An in vitro investigation of novel quinolone derivatives on selected pharmacological targets for diabetes mellitus and associated complications
- Authors: Ayodele, Omobolanle Opeyemi
- Date: 2023-03-29
- Subjects: Diabetes , Hyperglycemia , Quinolone antibacterial agents , Cardiovascular system Diseases , Diabetes Alternative treatment , In vitro experiment
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/409813 , vital:70632
- Description: Diabetes mellitus (DM) is a group of endocrine and metabolic disorders characterised and identified by the presence of hyperglycaemia over a long period and, to an extent, accompanied by hyperlipidaemia. CVD has been reported to be the leading cause of mortality in patients with DM. Several antidiabetic agents are available for managing DM, but these agents are not for curative therapy and present with undesirable side effects. In addition, these agents become less effective as the patient's condition progresses to complete beta-cell failure. Therefore, developing newer antidiabetic agents with minimal undesirable side effects, prolonged efficacy and protection against the development of DM complications are necessary. This study was conducted to identify potential novel antidiabetic agents with cardiovascular-protective activity. The compounds of interest for the study were quinolone derivatives since quinolones have been reported to have an antihyperglycaemic effect. , Thesis (MSc) -- Faculty of Pharmacy, 2023
- Full Text:
- Date Issued: 2023-03-29
- Authors: Ayodele, Omobolanle Opeyemi
- Date: 2023-03-29
- Subjects: Diabetes , Hyperglycemia , Quinolone antibacterial agents , Cardiovascular system Diseases , Diabetes Alternative treatment , In vitro experiment
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/409813 , vital:70632
- Description: Diabetes mellitus (DM) is a group of endocrine and metabolic disorders characterised and identified by the presence of hyperglycaemia over a long period and, to an extent, accompanied by hyperlipidaemia. CVD has been reported to be the leading cause of mortality in patients with DM. Several antidiabetic agents are available for managing DM, but these agents are not for curative therapy and present with undesirable side effects. In addition, these agents become less effective as the patient's condition progresses to complete beta-cell failure. Therefore, developing newer antidiabetic agents with minimal undesirable side effects, prolonged efficacy and protection against the development of DM complications are necessary. This study was conducted to identify potential novel antidiabetic agents with cardiovascular-protective activity. The compounds of interest for the study were quinolone derivatives since quinolones have been reported to have an antihyperglycaemic effect. , Thesis (MSc) -- Faculty of Pharmacy, 2023
- Full Text:
- Date Issued: 2023-03-29
Design of immunosensor for the detection of C-reactive protein using oriented antibody immobilization
- Authors: Adesina, Abiola Olanike
- Date: 2020
- Subjects: Immunochemistry , Biosensors , C-reactive protein , Immunoassay , Cardiovascular system Diseases
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/163080 , vital:41010 , https://dx.doi.org/10.21504/10962/163080
- Description: Early diagnosis of cardiovascular diseases (CVDs) has been a major challenge since CVDs are clinically silent. The current methods available for the diagnosis are not sensitive enough at the onset of the disease. Also, the use of sophisticated equipments and experts in the result interpretation has created a lot of barriers to the early diagnosis of CVDs. Biomarkers detection using electrochemical immunoassay offers great advantages in terms of sensitivity, miniaturization and low cost. This can be integrated into portable devices which can be made available in the remote areas for easy assessment of health care services. The fabrication of piezoelectric and electrochemical immunosensors