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Uddin KM, Meem MH, Akter M, Rahman S, Al-Gawati MA, Alarifi N, Albrithen H, Alodhayb A, Poirier RA, Bhuiyan MH. Design, synthesis, and bioevaluation of novel unsaturated cyanoacetamide derivatives: In vitro and in silico exploration. MethodsX 2024; 12:102691. [PMID: 38660042 PMCID: PMC11041845 DOI: 10.1016/j.mex.2024.102691] [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: 11/06/2023] [Accepted: 04/02/2024] [Indexed: 04/26/2024] Open
Abstract
In this study, we synthesized novel α,β-unsaturated 2-cyanoacetamide derivatives (1-5) using microwave-assisted Knoevenagel condensation. Characterization of these compounds was carried out using FTIR and 1H NMR spectroscopy. We then evaluated their in vitro antibacterial activity against both gram-positive and gram-negative pathogenic bacteria. Additionally, we employed in silico methods, including ADMET prediction and density functional theory (DFT) calculations of molecular orbital properties, to investigate these cyanoacetamide derivatives (1-5). Molecular docking was used to assess the binding interactions of these derivatives (1-5) with seven target proteins (5MM8, 4NZZ, 7FEQ, 5NIJ, ITM2, 6SE1, and 5GVZ) and compared them to the reference standard tyrphostin AG99. Notably, derivative 5 exhibited the most favorable binding affinity, with a binding energy of -7.7 kcal mol-1 when interacting with the staphylococcus aureus (PDB:5MM8), while also meeting all drug-likeness criteria. Additionally, molecular dynamics simulations were carried out to evaluate the stability of the interaction between the protein and ligand, utilizing parameters such as Root-Mean-Square Deviation (RMSD), Root-Mean-Square Fluctuation (RMSF), Radius of Gyration (Rg), and Principal Component Analysis (PCA). A 50 nanosecond molecular dynamics (MD) simulation was performed to investigate stability further, incorporating RMSD and RMSF analyses on compound 5 within the active binding site of the modeled protein across different temperatures (300, 305, 310, and 320 K). Among these temperatures, compound 5 exhibited an RMSD value ranging from approximately 0.2 to 0.3 nm at 310 K (body temperature) with the 5MM8 target, which differed from the other temperature conditions. The in silico results suggest that compound 5 maintained significant conformational stability throughout the 50 ns simulation period. It is consistent with its low docking energy and in vitro findings concerning α,β-unsaturated cyanoacetamides. Key insights from this study include:•The creation of innovative α,β-unsaturated 2-cyanoacetamide derivatives (1-5) employing cost-effective, licensed, versatile, and efficient software for both in silico and in vitro assessment of antibacterial activity.•Utilization of FTIR and NMR techniques for characterizing compounds 1-5.
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Affiliation(s)
- Kabir M. Uddin
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Mehnaz Hossain Meem
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Mokseda Akter
- Bioorganic and Medicinal Chemistry Laboratory, Department of Chemistry, University of Chittagong, Chattogram 4331, Bangladesh
| | - Shofiur Rahman
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mahmoud A. Al-Gawati
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nahed Alarifi
- Research Chair for Tribology, Surface, and Interface Sciences, Department of Physics and Astronomy, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Hamad Albrithen
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
- Research Chair for Tribology, Surface, and Interface Sciences, Department of Physics and Astronomy, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah Alodhayb
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
- Research Chair for Tribology, Surface, and Interface Sciences, Department of Physics and Astronomy, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Raymond A. Poirier
- Department of Chemistry, Memorial University, St. John's, Newfoundland A1B 3 × 7, Canada
| | - Md. Mosharef H. Bhuiyan
- Bioorganic and Medicinal Chemistry Laboratory, Department of Chemistry, University of Chittagong, Chattogram 4331, Bangladesh
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2
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Uddin KM, Sakib M, Siraji S, Uddin R, Rahman S, Alodhayb A, Alibrahim KA, Kumer A, Matin MM, Bhuiyan MMH. Synthesis of New Derivatives of Benzylidinemalononitrile and Ethyl 2-Cyano-3-phenylacrylate: In Silico Anticancer Evaluation. ACS OMEGA 2023; 8:25817-25831. [PMID: 37521603 PMCID: PMC10373203 DOI: 10.1021/acsomega.3c01123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/16/2023] [Indexed: 08/01/2023]
Abstract
