Inhibitory effects of selected cannabinoids against dipeptidyl peptidase IV, an enzyme linked to type 2 diabetes
- Mkabayi, Lithalethu, Viljoen, Zenobia, Krause, Rui W M, Lobb, Kevin A, Pletschke, Brett I, Frost, Carminita L
- Authors: Mkabayi, Lithalethu , Viljoen, Zenobia , Krause, Rui W M , Lobb, Kevin A , Pletschke, Brett I , Frost, Carminita L
- Date: 2024
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452760 , vital:75168 , xlink:href="https://doi.org/10.1016/j.heliyon.2023.e23289"
- Description: Ethnopharmacological relevance: In recent times the decriminalisation of cannabis globally has increased its use as an alternative medication. Where it has been used in modern medicinal practises since the 1800s, there is limited scientific investigation to understand the biological activities of this plant. Aim of the study: Dipeptidyl peptidase IV (DPP-IV) plays a key role in regulating glucose homeostasis, and inhibition of this enzyme has been used as a therapeutic approach to treat type 2 diabetes. However, some of the synthetic inhibitors for this enzyme available on the market may cause undesirable side effects. Therefore, it is important to identify new inhibitors of DPP-IV and to understand their interaction with this enzyme.
- Full Text:
- Date Issued: 2024
- Authors: Mkabayi, Lithalethu , Viljoen, Zenobia , Krause, Rui W M , Lobb, Kevin A , Pletschke, Brett I , Frost, Carminita L
- Date: 2024
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452760 , vital:75168 , xlink:href="https://doi.org/10.1016/j.heliyon.2023.e23289"
- Description: Ethnopharmacological relevance: In recent times the decriminalisation of cannabis globally has increased its use as an alternative medication. Where it has been used in modern medicinal practises since the 1800s, there is limited scientific investigation to understand the biological activities of this plant. Aim of the study: Dipeptidyl peptidase IV (DPP-IV) plays a key role in regulating glucose homeostasis, and inhibition of this enzyme has been used as a therapeutic approach to treat type 2 diabetes. However, some of the synthetic inhibitors for this enzyme available on the market may cause undesirable side effects. Therefore, it is important to identify new inhibitors of DPP-IV and to understand their interaction with this enzyme.
- Full Text:
- Date Issued: 2024
Crystal structure, Hirshfeld surface analysis and computational studies of (E)-2, 2-dimethyl-4-styryl-2, 3-dihydro-1H-benzo [b][1, 4] diazepine
- Odame, Felix, Madanhire, T, Hosten, Eric C, Lobb, Kevin A
- Authors: Odame, Felix , Madanhire, T , Hosten, Eric C , Lobb, Kevin A
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452677 , vital:75161 , xlink:href="https://doi.org/10.48317/IMIST.PRSM/morjchem-v11i3.40773"
- Description: The crystal structure, Hirshfeld surface analysis, and computational studies of (E)-2,2-dimethyl-4-styryl-2,3-dihydro-1H-benzo[b][1,4]diazepine have been presented. The compound crystallized in the monoclinic space group P21/c with 8 molecules in it unit cell. A comparison of the experimental and computed bond lengths and bond angles showed good agreement among the results with varying deviations from each other. A discussion of the Hirshfeld surface analysis of the compound have been carried out to provide insight into the structural properties of the compound.
- Full Text:
- Date Issued: 2023
- Authors: Odame, Felix , Madanhire, T , Hosten, Eric C , Lobb, Kevin A
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452677 , vital:75161 , xlink:href="https://doi.org/10.48317/IMIST.PRSM/morjchem-v11i3.40773"
- Description: The crystal structure, Hirshfeld surface analysis, and computational studies of (E)-2,2-dimethyl-4-styryl-2,3-dihydro-1H-benzo[b][1,4]diazepine have been presented. The compound crystallized in the monoclinic space group P21/c with 8 molecules in it unit cell. A comparison of the experimental and computed bond lengths and bond angles showed good agreement among the results with varying deviations from each other. A discussion of the Hirshfeld surface analysis of the compound have been carried out to provide insight into the structural properties of the compound.
- Full Text:
- Date Issued: 2023
Crystal Structure, Hirshfeld Surface Analysis and Computational Studies of Two Benzo [b][1, 4] Diazepine Derivatives
- Odame, Felix, Madanhire, T, Hosten, Eric C, Lobb, Kevin A
- Authors: Odame, Felix , Madanhire, T , Hosten, Eric C , Lobb, Kevin A
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452689 , vital:75162 , xlink:href="https://doi.org/10.1134/S0022476623120041"
- Description: The DFT computational studies, crystal structures and Hirshfeld surface analysis of (E)-4-(2-chlorostyryl)-2,2-dimethyl-2,3-dihydro-1H-benzo[b][1,4]diazepine (1) and (E)-4-(2-(2,2-dimethyl-2,3-dihydro-1H-benzo[b][1,4]diazepin-4-yl)vinyl)phenol (2) have been presented. The compounds crystallized in the monoclinic space group P21/c with 4 molecules in their unit cells each. The experimental and computed bond lengths and bond angles deviated from each other to some extent but also showed good agreement with each other in some cases. Hirshfeld surface analysis of the compounds provided further information about the structural properties of the compounds.
- Full Text:
- Date Issued: 2023
- Authors: Odame, Felix , Madanhire, T , Hosten, Eric C , Lobb, Kevin A
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452689 , vital:75162 , xlink:href="https://doi.org/10.1134/S0022476623120041"
- Description: The DFT computational studies, crystal structures and Hirshfeld surface analysis of (E)-4-(2-chlorostyryl)-2,2-dimethyl-2,3-dihydro-1H-benzo[b][1,4]diazepine (1) and (E)-4-(2-(2,2-dimethyl-2,3-dihydro-1H-benzo[b][1,4]diazepin-4-yl)vinyl)phenol (2) have been presented. The compounds crystallized in the monoclinic space group P21/c with 4 molecules in their unit cells each. The experimental and computed bond lengths and bond angles deviated from each other to some extent but also showed good agreement with each other in some cases. Hirshfeld surface analysis of the compounds provided further information about the structural properties of the compounds.
- Full Text:
- Date Issued: 2023
In silico substrate-binding profiling for SARS-CoV-2 Main protease (Mpro) using Hexapeptide substrates
- Zabo, Sophakama, Lobb, Kevin A
- Authors: Zabo, Sophakama , Lobb, Kevin A
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452711 , vital:75164 , xlink:href="https://doi.org/10.3390/v15071480"
- Description: The SARS-CoV-2 main protease (Mpro) is essential for the life cycle of the COVID-19 virus. It cleaves the two polyproteins at 11 positions to generate mature proteins for virion formation. The cleavage site on these polyproteins is known to be Leu-Gln↓(Ser/Ala/Gly). A range of hexapeptides that follow the known sequence for recognition and cleavage was constructed using RDKit libraries and complexed with the crystal structure of Mpro (PDB ID 6XHM) through extensive molecular docking calculations. A subset of 131 of these complexes underwent 20 ns molecular dynamics simulations. The analyses of the trajectories from molecular dynamics included principal component analysis (PCA), and a method to compare PCA plots from separate trajectories was developed in terms of encoding PCA progression during the simulations. The hexapeptides formed stable complexes as expected, with reproducible molecular docking of the substrates given the extensiveness of the procedure. Only Lys-Leu-Gln*** (KLQ***) sequence complexes were studied for molecular dynamics. In this subset of complexes, the PCA analysis identified four classifications of protein motions across these sequences. KLQ*** complexes illustrated the effect of changes in substrate on the active site, with implications for understanding the substrate recognition of Mpro and informing the development of small molecule inhibitors.