for the detection of C-reactive protein (a cardiac biomarker) are presented in this thesis. The electrochemical immunosensor investigates the effect of linkers chain length on the analytical performance of the immunosensor. The fabricated immunosensors were based on two simple and sensitive label-free impedimetric assay. Oriented immobilization of anti-CRP monoclonal antibody (mAb) unto gold surface was achieved using carbohydrate specific boronic ester reaction for enhanced capture and specific detection of CRP protein. Quartz crystal microbalance with dissipation (QCM-D) was employed to establish the immunocomplex formation between the mAb and CRP antigen. This was achieved by forming a self-assembled monolayer (SAM) of 4-mercaptophenylboronic acid (MPBA) onto the quartz crystal surface. The limit of detection (LoD) for the direct and sandwich immunoassay was 5.45 and 3.65 ng mL-1, respectively. The Au-MPBA-mAb/glucose immunosensor with the shortest chain length of boronic acid was fabricated. The use of SAM of 4-mercaptophenylboronic acid (MPBA) afforded a thio phenylboronic acid functionalized gold surface (Au-MPBA SAM). The anti-CRP-mAb capture antibody was immobilized in an oriented manner onto gold thiophenylboronic acid to yield an Au-MPBA-mAb surface. The non-specific boronic surface was blocked using glucose to yield an Au-MPBA-mAb/glucose. The modified gold surface could detect CRP antigen. The limit of detection (LoD) was found to be 9.82 and 6.23 ng mL-1 for the direct and sandwich immunoassay; respectively. The Au-MBA-APBA-mAb/glucose immunosensor was designed by forming a SAM of 4-mercaptobenzoic acid (MBA) onto gold electrode surface. The terminal -COOH group of the MBA SAM reacted with an amino (NH2) group the 4-aminophenylboronic acid (APBA) using EDC/NHS coupling. This was followed by the immobilization of the capture antibody and the blocking of non-specific binding sites using glucose. Improved analytical parameters were obtained with LoD for the direct and sandwich immunoassays found to be 2.90 and 1.20 ng mL-1; respectively. A more stable immunosensor utilizing electrochemical grafting was investigated for the fabrication of Au-PEA-SA-APBA-mAb/glucose. The enhanced stability of the immunosensor was through the electrochemical reduction of 4-aminoethyl benzene diazonium (AEBD) salt. The surface was further derivatized with succinic anhydride to have a carboxylic derivatized surface. Carbodiimide chemistry was used to form a covalent linkage between the APBA amine group and the surface -COOH terminal group to yield an Au-PEA-SA-APBA surface. The immobilization of mAb and glucose resulted in Au-PEA-SA-APBA-mAb/glucose immunosensor. For the detection and signal enhancement, the magnetic nanoparticles conjugated with anti-CRP polyclonal antibody (pAb) was prepared. The sandwich immunoassay was used to detect CRP by the first capture at Au-PEA-SA-APBA-mAb/glucose. This was followed by signal amplification using magnetic nanoparticles coated with a silica shell and conjugated to pAb (MNP-SiO-APTES-PBA-pAb/glucose). The limit of detection was found to be 560 pg mL-1 and much lower than sandwich immunosensor fabricated using SAMS. The signal enhancement, lower detection limits and high sensitivity were obtained due to the nanoparticles for the sandwich immunoassay. The linear range for all the fabricated immunosensor ranges from 10 – 100 ng mL-1. The sensitivity obtained for Au-MPBA-mAb/glucose, Au-MBA-APBA-mAb/glucose, and Au-PEA-SA-APBA-mAb/glucose were 0.691, 0.885, and 11.08 kΩ.ng-1.ml.cm-2 for the sandwich immunoassay. The piezoelectric immunosensor was regenerated using 0.1 M HCl without affecting the immobilized capture antibody. The real sample analysis was carried out in 10 % serum in a recovery study for all the fabricated immunosensor. The percentage of recovery was very close to 100 %. , Thesis (PhD)--Rhodes University, Science Faculty, Department of Chemistry, 2020.
