanities, Sahrdaya College of Engineering and Technology, Affiliated to APJ Abdul Kalam Technological University, Kodakara, Thrissur, Kerala, India
| | - Sudha George Valavi
- Department of Applied Science and Humanities, Sahrdaya College of Engineering and Technology, Affiliated to APJ Abdul Kalam Technological University, Kodakara, Thrissur, Kerala, India
| | - Amitha Joy
- Department of Biotechnology, Sahrdaya College of Engineering and Technology, Affiliated to APJ Abdul Kalam Technological University, Kodakara, Thrissur, Kerala, India
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Wang J, Zhang L, Sun J, Yang X, Wu W, Chen W, Zhao Q. Predicting drug-induced liver injury using graph attention mechanism and molecular fingerprints. Methods 2024; 221:18-26. [PMID: 38040204 DOI: 10.1016/j.ymeth.2023.11.014] [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: 10/21/2023] [Revised: 11/14/2023] [Accepted: 11/25/2023] [Indexed: 12/03/2023] Open
Abstract
Drug-induced liver injury (DILI) is a significant issue in drug development and clinical treatment due to its potential to cause liver dysfunction or damage, which, in severe cases, can lead to liver failure or even fatality. DILI has numerous pathogenic factors, many of which remain incompletely understood. Consequently, it is imperative to devise methodologies and tools for anticipatory assessment of DILI risk in the initial phases of drug development. In this study, we present DMFPGA, a novel deep learning predictive model designed to predict DILI. To provide a comprehensive description of molecular properties, we employ a multi-head graph attention mechanism to extract features from the molecular graphs, representing characteristics at the level of compound nodes. Additionally, we combine multiple fingerprints of molecules to capture features at the molecular level of compounds. The fusion of molecular fingerprints and graph features can more fully express the properties of compounds. Subsequently, we employ a fully connected neural network to classify compounds as either DILI-positive or DILI-negative. To rigorously evaluate DMFPGA's performance, we conduct a 5-fold cross-validation experiment. The obtained results demonstrate the superiority of our method over four existing state-of-the-art computational approaches, exhibiting an average AUC of 0.935 and an average ACC of 0.934. We believe that DMFPGA is helpful for early-stage DILI prediction and assessment in drug development.
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Affiliation(s)
- Jifeng Wang
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan 114051, China
| | - Li Zhang
- School of Life Science, Liaoning University, Shenyang 110036, China
| | - Jianqiang Sun
- School of Information Science and Engineering, Linyi University, Linyi 276000, China
| | - Xin Yang
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan 114051, China
| | - Wei Wu
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan 114051, China
| | - Wei Chen
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan 114051, China.
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Zekri A, Harkati D, Kenouche S, Saleh BA, Alnajjar R. A computational study of potent series of selective estrogen receptor degraders for breast cancer therapy. J Biomol Struct Dyn 2023; 41:11078-11100. [PMID: 36537313 DOI: 10.1080/07391102.2022.2159877] [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: 03/28/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
A detailed multistep framework combining quantitative structure-activity relationship, global reactivity, absorption, distribution, metabolism and elimination properties, molecular docking and molecular dynamics simulation (MD) on a series of Selective Estrogen Receptor Down-Regulators (SERDs) interacting with Estrogen Receptor α (ERα) has been performed. The partial least squares regression method derived an empirical model with better predictive capability. The results of global reactivity descriptors revealed that all the compounds are considered strong electrophiles, allowing them to participate in polar reactions more easily. The Brain Or IntestinaL EstimateD permeation diagram revealed that compounds 49 and 31 were predicted to be well absorbed by the human gastrointestinal tract and would not enter the brain. The elucidation of the binding mode between the most active compounds that comply with Lipinski's and Veber's rules from the dataset and ERα targets was explored by molecular docking. The MD simulations were performed for 100 ns on the best compounds, which indicated their stability state under dynamics simulations. These findings are expected to help predict the anticancer activities of the studied SERD compounds and better understand their binding mechanism with ERα targets.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Afaf Zekri
- Group of Computational and Pharmaceutical Chemistry, LMCE Laboratory, University of Biskra, Biskra, Algeria
| | - Dalal Harkati
- Group of Computational and Pharmaceutical Chemistry, LMCE Laboratory, University of Biskra, Biskra, Algeria
| | - Samir Kenouche
- Group of Modeling of Chemical Systems Using Quantum Calculations, Applied Chemistry Laboratory, University of Biskra, Biskra, Algeria
| | - Basil A Saleh
- Department of Chemistry, College of Science, University of Basrah, Basrah, Iraq
| | - Radwan Alnajjar
- Department of Chemistry, Faculty of Science, University of Benghazi, Benghazi, Libya
- Department of Chemistry, University of Cape Town, Rondebosch, South Africa
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Hadni H, Elhallaoui M. Discovery of anti-colon cancer agents targeting wild-type and mutant p53 using computer-aided drug design. J Biomol Struct Dyn 2023; 41:10171-10189. [PMID: 36533393 DOI: 10.1080/07391102.2022.2153919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022]
Abstract
Mutations in the p53 gene are common and occur in over 50% of all cancers, as it is involved in DNA damage repair, cell cycle regulation and apoptosis. Moreover, the p53 gene is mutated in 70% of colon cancers. Therefore, the development of drugs to combat this mutation requires urgent attention. With this in mind, in silico drug design approaches were applied on quinoline derivatives with anticancer activity. In 3D-QSAR study, steric, electrostatic, hydrophobic and H-bond acceptor fields (SEHA) play an important role in prediction and design of new colon cancer compounds. Indeed, the two best CoMSIA/SEHA models with (Q2 = 0.737, R2 = 0.914, R pred 2 = 0.720) and (Q2 = 0.738, R2 = 0.919, R pred 2 = 0.739) show good prediction of human colon carcinoma HCT 116 (p53+/+) and (p53-/-) activities, respectively. Furthermore, the predictive ability and robustness of these models were tested by several validation methods. Molecular docking analyses reveal crucial interactions with the active sites of the p53 protein in both wild type and mutant. Based on these theoretical studies, we designed 10 new compounds with good anticancer activity potential, which were evaluated using ADMET properties. Molecular dynamics simulations were performed to confirm the detailed binding mode of the docking results. Finally, the MM-GBSA based on molecular dynamics simulation confirmed that the designed compounds were able to form stable hydrogen bonding interactions with the crucial residues, which are essential to overcome the p53 mutation in colon cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hanine Hadni
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Menana Elhallaoui
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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10
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Chatterjee M, Roy K. "Data fusion" quantitative read-across structure-activity-activity relationships (q-RASAARs) for the prediction of toxicities of binary and ternary antibiotic mixtures toward three bacterial species. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132129. [PMID: 37506640 DOI: 10.1016/j.jhazmat.2023.132129] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/28/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023]
Abstract
Antibiotics are often found in the environment as pollutants. They are usually found as mixtures in the environment and may produce toxicity against different ecological species due to joint exposure in the sub-optimal range. Sometimes the degradation products of parent chemicals also interact with it and cause mixture toxicity. In this study, we have developed three different mixture-Quantitative Structure-Activity Relationship (mixture-QSAR) models for three different bacterial species (Vibrio fischeri, Escherichia coli, and Bacillus subtilis). The toxicity data were collected from a previous experimental report in the literature, which comprised binary and ternary mixtures of sulfonamides (SAs), sulfonamide potentiators (SAPs), and tetracyclines (TCs). We have also explored the interspecies modeling to find inter-correlation among the toxicity of these studied organisms and have developed quantitative structure activity-activity relationship (QSAAR) models by employing the "data fusion" quantitative read-across structure-activity-activity relationship (q-RASAAR) and partial least squares (PLS) regression algorithms. All the models are strictly validated using both internal and external validation tests as suggested in the OECD guidelines. Three different mixing rules have been used in this study for descriptor computations to incorporate the additive and interaction effects among the mixture components. To the best of our knowledge, this is the first report of interspecies mixture toxicity models which can predict the cellular toxicity of binary and ternary mixtures against any of the three above-mentioned organisms.
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Affiliation(s)
- Mainak Chatterjee
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Kunal Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India.