- Full Text:
- Date Issued: 2023
- Authors: Zabo, Sophakama , Lobb, Kevin A
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452711 , vital:75164 , xlink:href="https://doi.org/10.3390/v15071480"
- Description: The SARS-CoV-2 main protease (Mpro) is essential for the life cycle of the COVID-19 virus. It cleaves the two polyproteins at 11 positions to generate mature proteins for virion formation. The cleavage site on these polyproteins is known to be Leu-Gln↓(Ser/Ala/Gly). A range of hexapeptides that follow the known sequence for recognition and cleavage was constructed using RDKit libraries and complexed with the crystal structure of Mpro (PDB ID 6XHM) through extensive molecular docking calculations. A subset of 131 of these complexes underwent 20 ns molecular dynamics simulations. The analyses of the trajectories from molecular dynamics included principal component analysis (PCA), and a method to compare PCA plots from separate trajectories was developed in terms of encoding PCA progression during the simulations. The hexapeptides formed stable complexes as expected, with reproducible molecular docking of the substrates given the extensiveness of the procedure. Only Lys-Leu-Gln*** (KLQ***) sequence complexes were studied for molecular dynamics. In this subset of complexes, the PCA analysis identified four classifications of protein motions across these sequences. KLQ*** complexes illustrated the effect of changes in substrate on the active site, with implications for understanding the substrate recognition of Mpro and informing the development of small molecule inhibitors.
- Full Text:
- Date Issued: 2023
Inclusion complexation and liposomal encapsulation of an isoniazid hydrazone derivative in cyclodextrin for pH-dependent controlled release
- Safari, Justin B, Mona, Lamine B, Sekaleli, Bafokeng T, Avudi, Bénite K, Isamura, Bienfait K, Mukubwa, Grady K, Salami, Sodeeq A, Mbinze, Jérémie K, Lobb, Kevin A, Krause, Rui W M, Nkanga, Christian I
- Authors: Safari, Justin B , Mona, Lamine B , Sekaleli, Bafokeng T , Avudi, Bénite K , Isamura, Bienfait K , Mukubwa, Grady K , Salami, Sodeeq A , Mbinze, Jérémie K , Lobb, Kevin A , Krause, Rui W M , Nkanga, Christian I
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452727 , vital:75166 , xlink:href="https://doi.org/10.1016/j.jddst.2023.104302"
- Description: Tuberculosis, a predominantly pulmonary pathology, is currently the deadliest infection worldwide. Its treatment is based on combination therapy involving selected antimicrobials including Isoniazid. However, physicochemical properties of isoniazid negatively affect the clinical performance of current tuberculosis regimens, causing drug resistance development and increasing mortality rates. Liposomal encapsulation improves antituberculosis drug delivery; however, nano-formulation of isoniazid remains challenging due to its small molecular size and high hydrophilicity. Therefore, this study aimed to derivatize isoniazid and formulate a controlled delivery system using the concept of drug-in-cyclodextrins-in-liposomes to enhance drug biopharmaceutical properties. A prodrug of isoniazid was synthesized and screened for its ability to form stable complexes with α, β, and γ cyclodextrins. A selected inclusion complex with β-cyclodextrin was encapsulated in liposomes and assessed for controlled release of isoniazid. Successful formation of a 1:1 complex was established and characterized, followed by molecular modeling studies to demonstrate strength of the interactions within the complex and predicted complex structure. The inclusion complex was successfully encapsulated in liposomes using the thin film hydration method and the ethanol injection ultrasonic dispersion, with the latter giving the best results. These findings demonstrate the potential.
- Full Text:
- Date Issued: 2023
- Authors: Safari, Justin B , Mona, Lamine B , Sekaleli, Bafokeng T , Avudi, Bénite K , Isamura, Bienfait K , Mukubwa, Grady K , Salami, Sodeeq A , Mbinze, Jérémie K , Lobb, Kevin A , Krause, Rui W M , Nkanga, Christian I
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452727 , vital:75166 , xlink:href="https://doi.org/10.1016/j.jddst.2023.104302"
- Description: Tuberculosis, a predominantly pulmonary pathology, is currently the deadliest infection worldwide. Its treatment is based on combination therapy involving selected antimicrobials including Isoniazid. However, physicochemical properties of isoniazid negatively affect the clinical performance of current tuberculosis regimens, causing drug resistance development and increasing mortality rates. Liposomal encapsulation improves antituberculosis drug delivery; however, nano-formulation of isoniazid remains challenging due to its small molecular size and high hydrophilicity. Therefore, this study aimed to derivatize isoniazid and formulate a controlled delivery system using the concept of drug-in-cyclodextrins-in-liposomes to enhance drug biopharmaceutical properties. A prodrug of isoniazid was synthesized and screened for its ability to form stable complexes with α, β, and γ cyclodextrins. A selected inclusion complex with β-cyclodextrin was encapsulated in liposomes and assessed for controlled release of isoniazid. Successful formation of a 1:1 complex was established and characterized, followed by molecular modeling studies to demonstrate strength of the interactions within the complex and predicted complex structure. The inclusion complex was successfully encapsulated in liposomes using the thin film hydration method and the ethanol injection ultrasonic dispersion, with the latter giving the best results. These findings demonstrate the potential.
- Full Text:
- Date Issued: 2023
Inhibiting human dipeptidyl peptidase IV using cannabinoids and Leonotis leonurus extracts as a potential therapy for the management of diabetes
- Mkabayi, Lithalethu, Viljoen, Zenobia, Lobb, Kevin A, Pletschke, Brett I, Frost, Carminita L
- Authors: Mkabayi, Lithalethu , Viljoen, Zenobia , Lobb, Kevin A , Pletschke, Brett I , Frost, Carminita L
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452745 , vital:75167 , xlink:href="https://www.thieme-connect.com/products/ejournals/html/10.1055/s-0043-1773924"
- Description: Diabetes is a chronic metabolic disorder that has been shown to affect a growing number of people worldwide. Controlling blood glucose levels is one of the possible strategies to treat type 2 diabetes mellitus (T2DM). It has been established that the inhibition of dipeptidyl peptidase IV (DPP-IV) prolongs the activity of incretin hormones, which serve as key stimulators of insulin secretion and regulation of blood glucose levels. Although several synthetic DPP-IV inhibitors are available, there is still a need for naturally sourced inhibitors that have fewer to no undesirable side effects. In this study, cannabinoids and Leonotis leonurus aqueous extracts were evaluated for their inhibitory effects against recombinant human DPP-IV. Their potential inhibition mechanism was explored using in vitro and in silico approaches. All tested cannabinoids and L. leonurus aqueous extracts showed significant inhibitory activity against DPP-IV. Phytochemical analysis of L. leonurus extract indicated the presence of diterpenoids and alkaloids, which might contribute to the inhibitory activity. In molecular docking studies, among different constituents known in L. leonurus, luteolin and marrubiin showed binding energy of -7.2 kcal/mol and cannabinoids (cannabidiol, cannabigerol, cannabinol and Δ9-tetrahydrocannabinol) showed binding energies ranging from -6.5 to -8.2 kcal/mol. Molecular dynamics revealed that all tested compounds formed stable complexes with the enzyme during 100 ns simulation, indicating that they are good ligands. This study provided preliminary evidence for the potential application of the selected cannabinoids and L. leonurus in maintaining glucose homeostasis, suggesting that they could be suitable therapeutic candidates for managing T2DM.
