2D QSar studies on escherichia coli acrab tolc efflux pump inhibitors

MINISTRY OF EDUCATION AND TRAINING NGUYEN TAT THANH UNIVERSITY NGUYEN VU THUY VY 2D-QSAR STUDIES ON ESCHERICHIA COLI ACRAB-TOLC EFFLUX PUMP INHIBITORS DISSERTATION SUBMITTED IN FULFILMENT OF THE REQUIREMENTS FOR THE PHARMACIST ACADEMIC YEAR 2014 – 2019 HCM city – 2019 MINISTRY OF EDUCATION AND TRAINING NGUYEN TAT THANH UNIVERSITY NGUYEN VU THUY VY 2D-QSAR STUDIES ON ESCHERICHIA COLI ACRAB-TOLC EFFLUX PUMP INHIBITORS Field of study: Pharmaceutical manufacturing and development DISSERTATION SUBMITTED IN FULFILMENT OF THE REQUIREMENTS FOR THE PHARMACIST ACADEMIC YEAR 2014 – 2019 Scientific instructor: M.S Pharm PHAN THIEN VY HCM city – 2019 ACKNOWLEDGMENT Primarily, I would like to express my sincere gratitude to my instructor Mrs Phan Thien Vy Without your advice, concern and enthusiastic support, I can not complete this final essay I would like to thank my teachers work at Department of Pharmacognosy for your help and facilitation during this time Thanks to my teachers work at English Council: Prof PhD Nguyen Van Thanh, PhD Vo Hong Trung, PhD Vo Thị Ngoc My and M.S Huynh Tan for their helpful advices and comments to my dissertation Thanks also to Nhan, Cuong, Dai and Luan – Department of Pharmacognosy monitors and my team Ngan, Thy, Nhi and Ngoc for your encouragement and useful information Working together with you over the time is my great experience To my cousin Anh Thu and her husband Marlin Ray Weber for their advice on grammar, it is very helpful for me Thank you very much Last, but not least, my parent are always supporting and encouraging me all the time They are my inspirations I am extremely grateful for them ORIGINAL LITERARY WORK DECLARATION I assure you that this is my research work The data and results stated in this report are honest and never published in any other research STUDENT TABLE OF CONTENTS LIST OF ACRONYMS iii LIST OF FIGURE iv LIST OF TABLE v ABSTRACT i INTRODUCTION .1 CHAPTER LITERATURE REVIEW .3 1.1 Antibiotic resistance and multidrug efflux systems .3 1.1.1 Antibiotic resistance crisis .3 1.1.2 Multi-drug efflux systems 1.2 E coli AcrAB-TolC efflux pump 1.2.1 Structure of E coli AcrAB-TolC efflux pump .7 1.2.2 Substrates and mechanism of efflux pump 1.3 Inhibition of AcrAB-TolC efflux pump 1.3.1 In vitro biological assays 1.3.2 Synthetic compounds .9 1.3.3 Psychotropic medicines 10 1.3.4 Natural compounds 11 1.4 Virtual screening 13 1.4.1 Structural – based virtual screening 13 1.4.2 Ligand – based virtual screening 14 1.5 Partial Least Square regression 14 1.6 QSAR studies on E coli inhibitors 15 CHAPTER SUBJECTS – RESEARCH METHOD 17 2.1 Data sets 17 2.1.1 Data set of MPC4_ATB model 17 2.1.2 Data set of MPC4_LEV model 18 2.2 2D-QSAR study process 19 2.2.1 Preparation of the structure compounds 20 2.2.2 Preparation of the biological activity values 20 2.2.3 Dataset division 20 i 2.2.4 Calculated 2D-descriptors 20 2.2.5 Selected 2D-descriptors 21 2.2.6 Determining applicability domain (AD) of QSAR models 21 2.2.7 Linear regression based on QSAR models 23 2.2.8 Model validation 24 2.3 Virtual screening 26 CHAPTER RESULT AND DISCUSSION 29 3.1 MPC4_ATB model 29 3.1.1 ATB_1 QSAR model 29 3.1.2 ATB_2 QSAR model 32 3.2 MPC4_LEV model 35 3.2.1 LEV_1 QSAR model 35 3.2.2 LEV_2 QSAR model 38 3.3 Comparison with other QSAR models 41 3.4 Virtual screening 42 3.4.1 Screening on TCM database 42 3.4.2 Screening on approved medicines 45 3.4.3 Screening on Glinus oppositifolius and Chromolaena odorata 51 CHAPTER CONCLUSION AND SUGGESTION 54 REFERENCES APPENDIX ii LIST OF ACRONYMS 2D Dimensions 3D Dimensions ABC The ATP binding cassette AD Applicability domain ATB Antibiotic CV Cross-validation EPIs Efflux pump inhibitors LEV Levofloxacin LOO Leave-one-out MATE The multidrug and toxic compound extrusion MDR Multi-drug resistant MES Multi-drug efflux systems MFS The major facilitator MIC Minimum inhibitory concentration MLR Multiple Linear Regression MOE Molecular Operating Environment MPC4 The value of minimal concentration of an EPIs required to decrease the MIC of an antibiotic by 4-fold OLS Ordinary least squares PCA Principle component analysis PLS Partial Least Square regression QSAR Quantitative Structure – Activity Relationship RND The resistance nodulation division SMR The small multidrug resistance TCM Traditional Chinese Medical database TMDs Transmembrane domains TMHs Transmembrane helices WHO World Health Organization iii LIST OF FIGURE Figure 1.1 Five major families of efflux pump transporters Figure 1.2 Structure of E coli AcrAB TolC efflux pump Figure 1.3 Structure of some synthetic efflux pump inhibitors 10 Figure 1.4 Psychotropic medicines have efflux pump inhibitory activity 11 Figure 2.1 2D-QSAR study process 19 Figure 2.2 Determined outlier by 3D-scatter plot 23 Figure 2.3 Process of virtual screening 28 Figure 3.1 The correlation line between observed and predicted