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Wu JQ, Gong XQ, Wang Q, Yan F, Li JJ. A QSPR study for predicting θ(LCST) and θ(UCST) in binary polymer solutions. Chem Eng Sci 2023. [DOI: 10.1016/j.ces.2022.118326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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12
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Tabti K, Baammi S, Sbai A, Maghat H, Lakhlifi T, Bouachrine M. Molecular modeling study of pyrrolidine derivatives as novel myeloid cell leukemia-1 inhibitors through combined 3D-QSAR, molecular docking, ADME/Tox and MD simulation techniques. J Biomol Struct Dyn 2023; 41:13798-13814. [PMID: 36841617 DOI: 10.1080/07391102.2023.2183032] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 02/15/2023] [Indexed: 02/27/2023]
Abstract
A series of pyrrolidine derivatives have been used to study the main structural requirements for designing novel Mcl-1 inhibitors. For this purpose, three models CoMSIA, CoMFA and HQSAR were generated using QSAR molecular modeling techniques. The statistical results of the CoMFA (Q2 = 0.689; R = 0.999; R2pred = 0.986), CoMSIA (Q2 = 0.614; R2 = 0.923; R2pred = 0.815) and HQSAR (Q2= 0.603; R2 = 0.662; R2pred = 0.743) models showed good stability and predictability. The results of the models were presented as contours and colored fragments indicating the favorable and unfavorable contribution to the inhibitory activity of Mcl-1. Based on the obtained results, four new compounds were designed with more potent predicted pIC50 inhibitory activity. The ADME/Tox results and the pharmacokinetic properties revealed that these four compounds are orally bioavailable and show good permeability. In addition the four compounds showing non-inhibitors of CYP3A4 and CYP2D6 with the exception of Pred03. At the level of toxicity profile, the compounds Pred01, Pred02 and Pred03 showed interesting results and showed no AMES toxicity, no hERG inhibition and no skin sensitization. Molecular docking results were used to uncover the mode of interaction between the ligand and key residues of protein binding site. Molecular docking results were supported by molecular simulation and binding free energy estimation (MMPBSA). These results demonstrate the stability of the analyzed compounds in the target protein binding site during a 100 ns trajectory. Finally, all these results create a strong lead to develop promising new Pyrrolidine-based inhibitors against Mcl-1.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kamal Tabti
- Molecular Chemistry and Natural Substances Laboratory, Moulay Ismail University, Faculty of Science, Meknes, Morocco
| | - Soukayna Baammi
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Abdelouahid Sbai
- Molecular Chemistry and Natural Substances Laboratory, Moulay Ismail University, Faculty of Science, Meknes, Morocco
| | - Hamid Maghat
- Molecular Chemistry and Natural Substances Laboratory, Moulay Ismail University, Faculty of Science, Meknes, Morocco
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory, Moulay Ismail University, Faculty of Science, Meknes, Morocco
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory, Moulay Ismail University, Faculty of Science, Meknes, Morocco
- High School of Technology Khenifra, Sultan Moulay Sliman University, Benimellal, Morocco
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Hadni H, Bakhouch M, Elhallaoui M. 3D-QSAR, molecular docking, DFT and ADMET studies on quinazoline derivatives to explore novel DHFR inhibitors. J Biomol Struct Dyn 2023; 41:161-175. [PMID: 34825630 DOI: 10.1080/07391102.2021.2004233] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Resistance to folate antagonists is caused by mutations in the dihydrofolate reductase (DHFR) genes. These mutations affect the amino acids at positions 51, 59, 108 and 164 of DHFR, which appear to play a major role in malaria treatment failure. Therefore, the design of new drugs able to overcome the problem of antifolate drug resistance should receive urgent attention. In this study, a three-dimensional quantitative structure-activity relationship (3 D-QSAR) and molecular docking studies have been performed on antimalarial quinazoline derivatives. The CoMFA (Q2 = 0.63, R2 = 0.83 and Rpred2 = 0.70) and the CoMSIA (Q2 = 0.584, R2 = 0.816, and Rpred2= 0.73) models show a good prediction of antimalarial activity. The reliability and robustness of the proposed models have been tested using several validation methods, which showed that the steric, electrostatic, hydrophobic and H-bond acceptor fields of the CoMSIA model play a key role in the prediction of antimalarial activity. Molecular docking studies reveal important interactions between two isomeric compounds (meta and para) and the DHFR receptor in its wild and mutant forms. The obtained outcomes of molecular docking studies have been validated using a new method based on visual inspection. The DFT study of the two isomeric compounds confirms clearly the trends of 3 D-QSAR and molecular docking for the design of new compounds. Moreover, the consistency between theoretical, 3 D-QSAR and molecular docking analysis provides guidance for the design of new drug candidates, which have been tested using ADMET properties and drug likeness analysis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hanine Hadni
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohamed Bakhouch
- Laboratory of Bioorganic Chemistry, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, El Jadida, Morocco.,Engineering Laboratory of Organometallic and Molecular Materials and Environment, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Menana Elhallaoui
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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14
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Hedayatnasab Z, Ramazani Saadatabadi A, Shirgahi H, Mozafari M. Heat induction of iron oxide nanoparticles with rational artificial neural network design-based particle swarm optimization for magnetic cancer hyperthermia. MATERIALS RESEARCH BULLETIN 2023; 157:112035. [DOI: 10.1016/j.materresbull.2022.112035] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
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15
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Akash S, Hossain A, Mukerjee N, Sarker MMR, Khan MF, Hossain MJ, Rashid MA, Kumer A, Ghosh A, León-Figueroa DA, Barboza JJ, Padhi BK, Sah R. Modified coptisine derivatives as an inhibitor against pathogenic Rhizomucor miehei, Mycolicibacterium smegmatis (Black Fungus), Monkeypox, and Marburg virus by molecular docking and molecular dynamics simulation-based drug design approach. Front Pharmacol 2023; 14:1140494. [PMID: 37153804 PMCID: PMC10154673 DOI: 10.3389/fphar.2023.1140494] [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: 01/09/2023] [Accepted: 03/29/2023] [Indexed: 05/10/2023] Open
Abstract
During the second phase of SARS-CoV-2, an unknown fungal infection, identified as black fungus, was transmitted to numerous people among the hospitalized COVID-19 patients and increased the death rate. The black fungus is associated with the Mycolicibacterium smegmatis, Mucor lusitanicus, and Rhizomucor miehei microorganisms. At the same time, other pathogenic diseases, such as the Monkeypox virus and Marburg virus, impacted global health. Policymakers are concerned about these pathogens due to their severe pathogenic capabilities and rapid spread. However, no standard therapies are available to manage and treat those conditions. Since the coptisine has significant antimicrobial, antiviral, and antifungal properties; therefore, the current investigation has been designed by modifying coptisine to identify an effective drug molecule against Black fungus, Monkeypox, and Marburg virus. After designing the derivatives of coptisine, they have been optimized to get a stable molecular structure. These ligands were then subjected to molecular docking study against two vital proteins obtained from black fungal pathogens: Rhizomucor miehei (PDB ID: 4WTP) and Mycolicibacterium smegmatis (PDB ID 7D6X), and proteins found in Monkeypox virus (PDB ID: 4QWO) and Marburg virus (PDB ID 4OR8). Following molecular docking, other computational investigations, such as ADMET, QSAR, drug-likeness, quantum calculation and molecular dynamics, were also performed to determine their potentiality as antifungal and antiviral inhibitors. The docking score reported that they have strong affinities against Black fungus, Monkeypox virus, and Marburg virus. Then, the molecular dynamic simulation was conducted to determine their stability and durability in the physiological system with water at 100 ns, which documented that the mentioned drugs were stable over the simulated time. Thus, our in silico investigation provides a preliminary report that coptisine derivatives are safe and potentially effective against Black fungus, Monkeypox virus, and Marburg virus. Hence, coptisine derivatives may be a prospective candidate for developing drugs against Black fungus, Monkeypox and Marburg viruses.