- Full Text:
- Date Issued: 2023
- Authors: Mkabayi, Lithalethu , Viljoen, Zenobia , Lobb, Kevin A , Pletschke, Brett I , Frost, Carminita L
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452745 , vital:75167 , xlink:href="https://www.thieme-connect.com/products/ejournals/html/10.1055/s-0043-1773924"
- Description: Diabetes is a chronic metabolic disorder that has been shown to affect a growing number of people worldwide. Controlling blood glucose levels is one of the possible strategies to treat type 2 diabetes mellitus (T2DM). It has been established that the inhibition of dipeptidyl peptidase IV (DPP-IV) prolongs the activity of incretin hormones, which serve as key stimulators of insulin secretion and regulation of blood glucose levels. Although several synthetic DPP-IV inhibitors are available, there is still a need for naturally sourced inhibitors that have fewer to no undesirable side effects. In this study, cannabinoids and Leonotis leonurus aqueous extracts were evaluated for their inhibitory effects against recombinant human DPP-IV. Their potential inhibition mechanism was explored using in vitro and in silico approaches. All tested cannabinoids and L. leonurus aqueous extracts showed significant inhibitory activity against DPP-IV. Phytochemical analysis of L. leonurus extract indicated the presence of diterpenoids and alkaloids, which might contribute to the inhibitory activity. In molecular docking studies, among different constituents known in L. leonurus, luteolin and marrubiin showed binding energy of -7.2 kcal/mol and cannabinoids (cannabidiol, cannabigerol, cannabinol and Δ9-tetrahydrocannabinol) showed binding energies ranging from -6.5 to -8.2 kcal/mol. Molecular dynamics revealed that all tested compounds formed stable complexes with the enzyme during 100 ns simulation, indicating that they are good ligands. This study provided preliminary evidence for the potential application of the selected cannabinoids and L. leonurus in maintaining glucose homeostasis, suggesting that they could be suitable therapeutic candidates for managing T2DM.
- Full Text:
- Date Issued: 2023
Rationalising the retro-Diels-Alder fragmentation pattern of viscutins using electrospray interface-tandem mass spectrometry coupled to theoretical modelling
- Moyo, Babra, Novokoza, Yolanda, Tavengwa, Nikita T, Kuhnert, Nikolai, Lobb, Kevin A, Madala, Ntakadzeni E
- Authors: Moyo, Babra , Novokoza, Yolanda , Tavengwa, Nikita T , Kuhnert, Nikolai , Lobb, Kevin A , Madala, Ntakadzeni E
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452786 , vital:75170 , xlink:href="https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/epdf/10.1002/rcm.9592"
- Description: Although mass spectrometry (MS) is a powerful tool in structural elucidation of unknown flavonoids based on their unique fragmentation patterns, proposing the correct fragmentation mechanism is still a challenge from tandem mass spectrometry data only. In recent years, computational tools such as molecular networking and MS2LDA have played a major role in the identification of structurally related compounds through an in-depth survey of their fragmentation patterns.
- Full Text:
- Date Issued: 2023
- Authors: Moyo, Babra , Novokoza, Yolanda , Tavengwa, Nikita T , Kuhnert, Nikolai , Lobb, Kevin A , Madala, Ntakadzeni E
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452786 , vital:75170 , xlink:href="https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/epdf/10.1002/rcm.9592"
- Description: Although mass spectrometry (MS) is a powerful tool in structural elucidation of unknown flavonoids based on their unique fragmentation patterns, proposing the correct fragmentation mechanism is still a challenge from tandem mass spectrometry data only. In recent years, computational tools such as molecular networking and MS2LDA have played a major role in the identification of structurally related compounds through an in-depth survey of their fragmentation patterns.
- Full Text:
- Date Issued: 2023
Unveiling the reactivity of truxillic and truxinic acids (TXAs): deprotonation, anion center dot center dot center dot HO, cation center dot center dot center dot O and cation center dot center dot center dot pi interactions in TXA (0) center dot center dot center dot Y+ and TXA (0) center dot center dot center dot Z (-) complexes (Y= Li, Na, K; Z= F, Cl, Br)
- Isamura, Bienfait K, Patouossa, Issofa, Muya, Jules T, Lobb, Kevin A
- Authors: Isamura, Bienfait K , Patouossa, Issofa , Muya, Jules T , Lobb, Kevin A
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452827 , vital:75173 , xlink:href="https://link.springer.com/content/pdf/10.1007/s11224-022-01965-5.pdf"
- Description: Herein, we report a quantum chemistry investigation of the interaction between µ-truxinic acid, referred to as TXA0 , and Y+ (Y=Li, Na, K) and Z− (Z=F, Cl, Br) ions using M06-2X, B3LYP and 휔 B97XD functionals in conjunction with the 6–31+ +G(d,p), aug-cc-pVDZ(-X2C) and 6–311+ +G (d, p) basis sets. Our computations suggest that Y+ cations can bind to TXA0 through several combinations of cation…O and cation-π interactions, while Z− anions generally establish anion… H–O contacts. Predicted binding energies at the M06-2X/6–311+ +G(d,p) level range between−26.6 and−70.2 kcal/mol for cationic complexes and−20.4 and−62.3 kcal/mol for anionic ones. As such, TXA0 appears as an amphoteric molecule with a slight preference for electrophilic (cation... O) attacks. Furthermore, the most favourable binding site for cations allows for the formation of O…cation…O interactions where the cation is trapped between O37 and O38 atoms of TXA0 . Anions do not behave uniformly towards TXA0 : while the fuoride anion F− induces the deprotonation of TXA0 , Br− and Cl− do not. All of these structural insights are supported by topological calculations in the context of the quantum theory of atoms in molecules (QTAIM). Finally, SAPT0 analyses suggest that TXA0 …Y+ and TXA0 …Z− complexes are mainly stabilized by electrostatic and inductive efects, whose combined contributions account for more than 60 percent of the total interaction energy.
- Full Text:
- Date Issued: 2023
- Authors: Isamura, Bienfait K , Patouossa, Issofa , Muya, Jules T , Lobb, Kevin A
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452827 , vital:75173 , xlink:href="https://link.springer.com/content/pdf/10.1007/s11224-022-01965-5.pdf"
- Description: Herein, we report a quantum chemistry investigation of the interaction between µ-truxinic acid, referred to as TXA0 , and Y+ (Y=Li, Na, K) and Z− (Z=F, Cl, Br) ions using M06-2X, B3LYP and 휔 B97XD functionals in conjunction with the 6–31+ +G(d,p), aug-cc-pVDZ(-X2C) and 6–311+ +G (d, p) basis sets. Our computations suggest that Y+ cations can bind to TXA0 through several combinations of cation…O and cation-π interactions, while Z− anions generally establish anion… H–O contacts. Predicted binding energies at the M06-2X/6–311+ +G(d,p) level range between−26.6 and−70.2 kcal/mol for cationic complexes and−20.4 and−62.3 kcal/mol for anionic ones. As such, TXA0 appears as an amphoteric molecule with a slight preference for electrophilic (cation... O) attacks. Furthermore, the most favourable binding site for cations allows for the formation of O…cation…O interactions where the cation is trapped between O37 and O38 atoms of TXA0 . Anions do not behave uniformly towards TXA0 : while the fuoride anion F− induces the deprotonation of TXA0 , Br− and Cl− do not. All of these structural insights are supported by topological calculations in the context of the quantum theory of atoms in molecules (QTAIM). Finally, SAPT0 analyses suggest that TXA0 …Y+ and TXA0 …Z− complexes are mainly stabilized by electrostatic and inductive efects, whose combined contributions account for more than 60 percent of the total interaction energy.
