Dissertation/ Thesis
Validation of the computational simplification of the experimental molecule FR900359
| Τίτλος: | Validation of the computational simplification of the experimental molecule FR900359 |
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| Συγγραφείς: | Sultana, Brandon (2021) |
| Στοιχεία εκδότη: | University of Malta Faculty of Medicine and Surgery. Department of Pharmacy |
| Έτος έκδοσης: | 2021 |
| Συλλογή: | University of Malta: OAR@UM / L-Università ta' Malta |
| Θεματικοί όροι: | G proteins -- Antagonists, Drug development -- Computer simulation, Drugs -- Structure-activity relationships -- Computer simulation, Ligand binding (Biochemistry) -- Computer simulation, Pharmaceutical chemistry -- Computer simulation |
| Περιγραφή: | M.Pharm.(Melit.) ; Literature indicates that the experimental molecule FR900359 relieves bronchial spasm through G-alpha inhibition. This molecule however has a large molecular weight, and its magnitude precludes its systemic use. This study consequently aimed to use virtual screening and de novo design to identify and generate novel structures with a lower molecular weight based on a modelled optimal conformer of FR900359 capable of modulating the G-alpha subunit. The small molecule inhibitor YM254890 was extracted from its complex with the G-alpha subunit as described in PDB crystallographic deposition 3AH8 giving rise to an apo G-alpha subunit. FR900359 was subsequently docked into its ligand binding pocket, conformational analysis performed, and the optimal conformer of FR900359 identified. Pharmacophores of both these molecules were modelled in LigandScout (Wolber, 2005) and submitted to the online database ZincPharmer® for analogous hit identification with acceptance filters being set such that all recruited hits would conform to the Rule of 3 for lead likeness. This stringent search did not yield any hits. The de novo approach was applied next. Seeds were created from the best FR900359 conformer docked into a modelled G-alpha ligand binding pocket map, based on PDB crystallographic deposition 3AH8. De novo growth was attempted using the GROW and LINK algorithms of LigBuilder. Only 2 Lipinski Rule compliant structures were grown with, however, a ligand binding affinity (pKd 5.1 and 4.93 respectively) that was not high enough to guarantee endogenous molecule displacement in a competitive scenario. The implication of these results is that the FR900359 molecule with a molecular weight of 1001.53 Daltons was not suitable for the identification and design of lower weight G-alpha modulators owing to spatial and steric constraints. This result must also be taken into account in the context of future studies. Specifically, even though molecular weight reduction and structural simplification are sound strategies ... |
| Τύπος εγγράφου: | master thesis |
| Γλώσσα: | English |
| Relation: | Sultana, B. (2021). Validation of the computational simplification of the experimental molecule FR900359 (Master's dissertation).; https://www.um.edu.mt/library/oar/handle/123456789/88562 |
| Διαθεσιμότητα: | https://www.um.edu.mt/library/oar/handle/123456789/88562 |
| Rights: | info:eu-repo/semantics/restrictedAccess ; The copyright of this work belongs to the author(s)/publisher. The rights of this work are as defined by the appropriate Copyright Legislation or as modified by any successive legislation. Users may access this work and can make use of the information contained in accordance with the Copyright Legislation provided that the author must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the prior permission of the copyright holder. |
| Αριθμός Καταχώρησης: | edsbas.D9A8AC2A |
| Βάση Δεδομένων: | BASE |
| FullText | Text: Availability: 0 CustomLinks: – Url: https://www.um.edu.mt/library/oar/handle/123456789/88562# Name: EDS - BASE (ns324271) Category: fullText Text: View record from BASE |
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| Header | DbId: edsbas DbLabel: BASE An: edsbas.D9A8AC2A RelevancyScore: 758 AccessLevel: 3 PubType: Dissertation/ Thesis PubTypeId: dissertation PreciseRelevancyScore: 758.347900390625 |
| IllustrationInfo | |
