Design and Synthesis of potent benzimidazolone HIV Non-nucleoside reverse transcriptase inhibitors

Pribut, Nicole (2018-12)

Thesis (PhD)--Stellenbosch University, 2018.

Thesis

ENGLISH ABSTRACT: Since the 1980’s, HIV has plagued the population on a global scale, with millions of newly infected individuals reported every year. However, with the introduction of combination therapy, which can significantly suppress viremia to almost undetectable levels in the infected populace, the disease can be managed to a point where the infected population can live almost normal lives. Unfortunately, although able to improve quality of life and prevent the onset of AIDS, combination therapy is not curative as issues related to drug resistance and adherence can lead to the re-emergence of high viremia, AIDS and, inevitably, death. Consequently, there remains a need for the continued development of new and superior ARVs that are effective against wild-type and resistant strains of HIV and are well tolerated for chronic use. In an effort to address this need, our group has focused on the design and synthesis of new NNRTIs. In the clinic, NNRTIs are an important part of first-line regimens employed in the treatment of HIV. In particular, our group focused on the synthesis of a series of small benzimidazolone-containing NNRTIs which were initially designed to address lability issues exhibited by a series of potent indole-based NNRTIs. These first-generation benzimidazolones were readily synthesized over five steps and, following evaluation in an HIV whole cell assay, were found to be potent inhibitors of HIV RT, but were susceptible to clinically relevant resistant strains such as K103N and Y181C. As a result, we synthesized a series of second-generation benzimidazolone NNRTIs which were designed to overcome, specifically, the Y181C resistant strain. Starting from 2-amino-3-nitrophenol, the benzimidazolone precursor for these compounds was synthesized over six steps. This precursor was then coupled to various aryl or heteroaryl halides by way of an Ullmann reaction or SNAr. Of this small library, one compound in particular was found to be potent (with low nanomolar activity), not only against wildtype, but also against Y181C, Y188C and the double mutant K103N/Y181C. Furthermore, this compound, 3-chloro-5-((3-ethyl-2-oxo-1-((2-trimethylsilyl)ethoxy)methyl)-2,3-dihydro-1H-benzo[d]imidazol-4- yl)oxy)benzonitrile, exhibited only low levels of susceptibility against the most problematic K103N resistant strain. We envisaged that by introducing additional electrostatic interactions between our potent lead compound and the NNIBP we would succeed in optimizing the efficacy of our compound against wild-type and resistant strains of HIV. In order to achieve these additional interactions we adopted two different approaches. The first approach focused on targeting a lysine residue located at the top of a narrow hydrophobic chimney towards the back of the NNIBP. To this end, we installed a cyanovinyl substituent onto our lead compound which, based on docking studies, would protrude into the chimney and form a hydrogen bond with the targeted lysine. Installation of the cyanovinyl substituent was achieved using the well-established Heck coupling reaction. Although this compound, (E)-3-(2-cyanovinyl)-5-((3-ethyl-2-oxo-2,3-dihydro-1Hbenzo[ d]imidazol-4-yl)oxy)benzonitrile, was also a potent inhibitor of HIV RT, it was unfortunately not significantly more potent than our existing lead compound. The second approach employed a molecular hybridization technique to form a combination of our lead compound and efavirenz, in order to achieve additional hydrogen bonding to the backbone of Lys101. This new hybrid compound, 3-chloro-5-((4,4-dimethyl-2-oxo-1,4-dihydro-2H-benzo[d][1,3]oxazin-5- yl)oxy)benzonitrile, was successfully synthesized over seven steps and found to be slightly more potent than our lead compound with an improved selectivity index.