- Full Text:
- Date Issued: 2023
A multiscale ONIOM study of the buckminsterfullerene (C60) Diels–Alder reaction: from model design to reaction path analysis
- Isamura, Bienfait K, Lobb, Kevin A
- Authors: Isamura, Bienfait K , Lobb, Kevin A
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452517 , vital:75140 , xlink:href=" https://link.springer.com/article/10.1007/s00894-022-05319-0"
- Description: The hybrid ONIOM (Our own N-layered Integrated molecular Orbital and molecular Mechanics) formalism is employed to investigate the Diels–Alder reaction of the buckminsterfullerene C60. Our computa-tions suggest that the ONIOM2(M06-2X/6-31G(d): SVWN/STO3G) mod-el, enclosing both the diene and the pyracyclene fragment of C60 in the higher-layer, provides a reasonable trade-of between accuracy and computational cost as it comes to predicting reaction energetics. Moreover, the frontier molecular orbital (FMO) theory and activation strain model (ASM) are jointly relied on to rationalize the efect of –OH and –CN substituents on the activation barrier of this reaction. Finally, reaction paths are scrutinized to get insight into the various forces un-derpinning the process of cycloadduct formation.
- Full Text:
- Date Issued: 2022
- Authors: Isamura, Bienfait K , Lobb, Kevin A
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452517 , vital:75140 , xlink:href=" https://link.springer.com/article/10.1007/s00894-022-05319-0"
- Description: The hybrid ONIOM (Our own N-layered Integrated molecular Orbital and molecular Mechanics) formalism is employed to investigate the Diels–Alder reaction of the buckminsterfullerene C60. Our computa-tions suggest that the ONIOM2(M06-2X/6-31G(d): SVWN/STO3G) mod-el, enclosing both the diene and the pyracyclene fragment of C60 in the higher-layer, provides a reasonable trade-of between accuracy and computational cost as it comes to predicting reaction energetics. Moreover, the frontier molecular orbital (FMO) theory and activation strain model (ASM) are jointly relied on to rationalize the efect of –OH and –CN substituents on the activation barrier of this reaction. Finally, reaction paths are scrutinized to get insight into the various forces un-derpinning the process of cycloadduct formation.
- Full Text:
- Date Issued: 2022
Drug Resistance in the HIV-1 Subtype C Protease Enzyme: A High Throughput Virtual Screening Approach in Search of New Ligands with Activity
- Sarron, Arthur F D, Lobb, Kevin A
- Authors: Sarron, Arthur F D , Lobb, Kevin A
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452699 , vital:75163 , xlink:href="10.2174/1871520622666220202161543"
- Description: Background: HIV-1 subtype C protease is a strategic target for antiretroviral treatment. However, resistance to protease inhibi-tors appears after months of treatment. Chromones and 2- bis-coumarin derivatives show potential for inhibition of the HIV- subtype C protease. Objective: Different heterocyclic structures from the ZINC database were docked against Human Immuno-deficiency Virus-1 (HIV) subtype C protease crystal structure 2R5Q and 2R5P. The 5 best molecules were selected to be docked against 62 homology models based on HIV-protease se-quences from infants failing antiretroviral protease treatment. This experimentation was performed with two molecular docking programs: Autodock and Autodock Vina. These molecules were modified by substituting protons with different moieties, and the derivatives were docked against the same targets. Ligand-protein interactions, physical/chemical proprieties of the mole-cules, and dynamics simulations were analyzed.
- Full Text:
- Date Issued: 2022
- Authors: Sarron, Arthur F D , Lobb, Kevin A
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452699 , vital:75163 , xlink:href="10.2174/1871520622666220202161543"
- Description: Background: HIV-1 subtype C protease is a strategic target for antiretroviral treatment. However, resistance to protease inhibi-tors appears after months of treatment. Chromones and 2- bis-coumarin derivatives show potential for inhibition of the HIV- subtype C protease. Objective: Different heterocyclic structures from the ZINC database were docked against Human Immuno-deficiency Virus-1 (HIV) subtype C protease crystal structure 2R5Q and 2R5P. The 5 best molecules were selected to be docked against 62 homology models based on HIV-protease se-quences from infants failing antiretroviral protease treatment. This experimentation was performed with two molecular docking programs: Autodock and Autodock Vina. These molecules were modified by substituting protons with different moieties, and the derivatives were docked against the same targets. Ligand-protein interactions, physical/chemical proprieties of the mole-cules, and dynamics simulations were analyzed.
- Full Text:
- Date Issued: 2022
Insights into the Dynamics and Binding of Two Polyprotein Substrate Cleavage Points in the Context of the SARS-CoV-2 Main and Papain-like Proteases
- Sanusi, Zainab K, Lobb, Kevin A
- Authors: Sanusi, Zainab K , Lobb, Kevin A
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452773 , vital:75169 , xlink:href="https://doi.org/10.3390/molecules27238251"
- Description: It is well known that vital enzymes in the replication process of the coronavirus are the SARS-CoV-2 PLpro and SARS-CoV-2 3CLpro, both of which are important targets in the search for anti-coronavirus agents. These two enzymes are responsible for cleavage at various polyprotein sites in the SARS-CoV-2 lifecycle. Herein, the dynamics of the polyprotein cleavage sequences for the boundary between non-structural proteins Nsp1 and Nsp2 (CS1) and between Nsp2 and Nsp3 (CS2) in complex with both the papain-like protein PLpro and the main protease 3CLpro were explored using computational methods. The post dynamics analysis reveals that CS1 and CS2 both have greater stability when complexed with PLpro. Of these two, greater stability is observed for the CS1–PLpro complex, while destabilization resulting in loss of CS2 from the PLpro active site is observed for CS2-PLpro, suggesting the rate of exchange by the papain-like protease is faster for CS2 compared to CS1. On the other hand, the 3CLpro main protease also reveals stability for CS1 suggesting that the main protease could also play a potential role in the cleavage at point CS1. However, destabilization occurs early in the simulation for the complex CLpro–CS2 suggesting a poor interaction and non-plausible protease cleavage of the polyprotein at CS2 by the main protease. These findings could be used as a guide in the development and design of potent COVID-19 antiviral inhibitors that mimic the CS1 cleavage site.