- Full Text:
- Date Issued: 2020
- Authors: Adesina, Abiola Olanike
- Date: 2020
- Subjects: Immunochemistry , Biosensors , C-reactive protein , Immunoassay , Cardiovascular system Diseases
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/163080 , vital:41010 , https://dx.doi.org/10.21504/10962/163080
- Description: Early diagnosis of cardiovascular diseases (CVDs) has been a major challenge since CVDs are clinically silent. The current methods available for the diagnosis are not sensitive enough at the onset of the disease. Also, the use of sophisticated equipments and experts in the result interpretation has created a lot of barriers to the early diagnosis of CVDs. Biomarkers detection using electrochemical immunoassay offers great advantages in terms of sensitivity, miniaturization and low cost. This can be integrated into portable devices which can be made available in the remote areas for easy assessment of health care services. The fabrication of piezoelectric and electrochemical immunosensors for the detection of C-reactive protein (a cardiac biomarker) are presented in this thesis. The electrochemical immunosensor investigates the effect of linkers chain length on the analytical performance of the immunosensor. The fabricated immunosensors were based on two simple and sensitive label-free impedimetric assay. Oriented immobilization of anti-CRP monoclonal antibody (mAb) unto gold surface was achieved using carbohydrate specific boronic ester reaction for enhanced capture and specific detection of CRP protein. Quartz crystal microbalance with dissipation (QCM-D) was employed to establish the immunocomplex formation between the mAb and CRP antigen. This was achieved by forming a self-assembled monolayer (SAM) of 4-mercaptophenylboronic acid (MPBA) onto the quartz crystal surface. The limit of detection (LoD) for the direct and sandwich immunoassay was 5.45 and 3.65 ng mL-1, respectively. The Au-MPBA-mAb/glucose immunosensor with the shortest chain length of boronic acid was fabricated. The use of SAM of 4-mercaptophenylboronic acid (MPBA) afforded a thio phenylboronic acid functionalized gold surface (Au-MPBA SAM). The anti-CRP-mAb capture antibody was immobilized in an oriented manner onto gold thiophenylboronic acid to yield an Au-MPBA-mAb surface. The non-specific boronic surface was blocked using glucose to yield an Au-MPBA-mAb/glucose. The modified gold surface could detect CRP antigen. The limit of detection (LoD) was found to be 9.82 and 6.23 ng mL-1 for the direct and sandwich immunoassay; respectively. The Au-MBA-APBA-mAb/glucose immunosensor was designed by forming a SAM of 4-mercaptobenzoic acid (MBA) onto gold electrode surface. The terminal -COOH group of the MBA SAM reacted with an amino (NH2) group the 4-aminophenylboronic acid (APBA) using EDC/NHS coupling. This was followed by the immobilization of the capture antibody and the blocking of non-specific binding sites using glucose. Improved analytical parameters were obtained with LoD for the direct and sandwich immunoassays found to be 2.90 and 1.20 ng mL-1; respectively. A more stable immunosensor utilizing electrochemical grafting was investigated for the fabrication of Au-PEA-SA-APBA-mAb/glucose. The enhanced stability of the immunosensor was through the electrochemical reduction of 4-aminoethyl benzene diazonium (AEBD) salt. The surface was further derivatized with succinic anhydride to have a carboxylic derivatized surface. Carbodiimide chemistry was used to form a covalent linkage between the APBA amine group and the surface -COOH terminal group to yield an Au-PEA-SA-APBA surface. The immobilization of mAb and glucose resulted in Au-PEA-SA-APBA-mAb/glucose immunosensor. For the detection and signal enhancement, the magnetic nanoparticles conjugated with anti-CRP polyclonal antibody (pAb) was prepared. The sandwich immunoassay was used to detect CRP by the first capture at Au-PEA-SA-APBA-mAb/glucose. This was followed by signal amplification using magnetic nanoparticles coated with a silica shell and conjugated to pAb (MNP-SiO-APTES-PBA-pAb/glucose). The limit of detection was found to be 560 pg mL-1 and much lower than sandwich immunosensor fabricated using SAMS. The signal enhancement, lower detection limits and high sensitivity were obtained due to the nanoparticles for the sandwich immunoassay. The linear range for all the fabricated immunosensor ranges from 10 – 100 ng mL-1. The sensitivity obtained for Au-MPBA-mAb/glucose, Au-MBA-APBA-mAb/glucose, and Au-PEA-SA-APBA-mAb/glucose were 0.691, 0.885, and 11.08 kΩ.ng-1.ml.cm-2 for the sandwich immunoassay. The piezoelectric immunosensor was regenerated using 0.1 M HCl without affecting the immobilized capture antibody. The real sample analysis was carried out in 10 % serum in a recovery study for all the fabricated immunosensor. The percentage of recovery was very close to 100 %. , Thesis (PhD)--Rhodes University, Science Faculty, Department of Chemistry, 2020.
