Indole- and diaryl ether-derived non-nucleoside reverse transcriptase inhibitors
| dc.contributor.advisor | Van Otterlo, Willem | en_ZA |
| dc.contributor.advisor | Pelly, Stephen | en_ZA |
| dc.contributor.author | Wessels, Petronella Magdalena | en_ZA |
| dc.contributor.other | Stellenbosch University. Faculty of Science. Dept. of Chemistry and Polymer Science. | en_ZA |
| dc.date.accessioned | 2018-02-13T01:24:00Z | |
| dc.date.accessioned | 2018-04-09T10:52:17Z | |
| dc.date.available | 2021-02-01T03:00:08Z | |
| dc.date.issued | 2018-03 | |
| dc.description | Thesis (MSc)--Stellenbosch University, 2018. | en_ZA |
| dc.description.abstract | ENGLISH ABSTRACT: Since the discovery of the Human Immunodeficiency Virus (HIV) as the cause of Acquired Immune Deficiency Syndrome (AIDS) in the early 1980s, no cure has been found. This disease has thus claimed the lives of millions of people and has gained the reputation as one of the worst pandemics in human history. There has, however, been considerable success in reducing the viral load of infected individuals through the use of combination therapy, known as highly active antiretroviral therapy (HAART). A main target of this drug regimen is the reverse transcriptase (RT) enzyme, which is inhibited by two of the three drug classes typically employed by HAART, namely nucleoside RT inhibitors (NRTIs) and non-nucleoside RT inhibitors (NNRTIs). However, as the viral population diversifies through mutations introduced during viral replication, drug resistant viral strains emerge and limit the use of currently effective drugs. These resistant strains thus require new small molecule inhibitors to keep them in check. In light of the need for new therapeutic agents to continuously enter the drug development pipeline, we set out to improve upon current NNRTIs through the lead optimization of an indole core structure and the design of a diaryl ether NNRTI using molecular modelling. The first focus was to overcome the acid-catalysed indole-mediated degradation of the current lead compound, ethyl 5-chloro-3-[(methylthio)(phenyl)methyl]-1H-indole-2-carboxylate (designed in an earlier research project), thereby making the small molecule suitable for oral intake. We successfully synthesised twelve acid stable derivatives of this lead compound by replacing the thiomethyl group with an alkyl or alkene chain in the benzylic position. Four of these newly synthesised derivatives proved to be more potent (0.010 – 0.019 μM) than the lead compound (0.039 μM) against wild-type HIV-1, while six of these compounds were more potent than nevirapine (0.091 μM) under the same conditions. The next study involved modifications to the 2-position of a lead indole based NNRTI, ethyl 5-chloro- 3-[(3,5-dimethylphenyl)(methylthio)methyl]-1H-indole-2-carboxylate, through the introduction of various pyridinyl groups to determine the effects on efficacy. Three of the five resultant compounds performed better against wild-type HIV-1 (0.030 – 0.043 μM) than the lead compound, with an ethyl ester in the 2-position (0.060 μM), and two of these three compounds remained potent against HIV-1 viruses harbouring the prevalent NNRTI resistant mutations V106M, Y188C/H, G190A and K103N. Due to the positive results obtained when an indole was used as a core structure in NNRTIs, ethyl 3-(1-aminopropyl)-5-chloro-1H-indole-2-carboxylate was chosen for the incorporation of electrophilic warheads as amides with the aim of synthesising the first irreversible NNRTIs. Three proof-of-concept compounds were successfully synthesised with electrophilic warheads positioned to interact with the thiol of cysteine in the Y181C mutant strain of the virus. These compounds, however, proved to be toxic and thus ineffective as NNRTIs. Finally, molecular modelling was used to design flexible diaryl ether NNRTIs with the ability to form desirable interactions with residues in the binding pocket. We sought to achieve an improved resistance profile through π-π stacking interactions with conserved amino acid residues Trp229 and Tyr318 and additional interactions with Tyr188 and Lys101. Three proof-of-concept compounds were then synthesised, of which 3-(3-amino-2-methoxyphenoxy)-5-chlorobenzonitrile proved to be highly effective with an inhibition activity (IC50 value) of 5 nM against wild-type HIV-1. | en_ZA |