- Full Text:
- Date Issued: 2022
- Authors: Sanusi, Zainab K , Lobb, Kevin A
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452773 , vital:75169 , xlink:href="https://doi.org/10.3390/molecules27238251"
- Description: It is well known that vital enzymes in the replication process of the coronavirus are the SARS-CoV-2 PLpro and SARS-CoV-2 3CLpro, both of which are important targets in the search for anti-coronavirus agents. These two enzymes are responsible for cleavage at various polyprotein sites in the SARS-CoV-2 lifecycle. Herein, the dynamics of the polyprotein cleavage sequences for the boundary between non-structural proteins Nsp1 and Nsp2 (CS1) and between Nsp2 and Nsp3 (CS2) in complex with both the papain-like protein PLpro and the main protease 3CLpro were explored using computational methods. The post dynamics analysis reveals that CS1 and CS2 both have greater stability when complexed with PLpro. Of these two, greater stability is observed for the CS1–PLpro complex, while destabilization resulting in loss of CS2 from the PLpro active site is observed for CS2-PLpro, suggesting the rate of exchange by the papain-like protease is faster for CS2 compared to CS1. On the other hand, the 3CLpro main protease also reveals stability for CS1 suggesting that the main protease could also play a potential role in the cleavage at point CS1. However, destabilization occurs early in the simulation for the complex CLpro–CS2 suggesting a poor interaction and non-plausible protease cleavage of the polyprotein at CS2 by the main protease. These findings could be used as a guide in the development and design of potent COVID-19 antiviral inhibitors that mimic the CS1 cleavage site.
- Full Text:
- Date Issued: 2022
Photo-and thermoresponsive N-salicylideneaniline derivatives: solid-state studies and structural aspects
- Hulushe, Siyabonga T, Malan, Frederick P, Hosten, Eric C, Lobb, Kevin A, Khanye, Setshaba D, Watkins, Gareth M
- Authors: Hulushe, Siyabonga T , Malan, Frederick P , Hosten, Eric C , Lobb, Kevin A , Khanye, Setshaba D , Watkins, Gareth M
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/451137 , vital:75021 , xlink:href="https://pubs.rsc.org/en/content/articlehtml/2022/nj/d1nj03056f"
- Description: N-Salicylideneaniline (SA) and its derivatives are known to possess chromism upon exposure to external stimuli. Herein, we present mechanochemical synthesis of a series of photo-and thermoresponsive SAderivatives and report on solid-state stabilisation of their tautomeric forms either by change in temperature or by photoirradiation. The influence of UV light on proton transfer between the enol-imine (EI) and keto-amine (KA) forms was investigated at l1 = 254 and l2 = 365 nm. Differential scanning calorimetry (DSC) measurements provided extra information on the thermodynamic relationship between the prototropic tautomers, and their exposition to liquid nitrogen, combined with variable temperature single-crystal X-ray diffraction (VT-SCXRD) and spectroscopic data, ascertained structural reasons for the intrinsic thermo-optical properties of the compounds. A series of structural determinations between 150 and 300 K further shed light on the thermomechanical behaviour exhibited by the thermoresponsive compounds. By virtue of calorimetry we were able to demonstrate proton transfer via the intramolecular ON hydrogen bond over the temperature range 193–453 K. This present work demonstrates the importance of applying complementary analytical techniques and appropriate approaches for understanding the switching behaviour between the EI and KA forms. Furthermore, the assertion that it is predominantly the planarity (j o 251) that determines thermochromaticity is questioned.
- Full Text:
- Date Issued: 2022
- Authors: Hulushe, Siyabonga T , Malan, Frederick P , Hosten, Eric C , Lobb, Kevin A , Khanye, Setshaba D , Watkins, Gareth M
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/451137 , vital:75021 , xlink:href="https://pubs.rsc.org/en/content/articlehtml/2022/nj/d1nj03056f"
- Description: N-Salicylideneaniline (SA) and its derivatives are known to possess chromism upon exposure to external stimuli. Herein, we present mechanochemical synthesis of a series of photo-and thermoresponsive SAderivatives and report on solid-state stabilisation of their tautomeric forms either by change in temperature or by photoirradiation. The influence of UV light on proton transfer between the enol-imine (EI) and keto-amine (KA) forms was investigated at l1 = 254 and l2 = 365 nm. Differential scanning calorimetry (DSC) measurements provided extra information on the thermodynamic relationship between the prototropic tautomers, and their exposition to liquid nitrogen, combined with variable temperature single-crystal X-ray diffraction (VT-SCXRD) and spectroscopic data, ascertained structural reasons for the intrinsic thermo-optical properties of the compounds. A series of structural determinations between 150 and 300 K further shed light on the thermomechanical behaviour exhibited by the thermoresponsive compounds. By virtue of calorimetry we were able to demonstrate proton transfer via the intramolecular ON hydrogen bond over the temperature range 193–453 K. This present work demonstrates the importance of applying complementary analytical techniques and appropriate approaches for understanding the switching behaviour between the EI and KA forms. Furthermore, the assertion that it is predominantly the planarity (j o 251) that determines thermochromaticity is questioned.
- Full Text:
- Date Issued: 2022
Synthesis and conformational studies of 5-bromo-1-[(N-substituted-carbamoyl) methyl]-7-azabenzimidazoles
- Oluwafemi, Kola A, Klein, Rosalyn, Lobb, Kevin A, Tshiwawa, Tendamudzimu, Isaacs, Michelle, Hoppe, Heinrich C, Kaye, Perry T
- Authors: Oluwafemi, Kola A , Klein, Rosalyn , Lobb, Kevin A , Tshiwawa, Tendamudzimu , Isaacs, Michelle , Hoppe, Heinrich C , Kaye, Perry T
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452800 , vital:75171 , xlink:href="https://doi.org/10.1016/j.molstruc.2022.133811"
- Description: The Cs2CO3-catalysed condensation of 5-bromo-7-azabenzimidazole with a series of bromomethyl ketones has afforded a small library of ten, novel 5-bromo-1-[(N-substututed-carbamoyl)methyl]-7-azabenzimidazoles. Rotamerism in the products, as evidenced by the splitting of 1H- and 13C-NMR signals, is attributed to hindered internal rotation about the amide N-C(=O) bond, and has been explored using dynamic NMR (DNMR) analysis and computational methods at the GIAO B3LYP/6-311+G(2d,p) level of theory. Coalescence temperatures have been obtained for representative examples and rotational barriers determined experimentally and theoretically. A detailed theoretical analysis has been undertaken to explore conformations which may contribute to the relative populations of the s-cis and s-trans rotamers. The products have also been screened for cytotoxicity and activity against two parasitic protozoan strains (Plasmodium falciparum and Trypanosoma brucei).
- Full Text:
- Date Issued: 2022
- Authors: Oluwafemi, Kola A , Klein, Rosalyn , Lobb, Kevin A , Tshiwawa, Tendamudzimu , Isaacs, Michelle , Hoppe, Heinrich C , Kaye, Perry T
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452800 , vital:75171 , xlink:href="https://doi.org/10.1016/j.molstruc.2022.133811"
- Description: The Cs2CO3-catalysed condensation of 5-bromo-7-azabenzimidazole with a series of bromomethyl ketones has afforded a small library of ten, novel 5-bromo-1-[(N-substututed-carbamoyl)methyl]-7-azabenzimidazoles. Rotamerism in the products, as evidenced by the splitting of 1H- and 13C-NMR signals, is attributed to hindered internal rotation about the amide N-C(=O) bond, and has been explored using dynamic NMR (DNMR) analysis and computational methods at the GIAO B3LYP/6-311+G(2d,p) level of theory. Coalescence temperatures have been obtained for representative examples and rotational barriers determined experimentally and theoretically. A detailed theoretical analysis has been undertaken to explore conformations which may contribute to the relative populations of the s-cis and s-trans rotamers. The products have also been screened for cytotoxicity and activity against two parasitic protozoan strains (Plasmodium falciparum and Trypanosoma brucei).