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Affiliation(s)
- Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Arafat Hossain
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Nobendu Mukerjee
- Department of Microbiology, West Bengal State University, Kolkata, West Bengal, India
- Department of Health Sciences, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Md. Moklesur Rahman Sarker
- Health Med. Science Research Network, Dhaka, Bangladesh
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
| | | | - Md. Jamal Hossain
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
| | - Mohammad A. Rashid
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Ajoy Kumer
- Laboratory of Computational Research for Drug Design and Material Science, Department of Chemistry, European University of Bangladesh, Dhaka, Bangladesh
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, Assam, India
| | | | - Joshuan J. Barboza
- Escuela de Medicina, Universidad Cesar Vallejo, Trujillo, Peru
- *Correspondence: Joshuan J. Barboza, ; Ranjit Sah,
| | - Bijaya Kumar Padhi
- Department of Community Medicine, School of Public Health, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ranjit Sah
- Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
- Dr. D.Y Patil Medical College, Hospital and Research Centre, Pune, Maharashtra, India
- Green City Hospital, Tokha, Nepal
- *Correspondence: Joshuan J. Barboza, ; Ranjit Sah,
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3D-QSAR, drug-likeness, ADMET prediction, and molecular docking studies in silico of novel 5-oxo-1-thioxo-4,5-dihydro-1H-thiazolo[3,4-a]quinazoline derivatives as MALT1 protease inhibitors for the treatment of B cell lymphoma. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02627-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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17
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Ghasemi Gol A, Akbari J, Khalaj M, Mahmoud Mousavi-Safavi S, Esfahani S, Farahan N. DFT Investigation of a Zn-Doped Carbon Nanocone for the Drug Delivery of Methylated Aspirins. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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18
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Daghighi A, Casanola-Martin GM, Timmerman T, Milenković D, Lučić B, Rasulev B. In Silico Prediction of the Toxicity of Nitroaromatic Compounds: Application of Ensemble Learning QSAR Approach. TOXICS 2022; 10:toxics10120746. [PMID: 36548579 PMCID: PMC9786026 DOI: 10.3390/toxics10120746] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/10/2022] [Accepted: 11/28/2022] [Indexed: 06/02/2023]
Abstract
In this work, a dataset of more than 200 nitroaromatic compounds is used to develop Quantitative Structure-Activity Relationship (QSAR) models for the estimation of in vivo toxicity based on 50% lethal dose to rats (LD50). An initial set of 4885 molecular descriptors was generated and applied to build Support Vector Regression (SVR) models. The best two SVR models, SVR_A and SVR_B, were selected to build an Ensemble Model by means of Multiple Linear Regression (MLR). The obtained Ensemble Model showed improved performance over the base SVR models in the training set (R2 = 0.88), validation set (R2 = 0.95), and true external test set (R2 = 0.92). The models were also internally validated by 5-fold cross-validation and Y-scrambling experiments, showing that the models have high levels of goodness-of-fit, robustness and predictivity. The contribution of descriptors to the toxicity in the models was assessed using the Accumulated Local Effect (ALE) technique. The proposed approach provides an important tool to assess toxicity of nitroaromatic compounds, based on the ensemble QSAR model and the structural relationship to toxicity by analyzed contribution of the involved descriptors.
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Affiliation(s)
- Amirreza Daghighi
- Biomedical Engineering Program, North Dakota State University, Fargo, ND 58105, USA
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND 58102, USA
| | | | - Troy Timmerman
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND 58102, USA
- Department of Computer Science, North Dakota State University, Fargo, ND 58105, USA
| | - Dejan Milenković
- Department of Science, Institute for Information Technologies, University of Kragujevac, 34000 Kragujevac, Serbia
| | - Bono Lučić
- NMR Centre, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Bakhtiyor Rasulev
- Biomedical Engineering Program, North Dakota State University, Fargo, ND 58105, USA
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND 58102, USA
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Ahmadi S, Abdolmaleki A, Jebeli Javan M. In silico study of natural antioxidants. VITAMINS AND HORMONES 2022; 121:1-43. [PMID: 36707131 DOI: 10.1016/bs.vh.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Antioxidants are the body's defense system against the damage of reactive oxygen species, which are usually produced in the body through various physiological processes. There are various sources of these antioxidants such as endogenous antioxidants in the body and exogenous food sources. This chapter provides important information on methods used to investigate antioxidant activity and sources of plant antioxidants. Over the past two decades, numerous studies have demonstrated the importance of in silico research in the development of novel natural and synthesized antioxidants. In silico methods such as quantitative structure-activity relationships (QSAR), pharmacophore, docking, and virtual screenings are play critical roles in designing effective antioxidants that may be synthesized and tested later. This chapter introduces the available in silico approaches for different classes of antioxidants. Many successful applications of in silico methods in the development and design of novel antioxidants are thoroughly discussed. The QSAR, pharmacophore, molecular docking techniques, and virtual screenings process summarized here would help readers to find out the proper mechanism for the interaction between the free radicals and antioxidant compounds. Furthermore, this chapter focuses on introducing new QSAR models in combination with other in silico methods to predict antioxidants activity and design more active antioxidants. In silico studies are essential to explore largely unknown plant tissue, food sources for antioxidant synthesis, as well as saving time and money in such studies.
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Affiliation(s)
- Shahin Ahmadi
- Department of Chemistry, Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Azizeh Abdolmaleki
- Department of Chemistry, Tuyserkan Branch, Islamic Azad University, Tuyserkan, Iran
| | - Marjan Jebeli Javan
- Department of Chemistry, Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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20
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Hadni H, Elhallaouia M. In silico design of EGFRL858R/T790M/C797S inhibitors via 3D-QSAR, molecular docking, ADMET properties and molecular dynamics simulations. Heliyon 2022; 8:e11537. [DOI: 10.1016/j.heliyon.2022.e11537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/24/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
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21
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Diéguez-Santana K, Nachimba-Mayanchi MM, Puris A, Gutiérrez RT, González-Díaz H. Prediction of acute toxicity of pesticides for Americamysis bahia using linear and nonlinear QSTR modelling approaches. ENVIRONMENTAL RESEARCH 2022; 214:113984. [PMID: 35981614 DOI: 10.1016/j.envres.2022.113984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/19/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Globally, pesticides are toxic substances with wide applications. However, the widespread use of pesticides has received increasing attention from regulatory agencies due to their various acute and chronic effects on multiple organisms. In this study, Quantitative Structure-Toxicity Relationship (QSTR) models were established using Multiple Linear Regression (MLR) and five Machine Learning (ML) algorithms to predict pesticide toxicity in Americamysis bahia. The most influential descriptors included in the MLR model are RBF, JGI2, nCbH, nRCOOR, nRSR, nPO4 and 'Cl-090', with positive contributions to the dependent variable (negative decimal logarithm of median lethal concentration at 96-h). The Random Forest (RF) regression model was superior amongst the five ML models. We observed higher values of R2 (0.812) and lower values of RMSE (0.595) and MAE (0.462) in the cross-validation training set and external validation set. Similarly, this study had a high level of fitness and was internally robust and externally predictive compared to models presented in similar studies. The results suggest that the developed QSTR models are suitable for reliably predicting the aquatic toxicity of structurally diverse pesticides and can be used for screening, prioritising new pesticides, filling data gaps and overcoming the limitations of in vivo and in vitro tests.
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Affiliation(s)
- Karel Diéguez-Santana
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, 48940, Leioa, Spain; Universidad Regional Amazónica Ikiam, Tena, Ecuador.
| | | | - Amilkar Puris
- Facultad de Ciencias de la Ingeniería, Universidad Técnica Estatal de Quevedo, Ecuador
| | | | - Humberto González-Díaz
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, 48940, Leioa, Spain; Basque Center for Biophysics CSIC-UPVEH, University of Basque Country UPV/EHU, 48940, Leioa, Spain; IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Biscay, Spain
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22
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Zang J, Liu M, Liu H, Ding L. A molecular simulation study of hepatitis B virus core protein and the nuclear protein allosteric modulators of phthalazinone derivatives. Phys Chem Chem Phys 2022; 24:23209-23225. [PMID: 36129214 DOI: 10.1039/d2cp02946d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hepatitis B virus, causing hepatitis, cirrhosis, liver failure, and liver cancer, poses a serious threat to human health, and the currently approved drugs still cannot eliminate the virus completely. HBV core protein allosteric modulators (CpAMs) with a phthalazinone structure which targets the HBV core (HBc) protein have been seen as a new kind of drug because of their excellent antiviral effects. This study explores the structure-activity relationship and binding mechanism of phthalazinone molecules through three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking, molecular dynamics, and binding free energy calculation and decomposition studies. In addition, CoMFA and CoMSIA models revealed that the steric field, the hydrophobic field, and the hydrogen bond acceptor field may play important roles in the binding process. The molecular docking and dynamics disclosed the most likely binding pose of phthalazinone derivatives with the HBc protein. The binding free energy calculation and decomposition analysis indicated that the van der Waals force was the driving force and that ValE124, ThrD109, ThrE128, LeuD140, IleD105, PheD110, ThrD33, and TrpD102 were the key residues. This study provides an important theoretical basis for the design and optimization of phthalazinone compounds.
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Affiliation(s)
- Jieying Zang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, P. R. China.
| | - Min Liu
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, P. R. China.
| | - Huan Liu
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, P. R. China.
| | - Lina Ding
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, P. R. China.
