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:
- 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.
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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:
- 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.
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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:
- 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.
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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:
- 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.
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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:
- 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.
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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:
- 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.
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Synthesis, characterization, computational studies and DPPH scavenging activity of some triazatetracyclic derivatives
- Odame, Felix, Hosten, Eric C, Betz, Richard, Krause, Jason, Frost, Carminita L, Lobb, Kevin A, Tshentu, Zenixole R
- Authors: Odame, Felix , Hosten, Eric C , Betz, Richard , Krause, Jason , Frost, Carminita L , Lobb, Kevin A , Tshentu, Zenixole R
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/451186 , vital:75026 , xlink:href="https://doi.org/10.1007/s13738-021-02158-3"
- Description: Some dihydrobenzo[4,5]imidazo[1,2-c]quinazolines have been synthesized from aldehydes and ketones, using the ketones as both reagents and solvents and tetrahydrofuran (THF) as the solvent for the aldehydes, to yield the triazatetracyclics. The compounds have been characterized with spectroscopy and microanalysis. The crystal structures of 9,9-dimethyl-8,10,17- triazatetracyclo[8.7.02,7.011,16]heptadeca-1(17),2,4,6,11(16),12,14-heptaene (I), 9-butyl-9-methyl-8,10,17-triazatetracyclo[8.7.0.02 , 7 .011,16]heptadeca-(17),2,4,6,11(16),12,14-heptaene (III) and 9-phenyl-8,10,17-triazatetracyclo[8.7.0 02 7.011,16] heptadeca-1(17),2,4,6,11(16),12,14-heptaene (VIII) have been discussed. The computed NMR, IR, molecular electrostatic potential and frontier molecular orbitals of compounds I, III and VIII have been discussed. The M06 functional gave most of its values closest to the experimental values for the bond lengths and bond angles of compounds I and III. For compound VIII, none of the functionals gave values for bond lengths and bond angles that were consistent with the experimental values, but M06 gave values closest to experimental values. The 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging activity of the triazatetracyclics showed that compound I exhibits signifcant DPPH scavenging activity with an IC50 of 56.18 µM compared to 2.37 µM for ascorbic acid.
- Full Text:
- Authors: Odame, Felix , Hosten, Eric C , Betz, Richard , Krause, Jason , Frost, Carminita L , Lobb, Kevin A , Tshentu, Zenixole R
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/451186 , vital:75026 , xlink:href="https://doi.org/10.1007/s13738-021-02158-3"
- Description: Some dihydrobenzo[4,5]imidazo[1,2-c]quinazolines have been synthesized from aldehydes and ketones, using the ketones as both reagents and solvents and tetrahydrofuran (THF) as the solvent for the aldehydes, to yield the triazatetracyclics. The compounds have been characterized with spectroscopy and microanalysis. The crystal structures of 9,9-dimethyl-8,10,17- triazatetracyclo[8.7.02,7.011,16]heptadeca-1(17),2,4,6,11(16),12,14-heptaene (I), 9-butyl-9-methyl-8,10,17-triazatetracyclo[8.7.0.02 , 7 .011,16]heptadeca-(17),2,4,6,11(16),12,14-heptaene (III) and 9-phenyl-8,10,17-triazatetracyclo[8.7.0 02 7.011,16] heptadeca-1(17),2,4,6,11(16),12,14-heptaene (VIII) have been discussed. The computed NMR, IR, molecular electrostatic potential and frontier molecular orbitals of compounds I, III and VIII have been discussed. The M06 functional gave most of its values closest to the experimental values for the bond lengths and bond angles of compounds I and III. For compound VIII, none of the functionals gave values for bond lengths and bond angles that were consistent with the experimental values, but M06 gave values closest to experimental values. The 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging activity of the triazatetracyclics showed that compound I exhibits signifcant DPPH scavenging activity with an IC50 of 56.18 µM compared to 2.37 µM for ascorbic acid.
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