- Full Text:
- Date Issued: 2022
Synthesis, stereochemistry and in vitro STD NMR and in silico HIV-1 PR enzyme-binding potential of MBH-derived inhibitors
- Tukulula, Matshawandile, Olasupo, Idris A, Mugumbate, Grace C, Lobb, Kevin A, Klein, Rosalyn, Sayed, Yasien, Tshiwawa, Tendamudzimu, Kaye, Perry T
- Authors: Tukulula, Matshawandile , Olasupo, Idris A , Mugumbate, Grace C , Lobb, Kevin A , Klein, Rosalyn , Sayed, Yasien , Tshiwawa, Tendamudzimu , Kaye, Perry T
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452813 , vital:75172 , xlink:href="https://doi.org/10.1016/j.molstruc.2022.133716"
- Description: Aza-Michael reactions of a pyridine-3-carbaldehyde-derived Morita-Baylis-Hillman (MBH) adduct with various amines have afforded a series of 10 diastereomeric products, stereochemical analysis of which has been achieved using a combination of NMR (1D, 2D and NOESY) and computer modelling methods. Saturation Transfer Difference (STD) 1H NMR spectroscopy and in silico molecular docking studies have been used to explore the HIV-1 protease sub-type C enzyme binding potential of these compounds in five different HIV-1 PR enzyme receptors.
- Full Text:
- Date Issued: 2022
- Authors: Tukulula, Matshawandile , Olasupo, Idris A , Mugumbate, Grace C , Lobb, Kevin A , Klein, Rosalyn , Sayed, Yasien , Tshiwawa, Tendamudzimu , Kaye, Perry T
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452813 , vital:75172 , xlink:href="https://doi.org/10.1016/j.molstruc.2022.133716"
- Description: Aza-Michael reactions of a pyridine-3-carbaldehyde-derived Morita-Baylis-Hillman (MBH) adduct with various amines have afforded a series of 10 diastereomeric products, stereochemical analysis of which has been achieved using a combination of NMR (1D, 2D and NOESY) and computer modelling methods. Saturation Transfer Difference (STD) 1H NMR spectroscopy and in silico molecular docking studies have been used to explore the HIV-1 protease sub-type C enzyme binding potential of these compounds in five different HIV-1 PR enzyme receptors.
- Full Text:
- Date Issued: 2022
Arylquinolinecarboxamides: Synthesis, in vitro and in silico studies against Mycobacterium tuberculosis
- Bokosi, Fostino R B, Beteck, Richard M, Jordaan, Audrey, Seldon, Ronnett, Warner, Digby F, Tshiwawa, Tendamudzimu, Lobb, Kevin A, Khanye, Setshaba D
- Authors: Bokosi, Fostino R B , Beteck, Richard M , Jordaan, Audrey , Seldon, Ronnett , Warner, Digby F , Tshiwawa, Tendamudzimu , Lobb, Kevin A , Khanye, Setshaba D
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/451064 , vital:75015 , xlink:href="https://doi.org/10.1002/jhet.4340"
- Description: A series of fourteen 6-substituted-2-(methoxyquinolin-3-yl) methyl)-N-(pyridin-3-ylmethyl) benzamides was prepared from commercially available anilines infive simple and convenient synthetic steps. The structures of all new productswere confirmed by routine spectroscopic methods: IR,1Hand13 CNMR,andHRMS (electrospray ionization). The resulting arylquinolinecarboxamides weresubjected to biological screening assay forin vitroinhibitory activity againstMyco-bacterium tuberculosis (Mtb) H37Rv strain. Several compounds exhibited modestantitubercular activity with compounds8–11,15and19exhibiting MIC90valuesin the range of 32–85μM. The antitubercular data suggested that inhibition ofMtbcan be imparted by the introduction of a non-polar substituent on C-6 of thequinoline scaffold. Further, to understandthepossiblemodeofactionoftheseries, the reported compounds and bedaquiline were subjected toin silicodock-ing studies againstMtbATPase to determine their potential to interfere with themycobacterial adenosine triphosphate (ATP) synthase. The results showed thatthese compounds have the potential toserve as antimycobacterial agents.In silicoADME pharmacokinetic prediction results showed the ability of thesearylquinolinecarcboxamides to be absorbed, distributed, metabolized andexcreted efficiently.
- Full Text:
- Date Issued: 2021
- Authors: Bokosi, Fostino R B , Beteck, Richard M , Jordaan, Audrey , Seldon, Ronnett , Warner, Digby F , Tshiwawa, Tendamudzimu , Lobb, Kevin A , Khanye, Setshaba D
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/451064 , vital:75015 , xlink:href="https://doi.org/10.1002/jhet.4340"
- Description: A series of fourteen 6-substituted-2-(methoxyquinolin-3-yl) methyl)-N-(pyridin-3-ylmethyl) benzamides was prepared from commercially available anilines infive simple and convenient synthetic steps. The structures of all new productswere confirmed by routine spectroscopic methods: IR,1Hand13 CNMR,andHRMS (electrospray ionization). The resulting arylquinolinecarboxamides weresubjected to biological screening assay forin vitroinhibitory activity againstMyco-bacterium tuberculosis (Mtb) H37Rv strain. Several compounds exhibited modestantitubercular activity with compounds8–11,15and19exhibiting MIC90valuesin the range of 32–85μM. The antitubercular data suggested that inhibition ofMtbcan be imparted by the introduction of a non-polar substituent on C-6 of thequinoline scaffold. Further, to understandthepossiblemodeofactionoftheseries, the reported compounds and bedaquiline were subjected toin silicodock-ing studies againstMtbATPase to determine their potential to interfere with themycobacterial adenosine triphosphate (ATP) synthase. The results showed thatthese compounds have the potential toserve as antimycobacterial agents.In silicoADME pharmacokinetic prediction results showed the ability of thesearylquinolinecarcboxamides to be absorbed, distributed, metabolized andexcreted efficiently.
- Full Text:
- Date Issued: 2021
Force Field Parameters for Fe2+ 4S2− 4 Clusters of Dihydropyrimidine Dehydrogenase, the 5-Fluorouracil Cancer Drug Deactivation Protein: A Step towards In Silico Pharmacogenomics Studies
- Tendwa, Maureen B, Chebon-Bore, Lorna, Lobb, Kevin A, Musyoka, Thommas M, Taştan Bishop, Özlem
- Authors: Tendwa, Maureen B , Chebon-Bore, Lorna , Lobb, Kevin A , Musyoka, Thommas M , Taştan Bishop, Özlem
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/451078 , vital:75016 , xlink:href="https://doi.org/10.3390/molecules26102929 "
- Description: The dimeric dihydropyrimidine dehydrogenase (DPD), metalloenzyme, an adjunct anti-cancer drug target, contains highly specialized 4 × Fe2+4S2−4 clusters per chain. These clusters facilitate the catalysis of the rate-limiting step in the pyrimidine degradation pathway through a harmonized electron transfer cascade that triggers a redox catabolic reaction. In the process, the bulk of the administered 5-fluorouracil (5-FU) cancer drug is inactivated, while a small proportion is activated to nucleic acid antimetabolites. The occurrence of missense mutations in DPD protein within the general population, including those of African descent, has adverse toxicity effects due to altered 5-FU metabolism. Thus, deciphering mutation effects on protein structure and function is vital, especially for precision medicine purposes. We previously proposed combining molecular dynamics (MD) and dynamic residue network (DRN) analysis to decipher the molecular mechanisms of missense mutations in other proteins. However, the presence of Fe2+4S2−4 clusters in DPD poses a challenge for such in silico studies. The existing AMBER force field parameters cannot accurately describe the Fe2+ center coordination exhibited by this enzyme. Therefore, this study aimed to derive AMBER force field parameters for DPD enzyme Fe2+ centers, using the original Seminario method and the collation features Visual Force Field Derivation Toolkit as a supportive approach. All-atom MD simulations were performed to validate the results. Both approaches generated similar force field parameters, which accurately described the human DPD protein Fe2+4S2−4 cluster architecture. This information is crucial and opens new avenues for in silico cancer pharmacogenomics and drug discovery related research on 5-FU drug efficacy and toxicity issues.