In this study, microwave-assisted Knoevenagel condensation was used to produce two novel series of derivatives (1-6) from benzylidenemalononitrile and ethyl 2-cyano-3-phenylacrylate. The synthesized compounds were characterized using Fourier transform infrared (FT-IR) and 1H NMR spectroscopies. The pharmacodynamics, toxicity profiles, and biological activities of the compounds were evaluated through an in silico study using prediction of activity spectra for substances (PASS) and Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) studies. According to the PASS prediction results, compounds 1-6 showed greater antineoplastic potency for breast cancer than other types of cancer. Molecular docking was employed to investigate the binding mode and interaction sites of the derivatives (1-6) with three human cancer targets (HER2, EGFR, and human FPPS), and the protein-ligand interactions of these derivatives were compared to those reference standards Tyrphostin 1 (AG9) and Tyrphostin 23 (A23). Compound 3 showed a stronger effect on two cell lines (HER2 and FPPS) than the reference drugs. A 20 ns molecular dynamics (MD) simulation was also conducted to examine the ligand's behavior at the active binding site of the modeled protein, utilizing the lowest docking energy obtained from the molecular docking study. Enthalpies (ΔH), Gibbs free energies (ΔG), entropies (ΔS), and frontier molecular orbital parameters (highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gap, hardness, and softness) were calculated to confirm the thermodynamic stability of all derivatives. The consistent results obtained from the in silico studies suggest that compound 3 has potential as a new anticancer and antiparasitic drug. Further research is required to validate its efficacy.
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Affiliation(s)
- Kabir M. Uddin
- Department
of Biochemistry and Microbiology, North
South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Mohiuddin Sakib
- Department
of Biochemistry and Microbiology, North
South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Siam Siraji
- Department
of Biochemistry and Microbiology, North
South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Riaz Uddin
- Biorganic
and Medicinal Chemistry Laboratory, Department of Chemistry, University of Chittagong, Chattogram 4331, Bangladesh
| | - Shofiur Rahman
- Biological
and Environmental Sensing Research Unit, King Abdullah Institute for
Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah Alodhayb
- Biological
and Environmental Sensing Research Unit, King Abdullah Institute for
Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
- Research
Chair for Tribology, Surface, and Interface Sciences, Department of
Physics and Astronomy, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khuloud A. Alibrahim
- Department
of Chemistry, College of Science, Princess
Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Ajoy Kumer
- Department
of Chemistry, European University of Bangladesh, Gabtoli, Dhaka 1216, Bangladesh
| | - M. Mahbubul Matin
- Biorganic
and Medicinal Chemistry Laboratory, Department of Chemistry, University of Chittagong, Chattogram 4331, Bangladesh
| | - Md. Mosharef H. Bhuiyan
- Biorganic
and Medicinal Chemistry Laboratory, Department of Chemistry, University of Chittagong, Chattogram 4331, Bangladesh
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3
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Magar P, Parravicini O, Štěpánková Š, Svrčková K, Garro AD, Jendrzejewska I, Pauk K, Hošek J, Jampílek J, Enriz RD, Imramovský A. Novel Sulfonamide-Based Carbamates as Selective Inhibitors of BChE. Int J Mol Sci 2021; 22:9447. [PMID: 34502357 PMCID: PMC8430704 DOI: 10.3390/ijms22179447] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/28/2021] [Indexed: 11/16/2022] Open
Abstract
A series of 14 target benzyl [2-(arylsulfamoyl)-1-substituted-ethyl]carbamates was prepared by multi-step synthesis and characterized. All the final compounds were tested for their ability to inhibit acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) in vitro, and the selectivity index (SI) was determined. Except for three compounds, all compounds showed strong preferential inhibition of BChE, and nine compounds were even more active than the clinically used rivastigmine. Benzyl {(2S)-1-[(2-methoxybenzyl)sulfamoyl]-4-methylpentan-2-yl}carbamate (5k), benzyl {(2S)-1-[(4-chlorobenzyl)sulfamoyl]-4-methylpentan-2-yl}carbamate (5j), and benzyl [(2S)-1-(benzylsulfamoyl)-4-methylpentan-2-yl]carbamate (5c) showed the highest BChE inhibition (IC50 = 4.33, 6.57, and 8.52 µM, respectively), indicating that derivatives 5c and 5j had approximately 5-fold higher inhibitory activity against BChE than rivastigmine, and 5k was even 9-fold more effective than rivastigmine. In addition, the selectivity index of 5c and 5j was approx. 10 and that of 5k was even 34. The process of carbamylation and reactivation of BChE was studied for the most active derivatives 5k, 5j. The detailed information about the mode of binding of these compounds to the active site of both BChE and AChE was obtained in a molecular modeling study. In this study, combined techniques (docking, molecular dynamic simulations, and QTAIM (quantum theory of atoms in molecules) calculations) were employed.
