Montclair State University Montclair State University Digital Commons Theses, Dissertations and Culminating Projects 1-2020 A Comparative Study of Drug Affinities Determinedy b Thermofluor and Kinetic Analysis Oruba Shatnawi Montclair State University, [email protected] Follow this and additional works at: https://digitalcommons.montclair.edu/etd Part of the Other Chemistry Commons Recommended Citation Shatnawi, Oruba, "A Comparative Study of Drug Affinities Determined by Thermofluor and Kinetic Analysis" (2020). Theses, Dissertations and Culminating Projects. 330. https://digitalcommons.montclair.edu/etd/330 This Thesis is brought to you for free and open access by Montclair State University Digital Commons. It has been accepted for inclusion in Theses, Dissertations and Culminating Projects by an authorized administrator of Montclair State University Digital Commons. For more information, please contact [email protected]. Abstract Determining the binding affinity and potency in vitro is one of the significant steps that can give a clue for a new candidate drug during the drug discovery process. Thermofluor is a method used in measuring binding affinity (Kd) of protein-ligands interaction through determining the change in thermal denaturation temperature of protein using real time PCR (RT-PCR). Kinetic analysis assay is used to screen a library of compounds to calculate their potencies (IC50) and inhibition constants (Ki) and it can be performed by spectrophotometer technique. In this study, we used bovine carbonic anhydrase II (BCA II) enzyme, and four of its inhibitors as a model to compare drug affinities, which were determined either by Fluorescence Thermal Shift Assay (FTSA) using Sypro Orange dye or kinetic assay using 4-Nitrophenyl acetate as a substrate to measure the nonphysiologically esterase activity of CA. The inhibitors studied were Methazolamide, Brinzolamide, Dorzolamide HCl and Mafenide HCl. The Kd values were determined to be 5.4±0.085 µM, 1.2±0.44 µM, 2.08±0.63 µM, and IC50 values were 0.148±0.024 µM 0.129±0.015 µM 0.092±0.01 µM 1.715±0.16 µM whereas the Ki values were 4±0.55 nM, 3.5±0.5 nM, 2.5±0.5 nM and 46.5±6.5 nM for Methazolamide, Brinzolamide, Dorzolamide HCl and Mafenide HCl, respectively. The potencies (IC50) of the inhibitors were10-50 fold lower than that of the Kd values. In addition, Kd values were higher compared to Ki values. Therefore, kinetic analysis is a more sensitive technique and requires a lower amount of the enzyme to measure drug affinity than FTSA. I II A COMPARATIVE STUDY OF DRUG AFFINITIES DETERMINED BY THERMOFLUOR AND KINETIC ANALYSIS A THESIS Submitted in partial fulfillment of the requirements For the degree of Master of Science By ORUBA SHATNAWI Montclair State University Montclair, NJ 2020 III Acknowledgements I would like to express my deep gratitude to my supervisor, Dr. Siekierka for his invaluable advice, continuous encouragement and direction. I’m particularly thankful to my committees, Dr. Goody and Dr. Rotella for their support and encouragement throughout my study. I would like to thank Tamara Kriess, Tyler Eck, Brittany Hart and Thomas Candela for their technical instruction, patient troubleshooting assistance and support. I’m grateful to my husband, Salman for his inspiration, encouragement, moral help and patience while I completed my thesis. Without his support nothing could be done. I dedicate my work to my parents, this research work would not have come to light without their blessing, to my daughters, Layan, Kenda and Dariya. To my Family and friends IV Table of Contents Acknowledgements……………………...…………………………………...……IV List of Figures………………………………....……………………………….…VI Background: Literature Review……………………………………………………1 Materials and Methods………………….…………………………………………10 Results ……………………………………………………………………….….14 Discussion…………………………………………….……………………….….24 Conclusion……………………………………………………………….……….27 Bibliography…………………………………...…………………...………….....28 V List of Figures Figure 1: Drug discovery process ……………………………………………...2 Figure 2: The two-state transition curve ……………………………………….6 Figure 3: Comparison of fluorescence signal with Sypro Orange dye and Sybr Green dye………...……………………………………………………….11 Figure 4: Thermal unfolding of different concentrations of BCA II monitored by SYPRO Orange………………………………………………….15 Figure 5: (A) Thermal shift curves of unfolding transition of CA with Methazolamide …………………………………………………………...……17 Figure 5: (B) ∆Tm of CA and Methazolamide VS Methazolamide concentration ………………………………………………………………….17 Figure 6: (A) Thermal shift curves of unfolding transition of CA with Brinzolamide …………………………………………………………………...18 Figure 6: (B) ∆Tm of CA with Brinzolamide VS Brinzolamide concentration ……………………………………………………………………………….