- Full Text:
- Date Issued: 2021
- Authors: Tendwa, Maureen B , Chebon-Bore, Lorna , Lobb, Kevin A , Musyoka, Thommas M , Taştan Bishop, Özlem
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/451078 , vital:75016 , xlink:href="https://doi.org/10.3390/molecules26102929 "
- Description: The dimeric dihydropyrimidine dehydrogenase (DPD), metalloenzyme, an adjunct anti-cancer drug target, contains highly specialized 4 × Fe2+4S2−4 clusters per chain. These clusters facilitate the catalysis of the rate-limiting step in the pyrimidine degradation pathway through a harmonized electron transfer cascade that triggers a redox catabolic reaction. In the process, the bulk of the administered 5-fluorouracil (5-FU) cancer drug is inactivated, while a small proportion is activated to nucleic acid antimetabolites. The occurrence of missense mutations in DPD protein within the general population, including those of African descent, has adverse toxicity effects due to altered 5-FU metabolism. Thus, deciphering mutation effects on protein structure and function is vital, especially for precision medicine purposes. We previously proposed combining molecular dynamics (MD) and dynamic residue network (DRN) analysis to decipher the molecular mechanisms of missense mutations in other proteins. However, the presence of Fe2+4S2−4 clusters in DPD poses a challenge for such in silico studies. The existing AMBER force field parameters cannot accurately describe the Fe2+ center coordination exhibited by this enzyme. Therefore, this study aimed to derive AMBER force field parameters for DPD enzyme Fe2+ centers, using the original Seminario method and the collation features Visual Force Field Derivation Toolkit as a supportive approach. All-atom MD simulations were performed to validate the results. Both approaches generated similar force field parameters, which accurately described the human DPD protein Fe2+4S2−4 cluster architecture. This information is crucial and opens new avenues for in silico cancer pharmacogenomics and drug discovery related research on 5-FU drug efficacy and toxicity issues.
- Full Text:
- Date Issued: 2021
Interaction of silver nanoparticles with catechol O-methyltransferase: Spectroscopic and simulation analyses
- Usman, Aminu, Lobb, Kevin A, Pletschke, Brett I, Whiteley, Christopher G, Wilhelmi, Brendan S
- Authors: Usman, Aminu , Lobb, Kevin A , Pletschke, Brett I , Whiteley, Christopher G , Wilhelmi, Brendan S
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/451095 , vital:75018 , xlink:href=" https://doi.org/10.1016/j.bbrep.2021.101013"
- Description: Catechol O-methyltransferase, an enzyme involved in the metabolism of catechol containing compounds, catalyzes the transfer of a methyl group between S-adenosylmethionine and the hydroxyl groups of the catechol. Furthermore it is considered a potential drug target for Parkinson’s disease as it metabolizes the drug levodopa. Consequently inhibitors of the enzyme would increase levels of levodopa. In this study, absorption, fluorescence and infrared spectroscopy as well as computational simulation studies investigated human soluble catechol Omethyltransferase interaction with silver nanoparticles. The nanoparticles form a corona with the enzyme and quenches the fluorescence of Trp143. This amino acid maintains the correct structural orientation for the catechol ring during catalysis through a static mechanism supported by a non-fluorescent fluorophore–nanoparticle complex. The enzyme has one binding site for AgNPs in a thermodynamically spontaneous binding driven by electrostatic interactions as confirmed by negative ΔG and ΔH and positive ΔS values. Fourier transform infrared spectroscopy within the amide I region of the enzyme indicated that the interaction causes relaxation of its β− structures, while simulation studies indicated the involvement of six polar amino acids. These findings suggest AgNPs influence the catalytic activity of catechol O-methyltransferase, and therefore have potential in controlling the activity of the enzyme.
- Full Text:
- Date Issued: 2021
- Authors: Usman, Aminu , Lobb, Kevin A , Pletschke, Brett I , Whiteley, Christopher G , Wilhelmi, Brendan S
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/451095 , vital:75018 , xlink:href=" https://doi.org/10.1016/j.bbrep.2021.101013"
- Description: Catechol O-methyltransferase, an enzyme involved in the metabolism of catechol containing compounds, catalyzes the transfer of a methyl group between S-adenosylmethionine and the hydroxyl groups of the catechol. Furthermore it is considered a potential drug target for Parkinson’s disease as it metabolizes the drug levodopa. Consequently inhibitors of the enzyme would increase levels of levodopa. In this study, absorption, fluorescence and infrared spectroscopy as well as computational simulation studies investigated human soluble catechol Omethyltransferase interaction with silver nanoparticles. The nanoparticles form a corona with the enzyme and quenches the fluorescence of Trp143. This amino acid maintains the correct structural orientation for the catechol ring during catalysis through a static mechanism supported by a non-fluorescent fluorophore–nanoparticle complex. The enzyme has one binding site for AgNPs in a thermodynamically spontaneous binding driven by electrostatic interactions as confirmed by negative ΔG and ΔH and positive ΔS values. Fourier transform infrared spectroscopy within the amide I region of the enzyme indicated that the interaction causes relaxation of its β− structures, while simulation studies indicated the involvement of six polar amino acids. These findings suggest AgNPs influence the catalytic activity of catechol O-methyltransferase, and therefore have potential in controlling the activity of the enzyme.
- Full Text:
- Date Issued: 2021
Introducing DerivatizeME and its Application in the Augmentation of a Natural Product Library
- Sigauke, Lester T, Taştan Bishop, Özlem, Lobb, Kevin A
- Authors: Sigauke, Lester T , Taştan Bishop, Özlem , Lobb, Kevin A
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/451120 , vital:75020 , xlink:href="https://doi.org/10.1142/S2737416521500101"
- Description: The large chemical space universe can be traversed by screening libraries of compounds that possess novel medicinally relevant chemistries, properties and complexity criteria. These libraries can be populated with the use of exhaustive, de novo approaches or inspired, combinatorial approaches. By assuming that natural products within screening libraries may be classified as a source of feedstock for populating virtual libraries, they can act as scaffolds upon which exhaustive approaches may be used in exploring chemical space. In order to achieve this, we have built DerivatizeME as a tool that enumerates derivatives of query compounds in order to evaluate their relevance for further assessment and development. This technique was applied to natural products present in the South African natural compound database (SANCDB). By expanding the chemical space of SANCDB compounds through the generation of SANCDB derivatives, we were able to graduate some natural products that were in undesirable regions of medicinally relevant chemical space, to acceptable regions of this chemical space. These modified scaffolds are available for further development, testing and evaluation in a manner similar to natural product driven focused libraries. The natural product parent is used, through its derivatives, instead of being discarded from screening protocols. This approach has the potential to enhance the efficiency of the natural product library in providing successful hits, amplifying the potential that they possess to access both novel bioactives and privileged scaffolds which may have otherwise been overlooked.