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Affiliation(s)
- Pratibha Magar
- Institute of Organic Chemistry and Technology, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10 Pardubice, Czech Republic; (P.M.); (K.P.)
| | - Oscar Parravicini
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Chacabuco 915, 5700 San Luis, Argentina; (O.P.); (A.D.G.)
| | - Šárka Štěpánková
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10 Pardubice, Czech Republic; (Š.Š.); (K.S.)
| | - Katarina Svrčková
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10 Pardubice, Czech Republic; (Š.Š.); (K.S.)
| | - Adriana D. Garro
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Chacabuco 915, 5700 San Luis, Argentina; (O.P.); (A.D.G.)
| | | | - Karel Pauk
- Institute of Organic Chemistry and Technology, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10 Pardubice, Czech Republic; (P.M.); (K.P.)
| | - Jan Hošek
- Department of Pharmacology and Toxicology, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic;
| | - Josef Jampílek
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia;
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska Cesta 9, 845 10 Bratislava, Slovakia
| | - Ricardo D. Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Chacabuco 915, 5700 San Luis, Argentina; (O.P.); (A.D.G.)
| | - Aleš Imramovský
- Institute of Organic Chemistry and Technology, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10 Pardubice, Czech Republic; (P.M.); (K.P.)
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Arias F, Franco-Montalban F, Romero M, Carrión MD, Camacho ME. Synthesis, bioevaluation and docking studies of new imidamide derivatives as nitric oxide synthase inhibitors. Bioorg Med Chem 2021; 44:116294. [PMID: 34218000 DOI: 10.1016/j.bmc.2021.116294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 10/21/2022]
Abstract
In search of new Nitric Oxide Synthase (NOS) inhibitor agents, two isosteric series of derivatives with an imidamide scaffold (one of them with a hydroxyl group and the other with a carbonyl one) were synthesized and evaluated on inducible (iNOS) and neuronal (nNOS) isoforms. These compounds have been designed by combining a kynurenamine framework with an amidine moiety in order to improve selectivity for the inducible isoform. In general, the in vitro inhibitory assays exhibited better inhibition values on the iNOS isoform, being the N-(3-(2-amino-5-methoxyphenyl)-3-hydroxypropyl)-4-(trifluoromethyl)benzimidamide 4i the most active inhibitor with the highest iNOS selectivity, without inhibiting eNOS. Docking studies on the two most active compounds suggest a different binding mode on both isozymes, supporting the experimentally observed selectivity towards the inducible isoform. Physicochemical in silico studies suggest that these compounds possess good drug-likeness properties.
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Affiliation(s)
- Fabio Arias
- Departamento de Química Farmacéutica y Orgánica, Facultad de Farmacia, Universidad de Granada, Spain
| | | | - Miguel Romero
- Departamento de Farmacología, Facultad de Farmacia, Universidad de Granada, Spain; Instituto de Investigación Biosanitaria de Granada, ibs.GRANADA, Granada, Spain; Department of Pharmacology, School of Pharmacy and Center for Biomedical Research (CIBM), University of Granada, 18071 Granada, Spain; Ciber de Enfermedades Cardiovasculares (CIBERCV), Spain
| | - M Dora Carrión
- Departamento de Química Farmacéutica y Orgánica, Facultad de Farmacia, Universidad de Granada, Spain.
| | - M Encarnación Camacho
- Departamento de Química Farmacéutica y Orgánica, Facultad de Farmacia, Universidad de Granada, Spain.