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Investigation of [3H]diazepam derivatives as allosteric modulators of GABAA receptor α1β2γ2 subtypes: combination of molecular docking/dynamic simulations, pharmacokinetics/drug-likeness prediction, and QSAR analysis. Struct Chem 2022; 34:791-823. [PMID: 35971551 PMCID: PMC9365687 DOI: 10.1007/s11224-022-02029-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022]
Abstract
In this paper, a data set of [3H] diazepam derivatives was analyzed using various computational methods: molecular docking/dynamic simulations, and QSAR analysis. The main aims of these studies are to understand the binding mechanisms by which benzodiazepines allosterically modulate GABAA receptor α1β2γ2 subtypes, from inducing neuronal inhibition at lower doses to the anesthetic effect at higher doses, and also, to define the structural requirements that contribute to improving the response of GABAA/α1β2γ2 receptor to benzodiazepine drugs. The results of the molecular docking study allowed selecting Ro12-6377 and proflazepam as the best modulators for the four binding sites simultaneously. Subsequently, the stability of the selected complexes was investigated by performing molecular dynamics simulation. The latter confirmed the features of both modulators to exert direct effects on the chloride-channel lining residues. Pharmacokinetics and drug-likeness profile were assessed through in silico tool. Furthermore, a QSAR analysis was conducted using an improved vemolecular dynamics simulations proposed byrsion of PLS regression. The goodness of fit and the predictive power of the resulting PLS model were estimated according to internal and external validation parameters: R2 = 0.632, R2adj = 0.584, F = 12.806; p-value = 6.2050e − 07, Q2loo = 0.639, and Q2F3 = 0.813. Clearly, the obtained results ensure the predictive ability of the developed QSAR model for the design of new high-potency benzodiazepine drugs.
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De P, Kumar V, Kar S, Roy K, Leszczynski J. Repurposing FDA approved drugs as possible anti-SARS-CoV-2 medications using ligand-based computational approaches: sum of ranking difference-based model selection. Struct Chem 2022; 33:1741-1753. [PMID: 35692512 PMCID: PMC9171098 DOI: 10.1007/s11224-022-01975-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 12/19/2022]
Abstract
The worldwide burden of coronavirus disease 2019 (COVID-19) is still unremittingly prevailing, with more than 440 million infections and over 5.9 million deaths documented so far since the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic. The non-availability of treatment further aggravates the scenario, thereby demanding the exploration of pre-existing FDA-approved drugs for their effectiveness against COVID-19. The current research aims to identify potential anti-SARS-CoV-2 drugs using a computational approach and repurpose them if possible. In the present study, we have collected a set of 44 FDA-approved drugs of different classes from a previously published literature with their potential antiviral activity against COVID-19. We have employed both regression- and classification-based quantitative structure–activity relationship (QSAR) modeling to identify critical chemical features essential for anticoronaviral activity. Multiple models with the consensus algorithm were employed for the regression-based approach to improve the predictions. Additionally, we have employed a machine learning-based read-across approach using Read-Across-v3.1 available from https://sites.google.com/jadavpuruniversity.in/dtc-lab-software/home and linear discriminant analysis for the efficient prediction of potential drug candidate for COVID-19. Finally, the quantitative prediction ability of different modeling approaches was compared using the sum of ranking differences (SRD). Furthermore, we have predicted a true external set of 98 pharmaceuticals using the developed models for their probable anti-COVID activity and their prediction reliability was checked employing the “Prediction Reliability Indicator” tool available from https://dtclab.webs.com/software-tools. Though the present study does not target any protein of viral interaction, the modeling approaches developed can be helpful for identifying or screening potential anti-coronaviral drug candidates.
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Affiliation(s)
- Priyanka De
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata-700032, India
| | - Vinay Kumar
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata-700032, India
| | - Supratik Kar
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217 USA
| | - Kunal Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata-700032, India
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217 USA
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In Silico Antiprotozoal Evaluation of 1,4-Naphthoquinone Derivatives against Chagas and Leishmaniasis Diseases Using QSAR, Molecular Docking, and ADME Approaches. Pharmaceuticals (Basel) 2022; 15:ph15060687. [PMID: 35745607 PMCID: PMC9228275 DOI: 10.3390/ph15060687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 12/04/2022] Open
Abstract
Chagas and leishmaniasis are two neglected diseases considered as public health problems worldwide, for which there is no effective, low-cost, and low-toxicity treatment for the host. Naphthoquinones are ligands with redox properties involved in oxidative biological processes with a wide variety of activities, including antiparasitic. In this work, in silico methods of quantitative structure–activity relationship (QSAR), molecular docking, and calculation of ADME (absorption, distribution, metabolism, and excretion) properties were used to evaluate naphthoquinone derivatives with unknown antiprotozoal activity. QSAR models were developed for predicting antiparasitic activity against Trypanosoma cruzi, Leishmania amazonensis, and Leishmania infatum, as well as the QSAR model for toxicity activity. Most of the evaluated ligands presented high antiparasitic activity. According to the docking results, the family of triazole derivatives presented the best affinity with the different macromolecular targets. The ADME results showed that most of the evaluated compounds present adequate conditions to be administered orally. Naphthoquinone derivatives show good biological activity results, depending on the substituents attached to the quinone ring, and perhaps the potential to be converted into drugs or starting molecules.
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In silico design of novel PIN1 inhibitors by combined of 3D-QSAR, molecular docking, molecular dynamic simulation and ADMET studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132291] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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De P, Kar S, Ambure P, Roy K. Prediction reliability of QSAR models: an overview of various validation tools. Arch Toxicol 2022; 96:1279-1295. [PMID: 35267067 DOI: 10.1007/s00204-022-03252-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/14/2022] [Indexed: 01/20/2023]
Abstract
The reliability of any quantitative structure-activity relationship (QSAR) model depends on multiple aspects such as the accuracy of the input dataset, selection of significant descriptors, the appropriate splitting process of the dataset, statistical tools used, and most notably on the measures of validation. Validation, the most crucial step in QSAR model development, confirms the reliability of the developed QSAR models and the acceptability of each step in the model development. The present review deals with various validation tools that involve multiple techniques that improve the model quality and robustness. The double cross-validation tool helps in building improved quality models using different combinations of the same training set in an inner cross-validation loop. This exhaustive method is also integrated for small datasets (< 40 compounds) in another tool, namely the small dataset modeler tool. The main aim of QSAR researchers is to improve prediction quality by lowering the prediction errors for the query compounds. 'Intelligent' selection of multiple models and consensus predictions integrated in the intelligent consensus predictor tool were found to be more externally predictive than individual models. Furthermore, another tool called Prediction Reliability Indicator was explained to understand the quality of predictions for a true external set. This tool uses a composite scoring technique to identify query compounds as 'good' or 'moderate' or 'bad' predictions. We have also discussed a quantitative read-across tool which predicts a chemical response based on the similarity with structural analogues. The discussed tools are freely available from https://dtclab.webs.com/software-tools or http://teqip.jdvu.ac.in/QSAR_Tools/DTCLab/ and https://sites.google.com/jadavpuruniversity.in/dtc-lab-software/home (for read-across).
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Affiliation(s)
- Priyanka De
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Supratik Kar
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS, 39217, USA
| | | | - Kunal Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
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User-assisted methodology targeted for building structure interpretable QSPR models for boosting CO2 capture with ionic liquids. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Mukherjee RK, Kumar V, Roy K. Chemometric modeling of plant protection products (PPPs) for the prediction of acute contact toxicity against honey bees (A. mellifera): A 2D-QSAR approach. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127230. [PMID: 34844352 DOI: 10.1016/j.jhazmat.2021.127230] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Abstract
Honey bees (Apis mellifera) are vital for economic, viable agriculture and for food safety. Although Plant Protection Products (PPPs) are of undeniable importance in the global agricultural system, these have become potential threats for non-target organisms like pollinators (e.g., honey bees etc.), resulting in the disruption of the ecological balance. In the current work, we have used the 113 PPP analogs to develop a 2D-QSAR model and explored the structural features modulating the toxic effects on honey bees, following the Organization for Economic Co-operation and Development (OECD) guidelines. The extensive validation of the developed model has been performed using internal and external validation metrics to make sure that the model is statistically sound and interpretable enough to be acceptable. The obtained results (R2 = 0.666, Q2 = 0.594, Q2F1 = 0.647 and Q2F2 = 0.646) determine the predictability and reliability of the developed model. This model should be useful for the predictions (acute contact toxicity (LD50)) of the new and untested compounds located inside the applicability domain of the developed model. Moreover, we have performed the in-silico prediction of toxicity against honey bees of a total of 709 compounds obtained from the pesticide properties database (PPDB) using the developed model.