| dc.description.abstract | AFRIKAANSE OPSOMMING: Sedert verworwe immuniteitsgebreksindroom (VIGS) in die vroeë 1980s as oorsaak van die menslike immuniteitsvirus (MIV) geïdentifiseer is, is daar nog geen geneesmiddel beskikbaar teen MIV nie. As gevolg hiervan het hierdie siekte al die lewens van miljoene mense geëis en die reputasie as een van die ernstigste pandemies in menslike geskiedenis gekry. Ten spyte van bogenoemde is daar al heelwat sukses behaal in terme van ́n verlaging van die virale vlakke in besmette individue deur gebruik te maak van kombinasie terapie naamlik hoogsaktiewe antiretrovirale terapie (HAART). Twee uit die drie geneesmiddels wat oor die algemeen deur HAART gebruik word, naamlik nukleosied trutranskriptase inhibeerders (NRTIs) en nie-nukleosied trutranskriptase inhibeerders (NNRTIs), teiken die trutranskriptase ensiem deur inhibisie. Mutasies gedurende virale replikasie lei egter tot die diversivering van die virale bevolking en so ontwikkel weerstandige stamme wat dan die gebruik van hierdie huidige effektiewe middele belemmer. Weerstandige stamme benodig dus nuwe klein molekule inhibeerders om hulle in toom te hou. As gevolg van die konstante aanvraag na nuwe inhibeerders in die produksiepyplyn van geneesmiddels, is daar gepoog om te verbeter op die huidige beskikbare NNRTIs. Die indool- gebaseerde primêre-struktuur is gebruik, as ook die ontwerp van ́n di-ariel eter NNRTI deur die gebruik van molekulêre modelering. Die fokus was aanvanklik op die uitskakeling van suurgekataliseerde indool-bemiddelde degredasie van die huidige primêre-struktuur, etiel 5-chloor-3-[(metieltio)(feniel)metiel]-1H-indool-2-karboksilaat (gesintetiseer in ́n vorige navorsingsprojek). Hierdeur sal die klein molekule per mond geneem kan word. Twaalf suurstabiele variasies van die primêre-struktuur is daarna suksesvol gesintetiseer deur die tiometielgroep met ́n alkiel- of alkeenketting in die bensiliese posisie te vervang. Vier van hierdie nuut gesintetiseerde afgeleide molekules was meer aktief (0.010 – 0.019 μM) as die primêre- struktuur (0.039 μM) teen wilde-tipe MIV-1 bevind, terwyl ses uit die twaalf molekules meer aktief as nevirapine (0.091 μM) onder diesefde kondisies bevind is. Die volgende ondersoek het veranderinge tot die 2-posisie van die primêre-struktuur indool NNRTI, etiel 5-chloor-3-[(3,5-dimetielfeniel)(metieltio)metiel]-1H-indool-2-karboksilaat, behels. Verskeie piridiniel groepe is in hierdie posisie geplaas om die effek van die veranderinge op die doeltreffendheid teen MIV-1 te bepaal. Drie uit die vyf gesintetiseerde molekules was meer aktief bevind teen wilde-tipe MIV-1 (0.030 – 0.043 μM) as die primêre-middel (0.060 μM), wat ́n etiel ester in die 2-posisie het. Twee uit dié drie molekules het ook aktief getoets teen MIV-1 virusse met algemene NNRTI weerstandige mutasies V106M, Y188C/H, G190A en K103N. As gevolg van die positiewe resultate wat deur die indool-gebasseerde NNRTIs verkry is, kon etiel 3-(1-aminopropiel)-5-chloor-1H-indool-2-karboksilaat gebruik word vir die inkorporering van elektrofiliese lokvalle as amiede met die doel om die eerste onomkeerbare NNRTIs te sintetiseer. Drie bewys-van-konsep molekules is suksesvol gesintetiseer met die elektrofiliese lokvalle nagenoeg aan die tiol groep van sisteïen, in die Y181C mutante vorm van die virus, gepossisioneer om ́n binding te vorm. Daar was ongelukkig bevind dat hierdie verbindings giftig vir lewende selle is en dus onbruikbaar as NNRTIs is. Laastens is daar van molekulêre modelering gebruik gemaak om buigbare di-ariel eter NNRTIs te ontwerp wat die vermoë kan besit om gewensde interaksies met aminosuurresidue in die bindingsholte te hê. Ons het gemik om ́n verbeterde weerstands profiel te verkry deur middel van π-π stapelings interaksies met amienosuurresidue, Trp229 en Tyr318, wat nie maklik mutasie ondergaan nie, asook interaksies met Tyr188 en Lys101. Drie bewys-van-konsep molekules is toe gesintetiseer, waarvan 3-(3-amino-2-methoxyfenoxy)-5-chloorbenzonitriel hoogs aktief was met ́n inhibisie aktiwiteit van 5 nM teen wilde-tipe MIV-1. | af_ZA |
| dc.description.version | Masters | en_ZA |
| dc.embargo.terms | 2020-12-31 | |
| dc.format.extent | 177 pages | en_ZA |
| dc.identifier.uri | http://hdl.handle.net/10019.1/103835 | |
| dc.language.iso | en_ZA | en_ZA |
| dc.subject | Highly active antiretroviral therapy | en_ZA |
| dc.subject | Nucleosides | en_ZA |
| dc.subject | Reverse transcriptase inhibitors | en_ZA |
| dc.subject | HIV (Viruses) | en_ZA |
| dc.title | Indole- and diaryl ether-derived non-nucleoside reverse transcriptase inhibitors | en_ZA |
| dc.type | Thesis | en_ZA |