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5
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Kos J, Bak A, Kozik V, Jankech T, Strharsky T, Swietlicka A, Michnova H, Hosek J, Smolinski A, Oravec M, Devinsky F, Hutta M, Jampilek J. Biological Activities and ADMET-Related Properties of Novel Set of Cinnamanilides. Molecules 2020; 25:molecules25184121. [PMID: 32916979 PMCID: PMC7570544 DOI: 10.3390/molecules25184121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
A series of nineteen novel ring-substituted N-arylcinnamanilides was synthesized and characterized. All investigated compounds were tested against Staphylococcus aureus as the reference strain, two clinical isolates of methicillin-resistant S. aureus (MRSA), and Mycobacterium tuberculosis. (2E)-N-[3-Fluoro-4-(trifluoromethyl)phenyl]-3-phenylprop-2-enamide showed even better activity (minimum inhibitory concentration (MIC) 25.9 and 12.9 µM) against MRSA isolates than the commonly used ampicillin (MIC 45.8 µM). The screening of the cell viability was performed using THP1-Blue™ NF-κB cells and, except for (2E)-N-(4-bromo-3-chlorophenyl)-3-phenylprop-2-enamide (IC50 6.5 µM), none of the discussed compounds showed any significant cytotoxic effect up to 20 μM. Moreover, all compounds were tested for their anti-inflammatory potential; several compounds attenuated the lipopolysaccharide-induced NF-κB activation and were more potent than the parental cinnamic acid. The lipophilicity values were specified experimentally as well. In addition, in silico approximation of the lipophilicity values was performed employing a set of free/commercial clogP estimators, corrected afterwards by the corresponding pKa calculated at physiological pH and subsequently cross-compared with the experimental parameters. The similarity-driven property space evaluation of structural analogs was carried out using the principal component analysis, Tanimoto metrics, and Kohonen mapping.
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Affiliation(s)
- Jiri Kos
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 78371 Olomouc, Czech Republic; (J.K.); (T.S.); (H.M.); (J.H.)
| | - Andrzej Bak
- Department of Chemistry, University of Silesia, Szkolna 9, 40007 Katowice, Poland; (V.K.); (A.S.)
- Correspondence: (A.B.); (J.J.)
| | - Violetta Kozik
- Department of Chemistry, University of Silesia, Szkolna 9, 40007 Katowice, Poland; (V.K.); (A.S.)
| | - Timotej Jankech
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 84215 Bratislava, Slovakia; (T.J.); (M.H.)
| | - Tomas Strharsky
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 78371 Olomouc, Czech Republic; (J.K.); (T.S.); (H.M.); (J.H.)
| | - Aleksandra Swietlicka
- Department of Chemistry, University of Silesia, Szkolna 9, 40007 Katowice, Poland; (V.K.); (A.S.)
| | - Hana Michnova
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 78371 Olomouc, Czech Republic; (J.K.); (T.S.); (H.M.); (J.H.)
| | - Jan Hosek
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 78371 Olomouc, Czech Republic; (J.K.); (T.S.); (H.M.); (J.H.)
| | - Adam Smolinski
- Central Mining Institute, Pl. Gwarkow 1, 40166 Katowice, Poland;
| | - Michal Oravec
- Global Change Research Institute CAS, Belidla 986/4a, 60300 Brno, Czech Republic;
| | - Ferdinand Devinsky
- Faculty of Pharmacy, Comenius University, Odbojarov 10, 83232 Bratislava, Slovakia;
| | - Milan Hutta
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 84215 Bratislava, Slovakia; (T.J.); (M.H.)
| | - Josef Jampilek
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 84215 Bratislava, Slovakia; (T.J.); (M.H.)
- Correspondence: (A.B.); (J.J.)
