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
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