- Full Text:
- Date Issued: 2020
Development and assessment of gastroretentive sustained release captopril tablets
- Authors: Mukozhiwa, Samantha Yolanda
- Date: 2014-04-11
- Subjects: Captopril , Drug delivery systems , Drugs Controlled release , Cardiovascular system Diseases , Cardiovascular agents , Angiotensin converting enzyme Inhibitors
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/480301 , vital:78427
- Description: Cardiovascular diseases (CVD) are the leading cause of death worldwide and global projections predict that the number of deaths due to CVD will continue to increase over the next 17 years [1]. With the growing burden of CVD the design and development of formulations that optimise the delivery of existing therapeutic molecules may be an approach to improving the management of patients with CVD. Captopril (CPT) is an angiotensin converting enzyme (ACE) inhibitor used for the routine management of hypertension, cardiac failure and diabetic nephropathy [2-4]. However it has a relatively short half-life and typical therapeutic dosing regimens require multiple dosing [2]. CPT is a potential candidate for sustained oral drug delivery, however its poor stability profile and high water solubility present significant formulation challenges. CPT exhibits optimal stability at pH < 4 and is unstable in the alkaline environment of intestinal fluids [5]. A sustained release gastroretentive formulation is therefore proposed as an approach that may improve the in vivo stability of CPT in addition to slowly releasing the molecule at a desired rate that may also minimize the occurrence of drug-related adverse effects. A Capillary Zone Electrophoresis (CZE) method for the quantitation of CPT in pharmaceutical dosage forms was developed and optimised using a Central Composite Design (CCD) approach. The CZE method was found to have the necessary linearity, accuracy, precision, sensitivity and specificity for the analysis of CPT in pharmaceutical formulations. Preformulation studies were conducted as part of the preparative work required to manufacture high quality, stable gastroretentive sustained release CPT tablets. The experiments conducted were tailored for the development of CPT sustained release tablets using direct compression manufacture and included an analysis of particle size and shape, powder flow properties and CPT-excipient compatibility studies. The results revealed that there was no definite evidence of interactions between CPT and the excipients to be used to manufacture CPT tablets, and CPT formulations were developed using these excipients. A direct compression procedure was selected for tablet manufacture due to apparent simplicity and to avoid unnecessary exposure of CPT to the heat and moisture that would be encountered if a wet granulation manufacturing process was used. A numerical optimisation approach was used to predict a formulation composition that would produce minimal CPT release initially, a short floating lag time (FLT) and maximum CPT release after 12 hours of dissolution testing. The effect of increasing the agitation speed of USP Apparatus 2 on the release of CPT from the optimised formulation was also investigated. The results revealed that changing the speed of the paddle had only a relatively small impact on the in vitro release behaviour of CPT from the tablets. The optimised formulation was subjected to additional testing in an attempt to investigate the effects of pH and osmolarity on the swelling and erosion characteristics of the dosage form. It was important to evaluate the effects of pH and osmolarity from the perspective of the solubility and stability of CPT. The results generated from swelling studies revealed that the swelling characteristics of the proposed formulation were not significantly altered by a change in pH and osmolarity of the test medium and this is probably due to the non-ionic nature of HPMC. In addition, the results revealed that the solubility and/or stability of CPT in different dissolution media did not affect the water uptake and swelling of the tablet matrices. The results revealed the erosion rate constants were low and suggest that although polymer erosion does occur, the role of this phenomenon in the release of CPT may not be as significant as that of diffusion. The release kinetics of CPT from the tablets was established by fitting in vitro release data to several mathematical models. The in vitro release data were best described using the Korsmeyer-Peppas model and values of release exponent (n) suggest that the majority of the tablets exhibited an anomalous CPT transport mechanism. The short-term stability of the optimised formulation was established by undertaking stability studies at 25°/60% RH and 40°/75% RH. The results revealed that there was no significant change in appearance and physicochemical properties of the tablets over 60 days. In conclusion, gastroretentive sustained release CPT tablets with the potential for further development and optimisation have been successfully developed and assessed in these studies. A basis is thus provided for further development of this technology. , Thesis (MSc (Pharm)) -- Faculty of Pharmacy, 2014