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6
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Towards Intelligent Drug Design System: Application of Artificial Dipeptide Receptor Library in QSAR-Oriented Studies. Molecules 2018; 23:molecules23081964. [PMID: 30082652 PMCID: PMC6222794 DOI: 10.3390/molecules23081964] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 07/29/2018] [Accepted: 08/05/2018] [Indexed: 12/23/2022] Open
Abstract
The pharmacophore properties of a new series of potential purinoreceptor (P2X) inhibitors determined using a coupled neural network and the partial least squares method with iterative variable elimination (IVE-PLS) are presented in a ligand-based comparative study of the molecular surface by comparative molecular surface analysis (CoMSA). Moreover, we focused on the interpretation of noticeable variations in the potential selectiveness of interactions of individual inhibitor-receptors due to their physicochemical properties; therefore, the library of artificial dipeptide receptors (ADP) was designed and examined. The resulting library response to individual inhibitors was arranged in the array, preprocessed and transformed by the principal component analysis (PCA) and PLS procedures. A dominant absolute contribution to PC1 of the Glu attached to heptanoic gating acid and Phe bonded to the linker m-phenylenediamine/triazine scaffold was revealed by the PCA. The IVE-PLS procedure indicated the receptor systems with predominant Pro bonded to the linker and Glu, Gln, Cys and Val directly attached to the gating acid. The proposed comprehensive ligand-based and simplified structure-based methodology allows the in-depth study of the performance of peptide receptors against the tested set of compounds.
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7
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Bak A, Kozik V, Smolinski A, Jampilek J. In silico estimation of basic activity-relevant parameters for a set of drug absorption promoters. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:427-449. [PMID: 28573881 DOI: 10.1080/1062936x.2017.1327459] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
Finding a balance between a desired drug's potency and its physicochemical properties that are important for its molecule pharmacokinetic or pharmacodynamics profile is still a challenging issue in rational drug discovery. Quantitative assessment of the lipophilic characteristics of potential drug molecules is indispensable for efficient development of Absorption, Distribution, Metabolism, Excretion, Toxicity-tailored structure-activity models; therefore reliable procedures for deriving log P from molecular structure are desirable. In the current work a range of various software log P predictors for estimation of the numerical lipophilic values for a set of cholic acid derivatives were employed and subsequently cross-compared with the experimental parameters. Thus, the empirical lipophilicity (RM) was compared with the corresponding log P characteristics calculated using alternative methods for deducing the lipophilic features. The mean values of the selected molecular descriptors that were averaged over the chosen calculation methods (consensus clog P) were subsequently correlated with the RM parameter. As an additional experiment, the iterative variable elimination partial least squares (IVE-PLS) methodology for an ensemble of descriptors retrieved from Dragon 6.0 software was applied for a set of drug transporters. To investigate the variations within the ensemble of cholic acid derivatives principal component analysis (PCA) and self-organizing neural network (SOM) procedures were used to visualize the major differences in the performance of drug promoters with respect to their lipophilic profile.
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Affiliation(s)
- A Bak
- a Department of Organic Chemistry , University of Silesia , Katowice , Poland
| | - V Kozik
- b Department of Synthesis Chemistry , University of Silesia , Katowice , Poland
| | - A Smolinski
- c Department of Energy Saving and Air Protection , Central Mining Institute , Katowice , Poland
| | - J Jampilek
- d Department of Pharmaceutical Chemistry , Comenius University , Bratislava , Slovakia
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Kawabata T, Sugihara Y, Fukunishi Y, Nakamura H. LigandBox: A database for 3D structures of chemical compounds. Biophysics (Nagoya-shi) 2013; 9:113-21. [PMID: 27493549 PMCID: PMC4629684 DOI: 10.2142/biophysics.9.113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 07/11/2013] [Indexed: 12/22/2022] Open
Abstract
A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening.
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Affiliation(s)
- Takeshi Kawabata
- Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yusuke Sugihara
- Fujitsu Kyushu R&D Center, Life Science Systems Dept., Fujitsu Kyushu Systems Limited, 2-1, Momochihama 2-Chome, Sawara-ku, Fukuoka, 814-8589, Japan
| | - Yoshifumi Fukunishi
- Molecular Profiling Research Center for Drug Discovery (molprof), AIST, 2-3-26, Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
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