| Items | – Name: Title Label: Title Group: Ti Data: Validation of the computational simplification of the experimental molecule FR900359 – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Sultana%2C+Brandon+%282021%29%22">Sultana, Brandon (2021)</searchLink> – Name: Publisher Label: Publisher Information Group: PubInfo Data: University of Malta<br />Faculty of Medicine and Surgery. Department of Pharmacy – Name: DatePubCY Label: Publication Year Group: Date Data: 2021 – Name: Subset Label: Collection Group: HoldingsInfo Data: University of Malta: OAR@UM / L-Università ta' Malta – Name: Subject Label: Subject Terms Group: Su Data: <searchLink fieldCode="DE" term="%22G+proteins+--+Antagonists%22">G proteins -- Antagonists</searchLink><br /><searchLink fieldCode="DE" term="%22Drug+development+--+Computer+simulation%22">Drug development -- Computer simulation</searchLink><br /><searchLink fieldCode="DE" term="%22Drugs+--+Structure-activity+relationships+--+Computer+simulation%22">Drugs -- Structure-activity relationships -- Computer simulation</searchLink><br /><searchLink fieldCode="DE" term="%22Ligand+binding+%28Biochemistry%29+--+Computer+simulation%22">Ligand binding (Biochemistry) -- Computer simulation</searchLink><br /><searchLink fieldCode="DE" term="%22Pharmaceutical+chemistry+--+Computer+simulation%22">Pharmaceutical chemistry -- Computer simulation</searchLink> – Name: Abstract Label: Description Group: Ab Data: M.Pharm.(Melit.) ; Literature indicates that the experimental molecule FR900359 relieves bronchial spasm through G-alpha inhibition. This molecule however has a large molecular weight, and its magnitude precludes its systemic use. This study consequently aimed to use virtual screening and de novo design to identify and generate novel structures with a lower molecular weight based on a modelled optimal conformer of FR900359 capable of modulating the G-alpha subunit. The small molecule inhibitor YM254890 was extracted from its complex with the G-alpha subunit as described in PDB crystallographic deposition 3AH8 giving rise to an apo G-alpha subunit. FR900359 was subsequently docked into its ligand binding pocket, conformational analysis performed, and the optimal conformer of FR900359 identified. Pharmacophores of both these molecules were modelled in LigandScout (Wolber, 2005) and submitted to the online database ZincPharmer® for analogous hit identification with acceptance filters being set such that all recruited hits would conform to the Rule of 3 for lead likeness. This stringent search did not yield any hits. The de novo approach was applied next. Seeds were created from the best FR900359 conformer docked into a modelled G-alpha ligand binding pocket map, based on PDB crystallographic deposition 3AH8. De novo growth was attempted using the GROW and LINK algorithms of LigBuilder. Only 2 Lipinski Rule compliant structures were grown with, however, a ligand binding affinity (pKd 5.1 and 4.93 respectively) that was not high enough to guarantee endogenous molecule displacement in a competitive scenario. The implication of these results is that the FR900359 molecule with a molecular weight of 1001.53 Daltons was not suitable for the identification and design of lower weight G-alpha modulators owing to spatial and steric constraints. This result must also be taken into account in the context of future studies. Specifically, even though molecular weight reduction and structural simplification are sound strategies ... – Name: TypeDocument Label: Document Type Group: TypDoc Data: master thesis – Name: Language Label: Language Group: Lang Data: English – Name: NoteTitleSource Label: Relation Group: SrcInfo Data: Sultana, B. (2021). Validation of the computational simplification of the experimental molecule FR900359 (Master's dissertation).; https://www.um.edu.mt/library/oar/handle/123456789/88562 – Name: URL Label: Availability Group: URL Data: https://www.um.edu.mt/library/oar/handle/123456789/88562 – Name: Copyright Label: Rights Group: Cpyrght Data: info:eu-repo/semantics/restrictedAccess ; The copyright of this work belongs to the author(s)/publisher. The rights of this work are as defined by the appropriate Copyright Legislation or as modified by any successive legislation. Users may access this work and can make use of the information contained in accordance with the Copyright Legislation provided that the author must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the prior permission of the copyright holder. – Name: AN Label: Accession Number Group: ID Data: edsbas.D9A8AC2A |
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| RecordInfo | BibRecord: BibEntity: Languages: – Text: English Subjects: – SubjectFull: G proteins -- Antagonists Type: general – SubjectFull: Drug development -- Computer simulation Type: general – SubjectFull: Drugs -- Structure-activity relationships -- Computer simulation Type: general – SubjectFull: Ligand binding (Biochemistry) -- Computer simulation Type: general – SubjectFull: Pharmaceutical chemistry -- Computer simulation Type: general Titles: – TitleFull: Validation of the computational simplification of the experimental molecule FR900359 Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Sultana, Brandon (2021) IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 01 Type: published Y: 2021 Identifiers: – Type: issn-locals Value: edsbas |
| ResultId | 1 |