pMPC4 values in the training and the test set of ATB_1 model 31 Figure 3.2 The correlation line between observed and predicted pMPC4 values in the training and the test set of ATB_2 model 34 Figure 3.3 The correlation line between observed and predicted pMPC4 values in the training and the test set of LEV_1 model 37 Figure 3.4 The correlation line between observed and predicted pMPC4 values in the training and the test set of LEV_2 model 40 Figure 3.5 Virtual screening result of natural compounds 43 Figure 3.6 Virtual screening result of approved medicines 45 iv LIST OF TABLE Table 1.1 Some natural compounds have efflux pump inhibitory activity 12 Table 1.2 Some QSAR models on E coli inhibitors and theirs results 15 Table 2.1 Data set of MPC4_ATB model 17 Table 2.2 Data set of MPC4_LEV model 18 Table 2.3 Virtual screening database 27 Table 3.1 Two MPC4_ATB 2D-QSAR models 29 Table 3.2 Descriptors definition of ATB_1 model 29 Table 3.3 Correlation matrix between descriptors and pMPC4 of ATB_1 model 30 Table 3.4 Validation result of ATB_1 model 30 Table 3.5 Descriptors definition of ATB_2 model 32 Table 3.6 Correlation matrix between descriptors and pMPC4 of ATB_2 model 32 Table 3.7 Validation result of ATB_2 model 33 Table 3.8 Descriptors of MPC4_LEV models 35 Table 3.9 Descriptors definition of LEV_1 model 35 Table 3.10 Correlation matrix between descriptors and pMPC4 of LEV_1 model 36 Table 3.11 Validation result of LEV_1 model 36 Table 3.12 Descriptors definition of LEV_2 model 38 Table 3.13 Correlation matrix between descriptors and pMPC4 of LEV_2 model 38 Table 3.14 The validation result of LEV_2 model 39 Table 3.15 Comparison result of 2D-QSAR models 41 Table 3.16 Top natural compounds had strongest predicted values from virtual screening with theirs structures and natural materials 44 Table 3.17 Approved medicines had strongest predicted values from virtual screening and theirs structures 46 Table 3.18 Compounds extracted from Glinus oppositifolius and Chromolaena odorata with theirs structures 51 v ABSTRACT DISSERTATION SUBMITTED IN FULFILMENT OF THE REQUIREMENTS FOR THE PHARMACIST - ACADEMIC YEAR 2014 – 2019 2D-QSAR STUDIES ON ESCHERICHIA COLI ACRAB-TOLC EFFLUX PUMP INHIBITORS NGUYEN VU THUY VY Scientific instructor: M.S Pharm PHAN THIEN VY Introduction: In recent years, antimicrobial resistance rates in gram-negative bacteria are increasing rapidly and efflux pump has been found to be related to multi-drug resistance in clinical isolates ArcAB-TolC tripartite efflux pump, which belongs to the RND superfamily, are the main multi-drug efflux system of Escherichia coli because of the broad resistance on antibiotics With the discovering of efflux pump inhibitors (EPIs), the combination between these and antibiotics is one of the most promising therapies Therefore, the main objectives of this study are building 2D-QSAR models, which have predictive capabilities for efflux pump inhibitory activities of natural compounds and clinical medicines Materials and methods: The data sets of 2D-QSAR models included 115 compounds whose value of minimal concentration required to decrease the antibiotic minimum inhibitor y concentration by 4-fold (MPC4) These models were developed by Partial Least Squares method After that, best models were applied for predicting MPC4 values of virtual screening database Result and discussion: Four QSAR models whose dependent value was MPC4, were created with different descriptors Validation results showed that R2 values and Q2 values of all models were greater than 0.80 and 0.77, respectively The other values such as RMSE, 𝑅𝑝𝑟𝑒𝑑 , ̅̅̅ 𝑟𝑚2 and 𝑟𝑚2 were met the validation criteria Two best models of four were ATB_2 and LEV_2 would be applied to virtual screening database and the results indicated that 115 natural compounds had predicted MPC4 less than 10 μM on both models and met Five rules of Lipinski 14 approved medicines were forecasted to have predicted MPC4 less than 100 μΜ Conclusion: Both ATB_2 and LEV_2 models were the best predicted models Natural substances whose good predicted activity belonged to Diterpens and Lignans Approved medicines which possessed more nitrogen and sulfur groups or halogenic substitution at benzene ring would increase efflux pump inhibitory potency Key words: QSAR, efflux pump inhibitors, AcrAB-TolC, E coli, virtual screening i ... as AcrAB- TolC of E coli, MexAB-OprM of P aeruginosa and BpeAB-OprB of Burkholderia pseudomallei 1.2 E coli AcrAB- TolC efflux pump 1.2.1 Structure of E coli AcrAB- TolC efflux pump Although E coli. .. ABSTRACT DISSERTATION SUBMITTED IN FULFILMENT OF THE REQUIREMENTS FOR THE PHARMACIST - ACADEMIC YEAR 2014 – 2019 2D- QSAR STUDIES ON ESCHERICHIA COLI ACRAB- TOLC EFFLUX PUMP INHIBITORS NGUYEN VU...MINISTRY OF EDUCATION AND TRAINING NGUYEN TAT THANH UNIVERSITY NGUYEN VU THUY VY 2D- QSAR STUDIES ON ESCHERICHIA COLI ACRAB- TOLC EFFLUX PUMP INHIBITORS Field of study: Pharmaceutical