…18 Figure 7: (A) Thermal shift curves of unfolding transition of CA with Dorzolamide HCl …………………………………………………………………………….19 Figure 7: (B) ∆Tm of CA with Dorzolamide HCl VS Dorzolamide HCl concentration …………………………………………………………………...19 VI Figure 8: (A) Thermal shift curves of unfolding transition of CA with Mafenide HCl…………………………………………………………………………………...20 Figure 10: Figure 9: Plot of Michaels-Menten equation. Velocity vs N-NPA……….21 Figure 9: IC50 Curves of Methazolamide, Brinzolamide, Dorzolamide HCl and Mafenide HCl………………………………………………………………………...22 Table 1: Values of Kd and IC50...………………………...………………...………...23 VII Background: Literature Review Drug discovery The drug discovery process takes about 12-15 years, and more than 1 billion dollars to come up with any new candidate drug (Fig. 1). It may take many years to build up a body of supporting evidence before selecting a target for a costly drug discovery program. Many challenges are present in drug discovery and pharmaceutical industry, such as target identification, hit to lead optimization and evaluation of drug candidates (Hughes, Rees, Kalindjian, & Philpott, 2011).. The hit to lead to process is a valuable technique for distinguishing drug candidates. Determining the binding affinity and potency in vitro, is one of the hit to lead optimization steps that can give a clue for the candidate drug (Wang, Dong, & Sheng, 2019). Creating of methods for rapid screening of inhibitors of specific enzyme from compound library is one of the main challenges in drug discovery, especially for new targets where the goal is to study and recognize their potential inhibitors (Lo et al., 2004). 1 Figure 1: Drug discovery process. FDA, Food and Drug Administration; IND, Investigational New Drug; NDA, New Drug Application (Hughes et al., 2011). Universal and valid drug discovery assay technique are desired in order to get ahead with the latest developments in combinatorial chemistry and genomics-based target production (Pantoliano et al., 2001).Enzymatic assays (e.g. Fluorescence or absorbance spectroscopy) are commonly used in measuring the potencies of compounds in laboratories. While binding assay such as Fluorescence Thermal shift Assay (FTSA) is used to measure the compound affinity. Many compounds that are assumed to be potential drugs in treating human diseases, are firstly known through studying their binding properties like affinity and potency (FDA, 2003). Enzymatic assay (kinetic analysis): Enzymatic assays play critical roles in determining the reaction rate, binding affinity, catalytic constant, and inhibition rate as well as screening library of compounds. (FDA, 2003). 2 One of the major assays is used to estimate Vmax (the maximum velocity of the reaction) and KM (Michaelis-Menten constant), which is the substrate concentration at half of V max (Eq. 1) (Choi, Rempala, & Kim, 2017). Where the rate of the reaction is measured in time course by monitoring the absorbance of the product release or the substrate consumption over period of time ((Boeckx, Hertog, Geeraerd, & Nicolai, 2017).. 푽풎풂풙[푺] 흊 = Eq. 1 푲풎+[푺] Where [S] is the substrate constant; Vmax is the maximal velocity and Km is the Michaelis constant which is the substrate concentration of Vmax/2 IC50 Assay: Dose response relationship is displayed by fitting the response against the log of the inhibitor concentration through the application of the equation of Four- Parameter Logistic Function (Eq. 2), (Krohn & Link, 2003). 푻풐풑−푩풐풕풕풐풎 풚 = 푩풐풕풕풐풎 + Eq. 2 ퟏ+ퟏퟎ 풍풐품푰푪ퟓퟎ−풍풐품풙 ∗푯풊풍풍푺풍풐풑풆 Where y is: response, x: log of inhibitor concentration, Top and Bottom: plateaus in same unit as y, same log unit as x, Hillslope: slop factor or hill slop (unitless). High throughput screening assays are mainly used to examine enzyme activity and inhibitor efficacy. A total inhibitor concentration that decreases enzyme activity by 50% (IC50) is the most used pharmacokinetic measure of a drug's efficacy and potency. It is a quantitative measure that indicates the concentration of a drug or substance that is required to inhibit a specific biological activity by a half (Aykul & Martinez-Hackert, 2016). 3 Inhibition constant Ki: Inhibition constant (Ki) is a guide of how potent an inhibitor is, and it is the concentration of the inhibitor desired to produce half maximum inhibition. For competitive inhibitors It can be calculated by Cheng-Prusoff equation (Eq. 3) (Lazareno & Birdsall, 1993). 퐼퐶50 퐾푖 = Eq.3 1+ 푆 /퐾푚 Binding assays: Binding affinity is the strength of the binding interaction between protein and its ligands (like inhibitors or activators). It is generally estimated by the binding affinity constant also known as equilibrium dissociation constant (Kd). The smaller the Kd value, the greater the binding affinity of the ligand for its target(Pollard,