- Full Text:
- Date Issued: 2014-04-11
- Authors: Mukozhiwa, Samantha Yolanda
- Date: 2014-04-11
- Subjects: Captopril , Drug delivery systems , Drugs Controlled release , Cardiovascular system Diseases , Cardiovascular agents , Angiotensin converting enzyme Inhibitors
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/480301 , vital:78427
- Description: Cardiovascular diseases (CVD) are the leading cause of death worldwide and global projections predict that the number of deaths due to CVD will continue to increase over the next 17 years [1]. With the growing burden of CVD the design and development of formulations that optimise the delivery of existing therapeutic molecules may be an approach to improving the management of patients with CVD. Captopril (CPT) is an angiotensin converting enzyme (ACE) inhibitor used for the routine management of hypertension, cardiac failure and diabetic nephropathy [2-4]. However it has a relatively short half-life and typical therapeutic dosing regimens require multiple dosing [2]. CPT is a potential candidate for sustained oral drug delivery, however its poor stability profile and high water solubility present significant formulation challenges. CPT exhibits optimal stability at pH < 4 and is unstable in the alkaline environment of intestinal fluids [5]. A sustained release gastroretentive formulation is therefore proposed as an approach that may improve the in vivo stability of CPT in addition to slowly releasing the molecule at a desired rate that may also minimize the occurrence of drug-related adverse effects. A Capillary Zone Electrophoresis (CZE) method for the quantitation of CPT in pharmaceutical dosage forms was developed and optimised using a Central Composite Design (CCD) approach. The CZE method was found to have the necessary linearity, accuracy, precision, sensitivity and specificity for the analysis of CPT in pharmaceutical formulations. Preformulation studies were conducted as part of the preparative work required to manufacture high quality, stable gastroretentive sustained release CPT tablets. The experiments conducted were tailored for the development of CPT sustained release tablets using direct compression manufacture and included an analysis of particle size and shape, powder flow properties and CPT-excipient compatibility studies. The results revealed that there was no definite evidence of interactions between CPT and the excipients to be used to manufacture CPT tablets, and CPT formulations were developed using these excipients. A direct compression procedure was selected for tablet manufacture due to apparent simplicity and to avoid unnecessary exposure of CPT to the heat and moisture that would be encountered if a wet granulation manufacturing process was used. A numerical optimisation approach was used to predict a formulation composition that would produce minimal CPT release initially, a short floating lag time (FLT) and maximum CPT release after 12 hours of dissolution testing. The effect of increasing the agitation speed of USP Apparatus 2 on the release of CPT from the optimised formulation was also investigated. The results revealed that changing the speed of the paddle had only a relatively small impact on the in vitro release behaviour of CPT from the tablets. The optimised formulation was subjected to additional testing in an attempt to investigate the effects of pH and osmolarity on the swelling and erosion characteristics of the dosage form. It was important to evaluate the effects of pH and osmolarity from the perspective of the solubility and stability of CPT. The results generated from swelling studies revealed that the swelling characteristics of the proposed formulation were not significantly altered by a change in pH and osmolarity of the test medium and this is probably due to the non-ionic nature of HPMC. In addition, the results revealed that the solubility and/or stability of CPT in different dissolution media did not affect the water uptake and