- Full Text:
- Date Issued: 2021
- Authors: Sigauke, Lester T , Taştan Bishop, Özlem , Lobb, Kevin A
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/451120 , vital:75020 , xlink:href="https://doi.org/10.1142/S2737416521500101"
- Description: The large chemical space universe can be traversed by screening libraries of compounds that possess novel medicinally relevant chemistries, properties and complexity criteria. These libraries can be populated with the use of exhaustive, de novo approaches or inspired, combinatorial approaches. By assuming that natural products within screening libraries may be classified as a source of feedstock for populating virtual libraries, they can act as scaffolds upon which exhaustive approaches may be used in exploring chemical space. In order to achieve this, we have built DerivatizeME as a tool that enumerates derivatives of query compounds in order to evaluate their relevance for further assessment and development. This technique was applied to natural products present in the South African natural compound database (SANCDB). By expanding the chemical space of SANCDB compounds through the generation of SANCDB derivatives, we were able to graduate some natural products that were in undesirable regions of medicinally relevant chemical space, to acceptable regions of this chemical space. These modified scaffolds are available for further development, testing and evaluation in a manner similar to natural product driven focused libraries. The natural product parent is used, through its derivatives, instead of being discarded from screening protocols. This approach has the potential to enhance the efficiency of the natural product library in providing successful hits, amplifying the potential that they possess to access both novel bioactives and privileged scaffolds which may have otherwise been overlooked.
- Full Text:
- Date Issued: 2021
Potential repurposing of four FDA approved compounds with antiplasmodial activity identified through proteome scale computational drug discovery and in vitro assay
- Diallo, Bakary N, Swart, Tarryn, Hoppe, Heinrich C, Tastan Bishop, Özlem, Lobb, Kevin A
- Authors: Diallo, Bakary N , Swart, Tarryn , Hoppe, Heinrich C , Tastan Bishop, Özlem , Lobb, Kevin A
- Date: 2021
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/177531 , vital:42830 , https://doi.org/10.1038/s41598-020-80722-2
- Description: Malaria elimination can benefit from time and cost-efficient approaches for antimalarials such as drug repurposing. In this work, 796 DrugBank compounds were screened against 36 Plasmodium falciparum targets using QuickVina-W. Hits were selected after rescoring using GRaph Interaction Matching (GRIM) and ligand efficiency metrics: surface efficiency index (SEI), binding efficiency index (BEI) and lipophilic efficiency (LipE). They were further evaluated in Molecular dynamics (MD). Twenty-five protein–ligand complexes were finally retained from the 28,656 (36×796) dockings.
- Full Text:
- Date Issued: 2021
- Authors: Diallo, Bakary N , Swart, Tarryn , Hoppe, Heinrich C , Tastan Bishop, Özlem , Lobb, Kevin A
- Date: 2021
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/177531 , vital:42830 , https://doi.org/10.1038/s41598-020-80722-2
- Description: Malaria elimination can benefit from time and cost-efficient approaches for antimalarials such as drug repurposing. In this work, 796 DrugBank compounds were screened against 36 Plasmodium falciparum targets using QuickVina-W. Hits were selected after rescoring using GRaph Interaction Matching (GRIM) and ligand efficiency metrics: surface efficiency index (SEI), binding efficiency index (BEI) and lipophilic efficiency (LipE). They were further evaluated in Molecular dynamics (MD). Twenty-five protein–ligand complexes were finally retained from the 28,656 (36×796) dockings.
- Full Text:
- Date Issued: 2021
SANCDB: an update on South African natural compounds and their readily available analogs
- Diallo, Bakary N, Glenister, Michael, Musyoka, Thommas M, Lobb, Kevin A, Taştan Bishop, Özlem
- Authors: Diallo, Bakary N , Glenister, Michael , Musyoka, Thommas M , Lobb, Kevin A , Taştan Bishop, Özlem
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/451154 , vital:75023 , xlink:href="https://doi.org/10.1186/s13321-021-00514-2"
- Description: The dimeric dihydropyrimidine dehydrogenase (DPD), metalloenzyme, an adjunct anti-cancer drug target, contains highly specialized 4 × Fe2+4S2−4 clusters per chain. These clusters facilitate the catalysis of the rate-limiting step in the pyrimidine degradation pathway through a harmonized electron transfer cascade that triggers a redox catabolic reaction. In the process, the bulk of the administered 5-fluorouracil (5-FU) cancer drug is inactivated, while a small proportion is activated to nucleic acid antimetabolites. The occurrence of missense mutations in DPD protein within the general population, including those of African descent, has adverse toxicity effects due to altered 5-FU metabolism. Thus, deciphering mutation effects on protein structure and function is vital, especially for precision medicine purposes. We previously proposed combining molecular dynamics (MD) and dynamic residue network (DRN) analysis to decipher the molecular mechanisms of missense mutations in other proteins. However, the presence of Fe2+4S2−4 clusters in DPD poses a challenge for such in silico studies. The existing AMBER force field parameters cannot accurately describe the Fe2+ center coordination exhibited by this enzyme. Therefore, this study aimed to derive AMBER force field parameters for DPD enzyme Fe2+ centers, using the original Seminario method and the collation features Visual Force Field Derivation Toolkit as a supportive approach. All-atom MD simulations were performed to validate the results. Both approaches generated similar force field parameters, which accurately described the human DPD protein Fe2+4S2−4 cluster architecture. This information is crucial and opens new avenues for in silico cancer pharmacogenomics and drug discovery related research on 5-FU drug efficacy and toxicity issues.
- Full Text:
- Date Issued: 2021
- Authors: Diallo, Bakary N , Glenister, Michael , Musyoka, Thommas M , Lobb, Kevin A , Taştan Bishop, Özlem
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/451154 , vital:75023 , xlink:href="https://doi.org/10.1186/s13321-021-00514-2"
- Description: The dimeric dihydropyrimidine dehydrogenase (DPD), metalloenzyme, an adjunct anti-cancer drug target, contains highly specialized 4 × Fe2+4S2−4 clusters per chain. These clusters facilitate the catalysis of the rate-limiting step in the pyrimidine degradation pathway through a harmonized electron transfer cascade that triggers a redox catabolic reaction. In the process, the bulk of the administered 5-fluorouracil (5-FU) cancer drug is inactivated, while a small proportion is activated to nucleic acid antimetabolites. The occurrence of missense mutations in DPD protein within the general population, including those of African descent, has adverse toxicity effects due to altered 5-FU metabolism. Thus, deciphering mutation effects on protein structure and function is vital, especially for precision medicine purposes. We previously proposed combining molecular dynamics (MD) and dynamic residue network (DRN) analysis to decipher the molecular mechanisms of missense mutations in other proteins. However, the presence of Fe2+4S2−4 clusters in DPD poses a challenge for such in silico studies. The existing AMBER force field parameters cannot accurately describe the Fe2+ center coordination exhibited by this enzyme. Therefore, this study aimed to derive AMBER force field parameters for DPD enzyme Fe2+ centers, using the original Seminario method and the collation features Visual Force Field Derivation Toolkit as a supportive approach. All-atom MD simulations were performed to validate the results. Both approaches generated similar force field parameters, which accurately described the human DPD protein Fe2+4S2−4 cluster architecture. This information is crucial and opens new avenues for in silico cancer pharmacogenomics and drug discovery related research on 5-FU drug efficacy and toxicity issues.
- Full Text:
- Date Issued: 2021