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Affiliation(s)
- Rajendra Kumar Mukherjee
- Drug Theoretics and Cheminformatics (DTC) Laboratory,Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Vinay Kumar
- Drug Theoretics and Cheminformatics (DTC) Laboratory,Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Kunal Roy
- Drug Theoretics and Cheminformatics (DTC) Laboratory,Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India.
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Mukherjee RK, Kumar V, Roy K. Ecotoxicological QSTR and QSTTR Modeling for the Prediction of Acute Oral Toxicity of Pesticides against Multiple Avian Species. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:335-348. [PMID: 34905924 DOI: 10.1021/acs.est.1c05732] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The ever-increasing use of pesticides in response to the rising agricultural demand has threatened the existence of nontarget organisms like avian species, disrupting the global ecological integrity. Therefore, it is critical to protect and restore different endangered bird species from the perspective of ecosystem safety. In the present work, we have developed regression-based two-dimensional quantitative structure toxicity relationship (2D QSTR) and quantitative structure toxicity-toxicity relationship (QSTTR) models to estimate the toxicity of pesticides on five different avian species following the Organization for Economic Co-operation and Development (OECD) guidelines. Rigorous validation has been performed using different statistical internal and external validation parameters to ensure the robustness and interpretability of the developed models. From the developed models, it can be stated that the presence of electronegative and lipophilic features greatly enhance pesticide toxicity, whereas the hydrophilic characters are shown to have a detrimental impact on the toxicity of pesticides. Moreover, the developed QSTTR models have been employed to the in silico toxicity prediction of 124, 154, and 250 pesticides against bobwhite quail, ring-necked pheasant, and mallard duck species, respectively, extracted from the Office of Pesticides Program (OPP) Pesticide Ecotoxicity Database. The information obtained from the modeled descriptors might be used for pesticide risk assessment in the future, with the added benefit of providing an early caution of their possible negative impact on birds for regulatory purposes.
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Affiliation(s)
- Rajendra Kumar Mukherjee
- Drug Theoretics and Cheminformatics (DTC) Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Vinay Kumar
- Drug Theoretics and Cheminformatics (DTC) Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Kunal Roy
- Drug Theoretics and Cheminformatics (DTC) Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
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31
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Khaldan A, Bouamrane S, El-mernissi R, Alaqarbeh M, Hajji H, Alsakhen N, Maghat H, Ajana MA, Sbai A, Bouachrine M, Lakhlifi T. Computational study of quinoline-based thiadiazole compounds as potential antileishmanial inhibitors. NEW J CHEM 2022. [DOI: 10.1039/d2nj03253h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Leishmaniasis is a severe disease caused by protozoan parasites of the genus Leishmania and it is accountable for sizable morbidity and mortality worldwide.
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Affiliation(s)
- Ayoub Khaldan
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Soukaina Bouamrane
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Reda El-mernissi
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Marwa Alaqarbeh
- National Agricultural Research Center, Al-Baqa 19381, Jordan
| | - Halima Hajji
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Nada Alsakhen
- The Hashemite University, Department of Chemistry, Faculty of Science, Zarqa, Jordan
| | - Hamid Maghat
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Mohammed Aziz Ajana
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Abdelouahid Sbai
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
- EST Khenifra, Sultan Moulay Sliman University, Benimellal, Morocco
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
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32
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Gheidari D, Mehrdad M, Ghahremani M. Azole Compounds as Inhibitors of Candida albicans: QSAR Modelling. Front Chem 2021; 9:774416. [PMID: 34912782 PMCID: PMC8667819 DOI: 10.3389/fchem.2021.774416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 11/03/2021] [Indexed: 01/13/2023] Open
Abstract
Candida albicans is a pathogenic opportunistic yeast found in the human gut flora. It may also live outside of the human body, causing diseases ranging from minor to deadly. Candida albicans begins as a budding yeast that can become hyphae in response to a variety of environmental or biological triggers. The hyphae form is responsible for the development of multidrug resistant biofilms, despite the fact that both forms have been associated to virulence Here, we have proposed a linear and SPA-linear quantitative structure activity relationship (QSAR) modeling and prediction of Candida albicans inhibitors. A data set that consisted of 60 derivatives of benzoxazoles, benzimidazoles, oxazolo (4, 5-b) pyridines have been used. In this study, that after applying the leverage analysis method to detect outliers' molecules, the total number of these compounds reached 55. SPA-MLR model shows superiority over the multiple linear regressions (MLR) by accounting 90% of the Q 2 of anti-fungus derivatives 'activity. This paper focuses on investigating the role of SPA-MLR in developing model. The accuracy of SPA-MLR model was illustrated using leave-one-out (LOO). The mean effect of descriptors and sensitivity analysis show that RDF090u is the most important parameter affecting the as behavior of the inhibitors of Candida albicans.
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Affiliation(s)
- Davood Gheidari
- Department of Chemistry, Faculty of Science, University of Guilan, Rasht, Iran
| | - Morteza Mehrdad
- Department of Chemistry, Faculty of Science, University of Guilan, Rasht, Iran
| | - Mahboubeh Ghahremani
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
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Shahin R, Al-Hashimi NN, Daoud NEH, Aljamal S, Shaheen O. QSAR-guided pharmacophoric modeling reveals important structural requirements for Polo kinase 1 (Plk1) inhibitors. J Mol Graph Model 2021; 109:108022. [PMID: 34562852 DOI: 10.1016/j.jmgm.2021.108022] [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: 04/14/2021] [Revised: 09/02/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
Targeting Polo-like kinase 1 (Plk1) by molecular inhibitors is being a promising approach for tumor therapy. Nevertheless, insufficient methodical analyses have been done to characterize the interactions inside the Plk1 binding pocket. In this study, an extensive combined ligand and structure-based drug design workflow was conducted to data-mine the structural requirements for Plk1 inhibition. Consequently, the binding modes of 368 previously known Plk1 inhibitors were investigated by pharmacophore generation technique. The resulted pharmacophores were engaged in the context of Genetic function algorithm (GFA) and Multiple linear regression (MLR) analyses to search for a prognostic QSAR model. The most successful QSAR model was with statistical criteria of (r2277 = 0.76, r2adj = 0.76, r2pred = 0.75, Q2 = 0.73). Our QSAR-selected pharmacophores were validated by Receiver Operating Characteristic (ROC) curve analysis. Later on, the best QSAR model and its associated pharmacophoric hypotheses (HypoB-T4-5, HypoI-T2-7, HypoD-T4-3, and HypoC-T3-3) were used to identify new Plk1 inhibitory hits retrieved from the National Cancer Institute (NCI) database. The most potent hits exhibited experimental anti-Plk1 IC50 of 1.49, 3.79. 5.26 and 6.35 μM. Noticeably, our hits, were found to interact with the Plk1 kinase domain through some important amino acid residues namely, Cys67, Lys82, Cys133, Phe183, and Asp194.
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Affiliation(s)
- Rand Shahin
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, The Hashemite University, Zarqa, 13133, Jordan.
| | - Nabil N Al-Hashimi
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, The Hashemite University, Zarqa, 13133, Jordan.
| | - Nour El-Huda Daoud
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, The Hashemite University, Zarqa, 13133, Jordan.
| | - Salah Aljamal
- Faculty of Pharmacy, University of Jordan, Amman, Jordan.
| | - Omar Shaheen
- Department of Pharmacology, Faculty of Medicine, University of Jordan, Amman, Jordan.
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34
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Saavedra LM, Duchowicz PR. Predicting zebrafish (Danio rerio) embryo developmental toxicity through a non-conformational QSAR approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 796:148820. [PMID: 34328907 DOI: 10.1016/j.scitotenv.2021.148820] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/11/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
For many years, the frequent use of synthetic chemicals in the manufacture of veterinary drugs and plague control products has raised negative effects on human health and other non-target organisms, promoting the need to employ a practical and suitable methodology for early risk identification of several thousand commercial compounds. The zebrafish (Danio rerio) embryo has been emerged as one sustainable animal model for measuring developmental toxicity, an endpoint that is included in the regulatory procedures to approve chemicals, avoiding conventional and costly toxicity assays based on animal testing. In this context, the Quantitative Structure-Activity Relationships (QSAR) theory is applied to develop a predictive model based on a well-defined zebrafish embryo developmental toxicity database reported by the ToxCast™ Phase I chemical library of the Environmental Protection Agency (U.S. EPA). By means of four freely available softwares, a set with 28,038 non-conformational descriptors that encode the largest amount of permanent structural features are readily calculated. The Replacement Method (RM) variable subset selection technique provided the best regression models. Thereby, a linear QSAR model with proper statistical quality (Rtrain2 = 0.64, RMSEtrain = 0.49) is established in agreement with the Organization for Economic Co-operation and Development principles, accomplishing each internal (loo, l15 % o, VIF and Y-randomization) and external (Rtest2,Rm2, QF12, QF22, QF32 and CCC) validation criterion. The present QSAR approach provides a useful computational tool to estimate zebrafish developmental toxicity of new, untasted or hypothetical compounds, and it can contribute to the general lack of QSAR models in the literature to predict this endpoint.