swelling of the tablet matrices. The results revealed the erosion rate constants were low and suggest that although polymer erosion does occur, the role of this phenomenon in the release of CPT may not be as significant as that of diffusion. The release kinetics of CPT from the tablets was established by fitting in vitro release data to several mathematical models. The in vitro release data were best described using the Korsmeyer-Peppas model and values of release exponent (n) suggest that the majority of the tablets exhibited an anomalous CPT transport mechanism. The short-term stability of the optimised formulation was established by undertaking stability studies at 25°/60% RH and 40°/75% RH. The results revealed that there was no significant change in appearance and physicochemical properties of the tablets over 60 days. In conclusion, gastroretentive sustained release CPT tablets with the potential for further development and optimisation have been successfully developed and assessed in these studies. A basis is thus provided for further development of this technology. , Thesis (MSc (Pharm)) -- Faculty of Pharmacy, 2014
- Full Text:
- Date Issued: 2014-04-11
Insights: elucidation of squalene monooxygenase inhibitors for lowering cholesterol in cardiovascular diseases
- Authors: Leoma, Mofeli Benedict
- Date: 2024-04-04
- Subjects: Squalene monooxygenase , Cholesterol , Cardiovascular system Diseases , Anticholesteremic agents , Molecular dynamics , High throughput screening (Drug development) , Molecular Docking
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/434861 , vital:73111
- Description: Statins have been used to lower high cholesterol levels in the past few decades. However, several studies have shown that some people taking statins experience side effects over time, especially elderly patients, women of childbirth possibility, and children. Several studies have shown that the majority of people with underlying cardiovascular complications caused by high cholesterol are at a greater risk of fatality due to COVID-19, regardless of age and sex. The literature suggests that antimycotic squalene monooxygenase inhibitors, terbinafine and its derivatives, and anticholesterolemic squalene monooxygenase (SM) inhibitors could be another option and a safer remedy for lowering cholesterol in mammals. Molecular docking calculations, molecular dynamics (MD) simulations, molecular mechanics generalized born surface area (MM-GBSA) calculations, quantum mechanics/molecular mechanics calculations (QM/MM), and density functional theory (DFT) calculations were used in this study. An early stage in drug discovery, in which small molecular hits from high- throughput screening (HTS) are evaluated and undergo limited optimization to identify promising lead compounds, is referred to as lead generation. To address the first step of lead generation, the number of compounds to be tested was narrowed down, and the hit compounds that could be taken for further tests were obtained. Thus, the molecular docking technique was taken advantage of, which assisted us in identifying the antimycotic ligand SDZ 18, which had a good binding affinity of about -8,4 kcal mol−1. Another widely employed strategy, the molecular mechanics-generalized born surface area (MM-GBSA), was used to investigate the binding free energies of the protein-ligand complexes to validate the binding affinities obtained from molecular docking. Despite the excellent docking results, it must be emphasized that the stability of the ligand in the binding pocket must be investigated. To address this, the protein-ligand complexes were then taken through molecular dynamics for 100 ns simulations calculations which showed that the inhibitors stayed in the binding pocket with the RMSD values below 3.5 Å for most systems. This provided insight into a realistic model because the docked complexes were placed in conditions closer to the physiological environment at 300 K and 1.01325 bar, and in an explicitly solvated dynamic environment. Density functional theory (DFT) at the B3LPY level of theory using the standard 6-31G(d,p) basis set was used to assess the reactivity and other properties of the SM inhibitors. ONIOM calculations were performed to explain what was happening at the microscopic level by calculating the total energy of the complex. The aim of this project was to efficiently uncover the non-physical aspects of SM inhibitors with the help of computational techniques to identify new drugs that can lower high cholesterol levels. From a theoretical perspective, the results obtained from docking indicated that the antimycotic ligands SDZ SBA 586 18 and TNSA 84 (trisnor-squalene alcohol ) have good binding affinities, and the MM-GBSA method provided free energy calculations. MD results indicated that the stability of the ligand in the binding pocket was achieved during the 100 ns simulations. The HOMO-LUMO energy gaps obtained from DFT calculations provided information on the reactivity of the ligands. Other insights into the protein-ligand complexes were obtained from a hybrid ONIOM QM/MM study. , Thesis (MSc) -- Faculty of Science, Chemistry, 2024
- Full Text:
- Date Issued: 2024-04-04
- Authors: Leoma, Mofeli Benedict
- Date: 2024-04-04
- Subjects: Squalene monooxygenase , Cholesterol , Cardiovascular system Diseases , Anticholesteremic agents , Molecular dynamics , High throughput screening (Drug development) , Molecular Docking
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/434861 , vital:73111
- Description: Statins have been used to lower high cholesterol levels in the past few decades. However, several studies have shown that some people taking statins experience side effects over time, especially elderly patients, women of childbirth possibility, and children. Several studies have shown that the majority of people with underlying cardiovascular complications caused by high cholesterol are at a greater risk of fatality due to COVID-19, regardless of age and sex. The literature suggests that antimycotic squalene monooxygenase inhibitors, terbinafine and its derivatives, and anticholesterolemic squalene monooxygenase (SM) inhibitors could be another option and a safer remedy for lowering cholesterol in mammals. Molecular docking calculations, molecular dynamics (MD) simulations, molecular mechanics generalized born surface area (MM-GBSA) calculations, quantum mechanics/molecular mechanics calculations (QM/MM), and density functional theory (DFT) calculations were used in this study. An early stage in drug discovery, in which small molecular hits from high- throughput screening (HTS) are evaluated and undergo limited optimization to identify promising lead compounds, is referred to as lead generation. To address the first step of lead generation, the number of compounds to be tested was narrowed down, and the hit compounds that could be taken for further tests were obtained. Thus, the molecular docking technique was taken advantage of, which assisted us in identifying the antimycotic ligand SDZ 18, which had a good binding affinity of about -8,4 kcal mol−1. Another widely employed strategy, the molecular mechanics-generalized born surface area (MM-GBSA), was used to investigate the binding free energies of the protein-ligand complexes to validate the binding affinities obtained from molecular docking. Despite the excellent docking results, it must be emphasized that the stability of the ligand in the binding pocket must be investigated. To address this, the protein-ligand complexes were then taken through molecular dynamics for 100 ns simulations calculations which showed that the inhibitors stayed in the binding pocket with the RMSD values below 3.5 Å for most systems. This provided insight into a realistic model because the docked complexes were placed in conditions closer to the physiological environment at 300 K and 1.01325 bar, and in an explicitly solvated dynamic environment. Density functional theory (DFT) at the B3LPY level of theory using the standard 6-31G(d,p) basis set was used to assess the reactivity and other properties of the SM inhibitors. ONIOM calculations were performed to explain what was happening at the microscopic level by calculating the total energy of the complex. The aim of this project was to efficiently uncover the non-physical aspects of SM inhibitors with the help of computational techniques to identify new drugs that can lower high cholesterol levels. From a theoretical perspective, the results obtained from docking indicated that the antimycotic ligands SDZ SBA 586 18 and TNSA 84 (trisnor-squalene alcohol ) have good binding affinities, and the MM-GBSA method provided free energy calculations. MD results indicated that the stability of the ligand in the binding pocket was achieved during the 100 ns simulations. The HOMO-LUMO energy gaps obtained from DFT calculations provided information on the reactivity of the ligands. Other insights into the protein-ligand complexes were obtained from a hybrid ONIOM QM/MM study. , Thesis (MSc) -- Faculty of Science, Chemistry, 2024
- Full Text:
- Date Issued: 2024-04-04
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