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Affiliation(s)
- Laura M Saavedra
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), CONICET, UNLP, Diag. 113 y 64, C.C. 16, Sucursal 4, 1900 La Plata, Argentina.
| | - Pablo R Duchowicz
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), CONICET, UNLP, Diag. 113 y 64, C.C. 16, Sucursal 4, 1900 La Plata, Argentina.
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35
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Vincze A, Dargó G, Rácz A, Balogh GT. A corneal-PAMPA-based in silico model for predicting corneal permeability. J Pharm Biomed Anal 2021; 203:114218. [PMID: 34166924 DOI: 10.1016/j.jpba.2021.114218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 12/23/2022]
Abstract
The capability to predict corneal permeability based on physicochemical parameters has always been a desirable objective of ophthalmic drug development. However, previous work has been limited to cases where either the diversity of compounds used was lacking or the performance of the models was poor. Our study provides extensive quantitative structure-property relationship (QSPR) models for corneal permeability predictions. The models involved in vitro corneal permeability measurements of 189 diverse compounds. Preliminary analysis of data showed that there is no significant correlation between corneal-PAMPA (Parallel Artificial Membrane Permeability Assay) permeability values and other pharmacokinetically relevant in silico drug transport parameters like Caco-2, jejunal permeability and blood-brain partition coefficient (logBB). Two different QSPR models were developed: one for corneal permeability and one for corneal membrane retention, based on experimental corneal-PAMPA permeability data. Partial least squares regression was applied for producing the models, which contained classical molecular descriptors and ECFP fingerprints in combination. A complex validation protocol (including internal and external validation) was carried out to provide robust and appropriate predictions for the permeability and membrane retention values. Both models had an overall fit of R2 > 0.90, including R2-values not lower than 0.85 for validation runs, and provide quick and accurate predictions of corneal permeability values for a diverse set of compounds.
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Affiliation(s)
- Anna Vincze
- Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, Műegyetem Rakpart 3., 1111, Budapest, Hungary
| | - Gergő Dargó
- Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, Műegyetem Rakpart 3., 1111, Budapest, Hungary
| | - Anita Rácz
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2., 1117, Budapest, Hungary.
| | - György T Balogh
- Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, Műegyetem Rakpart 3., 1111, Budapest, Hungary; Department of Pharmacodynamics and Biopharmacy, University of Szeged, Eötvös u. 6., 6720, Szeged, Hungary.
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36
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Ishola AA, Adedirin O, Joshi T, Chandra S. QSAR modeling and pharmacoinformatics of SARS coronavirus 3C-like protease inhibitors. Comput Biol Med 2021; 134:104483. [PMID: 34020129 PMCID: PMC8111888 DOI: 10.1016/j.compbiomed.2021.104483] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/24/2021] [Accepted: 05/07/2021] [Indexed: 11/30/2022]
Abstract
The search for effective treatment against novel coronavirus (COVID-19) remains a global challenge due to controversies on available vaccines. In this study, data of SARS coronavirus 3C-like protease (3CLpro) inhibitors; a key drug target in the coronavirus genome was retrieved from CHEMBL database. Quantitative Structure-Activity Relationship (QSAR) studies, Molecular docking, Absorption-Distribution-Metabolism-Excretion-Toxicity (ADMET) and molecular dynamics simulation (MDS) were carried out using these 3CLpro inhibitors. QSAR model constructed using the data had correlation coefficient R2 value of 0.907; cross-validated correlation coefficient Q2 value of 0.866 and test set predicted correlation coefficient R2pred value of 0.517. Variance inflation factor (VIF) values for descriptors contained in the model ranged from 1.352 to 1.68, hence, these descriptors were orthogonal to one another. Therefore, the model was statistically significant and can be used to screen and design new molecules for their inhibitory activity against 3CLpro. Molecular docking showed that seven of the compounds (inhibitors) used in the study had a remarkable binding affinity (-9.2 to -10.3 kcal/mol) for 3CLpro. ADMET study revealed that five (CHEMBL Accession IDs 19438, 196635, 377150, 208763, and 210097) of the seven compounds with good binding ability obeyed Lipinski's rule of five. Hence, they were compounds with drug-like properties. MDS analysis revealed that 3CLpro-compound 21, 3CLpro-compound 22, 3CLpro-compound 40 complexes are very stable as compared to the reference 3CLpro-X77 complex. Therefore, this study identified three potent inhibitors of 3CLpro viz. CHEMBL194398, CHEMBL196635, and CHEMBL210097 that can be further explored for the treatment of COVID-19.
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Affiliation(s)
- Ahmed Adebayo Ishola
- Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Nigeria.
| | - Oluwaseye Adedirin
- Chemistry Advance Laboratory, Sheda Science and Technology Complex (SHESTCO), P.M.B. 186, Garki, Abuja, Federal Capital Territory, Nigeria
| | - Tanuja Joshi
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India.
| | - Subhash Chandra
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India; Formerly Department of Botany, Kumaun University, S.S.J Campus, Almora, 263601, Uttarakhand, India.
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Hou Y, Li Q, He W, Li M, Xue J, Li X, Li Y. Enhanced biodegradation of modified fluoroquinolone for aerobic, facultative, and anaerobic processes using quantitative structure-activity relationship, molecular docking, and molecular dynamics. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Banjare P, Matore B, Singh J, Roy PP. In silico local QSAR modeling of bioconcentration factor of organophosphate pesticides. In Silico Pharmacol 2021; 9:28. [PMID: 33868896 PMCID: PMC8019672 DOI: 10.1007/s40203-021-00087-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/15/2021] [Indexed: 11/30/2022] Open
Abstract
The persistent and accumulative nature of the pesticide of indiscriminate use emerged as ecotoxicological hazards. The bioconcentration factor (BCF) is one of the key elements for environmental assessments of the aquatic compartment. Limitations of prediction accuracy of global model facilitate the use of local predictive models in toxicity modeling of emerging compounds. The BCF data of diverse organophosphate (n = 55) was collected from the Pesticide Properties Database and used as a model data set in the present study to explore physicochemical properties and structural alert concerning BCF. The structures were downloaded from Pubchem, ChemSpider database. Two splitting techniques (biological sorting and structure-based) were used to divide the whole dataset into training and test set compounds. The QSAR study was carried out with two-dimensional descriptors (2D) calculated from PaDEL by applying genetic algorithm (GA) as chemometric tools using QSARINS software. The models were statistically robust enough both internally as well as externally (Q2: 0.709-0.722, Q2 Ext: 0.717-0.903, CCC: 0.857-0.880). Overall molecular mass, presence of fused, and heterocyclic ring with electron-withdrawing groups affect the BCF value. The developed models reflected extended applicability domain (AD) and reliable predictions than the reported models for the studied chemical class. Finally, predictions of unknown organophosphate pesticides and the toxic nature of unknown organophosphate pesticides were commented on. These findings may be useful for the scientific community in prioritizing high potential pesticides of organophosphate class.
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Affiliation(s)
- Purusottam Banjare
- Department of Pharmacy, Guru GhasidasVishwavidyalaya (A Central University), Bilaspur, 495009 India
| | - Balaji Matore
- Department of Pharmacy, Guru GhasidasVishwavidyalaya (A Central University), Bilaspur, 495009 India
| | - Jagadish Singh
- Department of Pharmacy, Guru GhasidasVishwavidyalaya (A Central University), Bilaspur, 495009 India
| | - Partha Pratim Roy
- Department of Pharmacy, Guru GhasidasVishwavidyalaya (A Central University), Bilaspur, 495009 India
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39
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Wu J, Yan F, Jia Q, Wang Q. QSPR for predicting the hydrophile-lipophile balance (HLB) of non-ionic surfactants. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2020.125812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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40
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Fuentes JV, Zamora EB, Li Z, Xu Z, Chakraborty A, Zavala G, Vázquez F, Flores C. Alkylacrylic-carboxyalkylacrylic random bipolymers as demulsifiers for heavy crude oils. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2020.117850] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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41
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Shirvani P, Fassihi A. In silico design of novel FAK inhibitors using integrated molecular docking, 3D-QSAR and molecular dynamics simulation studies. J Biomol Struct Dyn 2021; 40:5965-5982. [PMID: 33475043 DOI: 10.1080/07391102.2021.1875880] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Focal adhesion kinase (FAK) is a cytoplasmic tyrosine kinase that plays a crucial role in integrin signaling that regulates essential cellular functions including growth, motility, proliferation and survival in different types of cells. Interestingly, it has also shown to be up-regulated in various types of tumors, hence it has emerged as a significant therapeutic target for the development of selective inhibitors. In present work, with the aim of achieving further insight into the structural characteristics required for the FAK inhibitory activity, a combined approach of molecular modeling studies including molecular docking, three-dimensional quantitative structure activity relationship (3D-QSAR) and molecular dynamics (MD) simulation were carried out on a series of 7H-pyrrolo[2,3-d]pyrimidine and thieno[3,2-d]pyrimidine FAK inhibitors. The probable binding modes and interactions of inhibitors into the FAK active site were predicted by molecular docking. The 3D-QSAR models were developed using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods, with three ligand-based, docking-based and receptor-based alignment techniques. Both CoMFA and CoMSIA models obtained from receptor-based alignment were superior to the ones obtained by other alignment methods. However, the CoMSIA model (q2 = 0.679, r2 = 0.954 and r2pred = 0.888) depicted almost better predictive ability than the CoMFA model (q2 = 0.617, r2 = 0.932 and r2pred = 0.856). The contour map analysis revealed the relationship between the structural features and inhibitory activity. The docking results and CoMFA and CoMSIA contour maps were in good accordance. Based on the information obtained from the molecular docking and contour map analysis, a series of novel FAK inhibitors were designed that showed better predicted inhibitory activity than the most potent compound 31 in the data set. Finally, the stability of the reference molecule 31 and the designed compounds D15 and D27 were evaluated through a 30 ns of MD simulation and their binding free energies were calculated using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. The result of MD simulation and binding free energy decomposition demonstrated the important role of van der Waals interactions alongside H-bond ones that were in consistent with the docking and contour maps analysis results. In sum, the results from this study may provide a significant insight for developing more effective novel FAK inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pouria Shirvani
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Isfahan, Iran
| | - Afshin Fassihi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Isfahan, Iran.,Bioinformatics Research Center, Isfahan university of Medical Science, Isfahan, Iran
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42
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Rosell-Hidalgo A, Young L, Moore AL, Ghafourian T. QSAR and molecular docking for the search of AOX inhibitors: a rational drug discovery approach. J Comput Aided Mol Des 2020; 35:245-260. [PMID: 33289903 PMCID: PMC7904559 DOI: 10.1007/s10822-020-00360-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 11/12/2020] [Indexed: 11/24/2022]
Abstract
The alternative oxidase (AOX) is a monotopic diiron carboxylate protein that catalyses the oxidation of ubiquinol and the reduction of oxygen to water. Although a number of AOX inhibitors have been discovered, little is still known about the ligand–protein interaction and essential chemical characteristics of compounds required for a potent inhibition. Furthermore, owing to the rapidly growing resistance to existing inhibitors, new compounds with improved potency and pharmacokinetic properties are urgently required. In this study we used two computational approaches, ligand–protein docking and Quantitative Structure–Activity Relationships (QSAR) to investigate binding of AOX inhibitors to the enzyme and the molecular characteristics required for inhibition. Docking studies followed by protein–ligand interaction fingerprint (PLIF) analysis using the AOX enzyme and the mutated analogues revealed the importance of the residues Leu 122, Arg 118 and Thr 219 within the hydrophobic cavity. QSAR analysis, using stepwise regression analysis with experimentally obtained IC50 values as the response variable, resulted in a multiple regression model with a good prediction accuracy. The model highlighted the importance of the presence of hydrogen bonding acceptor groups on specific positions of the aromatic ring of ascofuranone derivatives, acidity of the compounds, and a large linker group on the compounds on the inhibitory effect of AOX.
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Affiliation(s)
- Alicia Rosell-Hidalgo
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Luke Young
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Anthony L Moore
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Taravat Ghafourian
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK. .,School of Life Sciences, Faculty of Creative Arts, Technologies and Science, University of Bedfordshire, Luton, Bedfordshire, LU1 3JU, UK.
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43
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Akabli T, Toufik H, Lamchouri F. In silico modeling studies of N9-substituted harmine derivatives as potential anticancer agents: combination of ligand-based and structure-based approaches. J Biomol Struct Dyn 2020; 40:3965-3978. [PMID: 33252029 DOI: 10.1080/07391102.2020.1852118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A computational study was carried out to develop quantitative-structure activity relationship (QSAR), pharmacophore, molecular docking and molecular dynamics simulations of a series of N9-substituted harmine derivatives in order to investigate the structural factors involved in the cytotoxic activity and thus design new active derivatives. A valid 3 D-QSAR (R2= 0.89, q2=0.67, R2pred = 0.72) and 2 D-QSAR (R2= 0.81, q2=0.69, R2pred = 0.76) models were obtained correlating the cytotoxic activity with hydrophobic and hydrogen bond acceptor (HBA) features for 3 D-QSAR and SlogP and a_acc descriptors for 2 D-QSAR. Analysis of the selected descriptors for both models highlighted that lipophilicity and hydrogen bonding acceptor atoms remain the crucial properties and those on which cytotoxic activity depends. Also, these findings are in agreement with the characteristics of the generated pharmacophore. Furthermore, molecular docking revealed that the binding energy (-9.74 kcal/mol) and inhibition constant (0.071 µmol) correlate with the activity of the most active compound that forms hydrophobic interactions and two hydrogen bonds with the the dual specificity tyrosine phosphorylation regulated kinase 1 A (DYRK1A). The molecular dynamics simulations revealed that the protein-ligand equilibrium is stable after 100000 fs of trajectories. Based on these results, we designed new N9-substituted harmine derivatives with improved properties: predicted cytotoxic activities, estimated binding energies, estimated inhibition constants and interaction modes with amino acid residues of DYRK1A, compared to the best compound in the studied dataset. Additionally, these newly designed inhibitors showed promising results in the preliminary in silico Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) evaluations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Taoufik Akabli
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health & Quality of Life (SNAMOPEQ), Polydisciplinary Faculty of Taza, Sidi Mohamed Ben Abdellah University of Fez, Taza, Morocco
| | - Hamid Toufik
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health & Quality of Life (SNAMOPEQ), Polydisciplinary Faculty of Taza, Sidi Mohamed Ben Abdellah University of Fez, Taza, Morocco
| | - Fatima Lamchouri
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health & Quality of Life (SNAMOPEQ), Polydisciplinary Faculty of Taza, Sidi Mohamed Ben Abdellah University of Fez, Taza, Morocco
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44
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Bouhedjar K, Benfenati E, Nacereddine AK. Modelling quantitative structure activity-activity relationships (QSAARs): auto-pass-pass, a new approach to fill data gaps in environmental risk assessment under the REACH regulation. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:785-801. [PMID: 32878491 DOI: 10.1080/1062936x.2020.1810770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
Reviewing the toxicological literature for over the past decades, the key elements of QSAR modelling have been the mechanisms of toxic action and chemical classes. As a result, it is often hard to design an acceptable single model for a particular endpoint without clustering compounds. The main aim here was to develop a Pass-Pass Quantitative Structure-Activity-Activity Relationship (PP QSAAR) model for direct prediction of the toxicity of a larger set of compounds, combing the application of an already predicted model for another species, and molecular descriptors. We investigated a large acute toxicity data set of five aquatic organisms, fish, Daphnia magna, and algae from the VEGA-Hub, as well as Tetrahymena pyriformis and Vibrio fischeri. The statistical quality of the models encouraged us to consider this alternative for the prediction of toxicity using interspecies extrapolation QSAAR models without regard to the toxicity mechanism or chemical class. In the case of algae, the use of activity values from a second species did not improve the models. This can be attributed to the weak interspecies relationships, due to different aquatic toxicity mechanisms in species.
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Affiliation(s)
- K Bouhedjar
- Laboratoire de Synthèse et Biocatalyse Organique, Département de Chimie, Faculté des Sciences, Université Badji Mokhtar Annaba , Annaba, Algeria
- Laboratoire Bioinformatique, Centre de Recherche en Biotechnologie (CRBt) , Constantine, Algeria
- Laboratory of Environmental Chemistry and Toxicology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS , Milano, Italy
| | - E Benfenati
- Laboratory of Environmental Chemistry and Toxicology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS , Milano, Italy
| | - A K Nacereddine
- Laboratory of Physical Chemistry and Biology of Materials, Department of Physics and Chemistry, Higher Normal School of Technological Education-Skikda , Skikda, Algeria
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45
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Zivkovic M, Zlatanovic M, Zlatanovic N, Golubović M, Veselinović AM. The Application of the Combination of Monte Carlo Optimization Method based QSAR Modeling and Molecular Docking in Drug Design and Development. Mini Rev Med Chem 2020; 20:1389-1402. [DOI: 10.2174/1389557520666200212111428] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 01/18/2023]
Abstract
In recent years, one of the promising approaches in the QSAR modeling Monte Carlo optimization
approach as conformation independent method, has emerged. Monte Carlo optimization has
proven to be a valuable tool in chemoinformatics, and this review presents its application in drug discovery
and design. In this review, the basic principles and important features of these methods are discussed
as well as the advantages of conformation independent optimal descriptors developed from the
molecular graph and the Simplified Molecular Input Line Entry System (SMILES) notation compared
to commonly used descriptors in QSAR modeling. This review presents the summary of obtained results
from Monte Carlo optimization-based QSAR modeling with the further addition of molecular
docking studies applied for various pharmacologically important endpoints. SMILES notation based
optimal descriptors, defined as molecular fragments, identified as main contributors to the increase/
decrease of biological activity, which are used further to design compounds with targeted activity
based on computer calculation, are presented. In this mini-review, research papers in which molecular
docking was applied as an additional method to design molecules to validate their activity further,
are summarized. These papers present a very good correlation among results obtained from Monte
Carlo optimization modeling and molecular docking studies.
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Affiliation(s)
| | | | | | - Mladjan Golubović
- Clinic for Anesthesiology and Intensive Care, Clinical Center Nis, Nis, Serbia
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Serra A, Önlü S, Festa P, Fortino V, Greco D. MaNGA: a novel multi-niche multi-objective genetic algorithm for QSAR modelling. Bioinformatics 2020; 36:145-153. [PMID: 31233136 DOI: 10.1093/bioinformatics/btz521] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/27/2019] [Accepted: 06/19/2019] [Indexed: 01/19/2023] Open
Abstract
SUMMARY Quantitative structure-activity relationship (QSAR) modelling is currently used in multiple fields to relate structural properties of compounds to their biological activities. This technique is also used for drug design purposes with the aim of predicting parameters that determine drug behaviour. To this end, a sophisticated process, involving various analytical steps concatenated in series, is employed to identify and fine-tune the optimal set of predictors from a large dataset of molecular descriptors (MDs). The search of the optimal model requires to optimize multiple objectives at the same time, as the aim is to obtain the minimal set of features that maximizes the goodness of fit and the applicability domain (AD). Hence, a multi-objective optimization strategy, improving multiple parameters in parallel, can be applied. Here we propose a new multi-niche multi-objective genetic algorithm that simultaneously enables stable feature selection as well as obtaining robust and validated regression models with maximized AD. We benchmarked our method on two simulated datasets. Moreover, we analyzed an aquatic acute toxicity dataset and compared the performances of single- and multi-objective fitness functions on different regression models. Our results show that our multi-objective algorithm is a valid alternative to classical QSAR modelling strategy, for continuous response values, since it automatically finds the model with the best compromise between statistical robustness, predictive performance, widest AD, and the smallest number of MDs. AVAILABILITY AND IMPLEMENTATION The python implementation of MaNGA is available at https://github.com/Greco-Lab/MaNGA. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, Tampere 33200, Finland
| | - Serli Önlü
- Faculty of Medicine and Health Technology, Tampere University, Tampere 33200, Finland
| | - Paola Festa
- Department of Mathematics and Applications, University of Napoli Federico II, Naples 80138, Italy
| | - Vittorio Fortino
- Institute of Biomedicine, University of Eastern Finland, Kuopio, 80101 Finland
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, Tampere 33200, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, 00014 Finland.,BioMediTech Institute, Tampere University, Tampere 33200, Finland
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Kasmi R, Hadaji E, Chedadi O, El Aissouq A, Bouachrine M, Ouammou A. 2D-QSAR and docking study of a series of coumarin derivatives as inhibitors of CDK (anticancer activity) with an application of the molecular docking method. Heliyon 2020; 6:e04514. [PMID: 32817887 PMCID: PMC7424200 DOI: 10.1016/j.heliyon.2020.e04514] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/14/2020] [Accepted: 07/16/2020] [Indexed: 11/01/2022] Open
Abstract
Quantitative Structure Activity Relationship (QSAR) analysis techniques are tools largely utilized in many research fields, including drug discovery processes. In this work electronic descriptors are calculated with the Gaussian 03W software using the DFT method with the BecKe 3-parameters exchange functional and Lee-Yang-Parr correlation functional, with Kohn and Sham orbitals (KS) developed on a Gaussian Basis of type 6-31G (d), in combination with five Lipinski parameters that have been calculated with ChemOffice software, in order to develop a statistically verified 2D-QSAR model able to predict the biological activity of new molecules belonging to the same range of coumarins rather than chemical synthesis and biological evaluations that require more time and resources. Two QSAR models against both MCF-7 and HepG-2 cell lines are obtained using the multiple linear regression method. The predictive power of these models has been confirmed by internal and external validation. The Leverage method was used to determine the domain of applicability of the 2D-QSAR models developed. The results indicate that the best QSAR model is the one that links the 2D descriptors with the CDK inhibitory activity of the cell line (HepG-2) R2 = 0.748, R2cv = 0.618, MSE = 0.03 for the learning series and R2 = 0.73, MSE = 0.18 for the test series. This model implies that coumarin inhibitory activity is strongly related to dipole moment and the number of hydrogen bond donors. The results obtained suggest the importance of studying structure-activity relationships as a principal axis in drug design. The docking procedure using AutoDOCK Tools was also used to understand the mechanisms of molecular interactions and consequently, to develop new inhibitors.
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Affiliation(s)
- Rania Kasmi
- LIMOME Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Elghalia Hadaji
- LIMOME Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Oussama Chedadi
- LIMOME Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Abdellah El Aissouq
- LIMOME Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohammed Bouachrine
- MCNS Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco.,EST Khenifra, Sultan Moulay Sliman University, Morocco
| | - Abdelkrim Ouammou
- LIMOME Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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Pandey SK, Ojha PK, Roy K. Exploring QSAR models for assessment of acute fish toxicity of environmental transformation products of pesticides (ETPPs). CHEMOSPHERE 2020; 252:126508. [PMID: 32240857 DOI: 10.1016/j.chemosphere.2020.126508] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/14/2020] [Accepted: 03/14/2020] [Indexed: 06/11/2023]
Abstract
Environmental transformation products of pesticides (ETPPs) have a great deal of ecological impact owing to their ability to cause toxicity to the aquatic organisms, which can then be translated to the humans. The limited experimental data on biochemical and toxic effects of ETPPs, the high test costs together with regulatory limitations and the international push to reduce animal testing encourage greater dependence on predictive in silico techniques like quantitative structure-activity relationship (QSAR) models. The aim of the present work was to explore the key structural features, which regulate the toxicity towards fishes, for 85 ETPPs using a partial least squares (PLS) regression based chemometric model developed according to Organisation for Economic Co-operation and Development (OECD) guidelines. The model was extensively validated using both internal and external validation metrics, and the results so obtained justify the reliability and usefulness of the developed model (Q2 = 0.648, R2pred or Q2F1 = 0.734 and Q2F2 = 0.733). From the developed model, we can conclude that lipophilicity, polarity, presence of branching and the functional form of O-atom in the transformed structures of pesticides are the important features that are to be considered during ecotoxicity assessment of ETPPs. The information obtained from the descriptors of the developed model could be utilized in the future for assessing ETPPs with the benefit of providing an early warning of their potentially detrimental effect on fishes for regulatory purposes.
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Affiliation(s)
- Sapna Kumari Pandey
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Probir Kumar Ojha
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Kunal Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
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QSAR investigations and structure-based virtual screening on a series of nitrobenzoxadiazole derivatives targeting human glutathione-S-transferases. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
At the end of her academic career, the author summarizes the main aspects of QSAR modeling, giving comments and suggestions according to her 23 years' experience in QSAR research on environmental topics. The focus is mainly on Multiple Linear Regression, particularly Ordinary Least Squares, using a Genetic Algorithm for variable selection from various theoretical molecular descriptors, but the comments can be useful also for other QSAR methods. The need for rigorous validation, also external, and for applicability domain check to guarantee predictivity and reliability of QSAR models is particularly highlighted. The commented approach is the “predictive” one, based on chemometrics, and is usefully applied to the prioritization of environmental pollutants. All the discussed points and the author's ideas are implemented in the software QSARINS, as a legacy to the QSAR community.
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