AFRIKAANSE OPSOMMING: Sedert die 1980’s het MIV in ‘n globale pandemie geraak waar miljoene mense jaarliks gediagnoseer word. Die gebruik van kombinasie terapie het gelei tot grootskaalse onderdrukking van viremie in so ‘n mate dat dit gevolglik onopspoorbaar is, en dus sorg dat mense met HIV amper ‘n normale lewe kan lei. Alhoewel die behandeling van mense met HIV hulle lewens gehalte verbeter het en die aanvang van VIGS verhoed, is hedendaagse behandeling nie genesend nie, en as gevolg van dwelm-bestandhied moontlik kan lei to die herverskyning van ‘n hoë viralelading, VIGS en dan dood. As gevolg van hierdie dilemma, is daar tans ‘n groot nood vir navorsing en onwikkeling vir nuwe ARV medisyne wat effektief is teen wilde-tipe en dwelm-bestande MIV stamme, tesame met minimale newe effekte wat ‘n resultaat is van daaglikse gebruik. Om die tekort aan nuwe en effektiewe antiretrovirale medisyne aan te spreek, het ons groep gefokus op om nuwe nie-nukleosied-omgekeerde transkriptase-inhibeerders (NNRTI’s) te ontwerp en te sintetiseer, sedert NNRTI’s beskou word as ‘n belangrike gedeelte vir die behandeling van MIV. Ons groep het onder andere gefokus op die sintesise van ‘n klein reeks molekules wat ‘n bensimidasoloon kern bevat. Die reeks was aanvanklik gesintetiseer om probleme rakend die chemiese stabiliteit van ‘n voorheen gesintetiseerde reeks indool NNRTI’s, ook deur ons groep ontwikkel, aan te spreek. Die eerste generasie reeks bensimidasoloon molekules was maklik geskep oor vyf stappe, en heel sel toetse teenoor MIV omgekeerde transkriptase het getoon dat hulle kragtige inhibeerders van die ensiem was, maar was ook onder andere vatbaar vir relevante MIV stamme soos K103N en Y181C. As gevolg daarvan het ons ‘n tweede generasie reeks bensimidasoloon NNRTI’s ontwerp om hierdie tekortkoming teenoor K103N en spesifiek die Y181C weerstandige stam te verbeter. Deur te begin met 2- amino-3-nitro fenol was die bensimidasoloon voorloper gesintetiseer in ses stappe. Die voorloper was dan gekoppel met menigte aromatiese en heteroaromatiese haliede deur middel van of die Ullmann-koppel reaksie of SNAr. Een molekule uit hierdie reeks, 3-chloro-5-((3-ethyl-2-oxo-1-((2- trimethylsilyl)ethoxy)methyl)-2,3-dihydro-1H-benzo[d]imidazol-4-yl)oxy)benzonitrile, was aktief gewees met lae nanomolaar aktiwiteit teenoor die wilde-tipe MIV maar ook teenoor Y181C, Y188C en die dubbel mutant K103N/Y181C, met net ‘n klein hoeveelheid weerstand teenoor die problematiese K103N MIV stam. Deur addisionele elektrostatiese interaksies by te voeg tussen ons aktiefste molekule en die NNIBP, het ons probeer bevestig of ons die aktiwitiet teenoor die wilde tipe MIV stam sal kan verbeter. Om hierdie idee van addisionele interaksies te laat realiseer het ons twee verskillende metodes benader. In die eerste metode het ons daarop gefokus om ‘n lisien residu te teiken wat in die boonste gedeelte van die smal hidrofobiese skoorsteen in die aktiewe setel van die NNIBP geleë is. Ons het ‘n nitriel-viniel groep geïnstalleer op ons mees aktiefste molekule wat, deur middle van dokstudies, getoon het dat die nitrielviniel groep moontlik sal inbeweeg in die skoorsteen gedeelte en ‘n waterstof-binding vorm met die lisien residu. Inkorporering van die nitriel-viniel substituent was gedoen deur die uitvoering van ‘n Heck-koppel reaksie. Alhoewel die nitriel-viniel molecule, (E)-3-(2-cyanovinyl)-5-((3-ethyl-2-oxo-2,3-dihydro-1Hbenzo[ d]imidazol-4-yl)oxy)benzonitrile, goeie aktiwiteit getoon het teenoor MIV omgekeerde transkriptase, was dit nie moontlik om die oorspronlike aktiewe molekuul se aktiwiteit drasties te verbeter nie. Die tweede benadering het ‘n molekulêre hibridisasie tegniek ingesluit waar ons ons aktiewe molekuul en efavirenz gebaster het sodat daar moontlik ‘n addisionele waterstof-binding gemaak kan word met ‘n Lys101 residu in die aktiewe setel. Hierdie hibried molekuul, 3-chloro-5-((4,4-dimethyl-2-oxo-1,4-dihydro- 2H-benzo[d][1,3]oxazin-5-yl)oxy)benzonitrile, was suksesvol gesintetiseer oor sewe stappe, en was meer aktief as die oorspronglike aktiewe molekuul, maar het ook ‘n verbeterde selektiwiteits indeks getoon in vergelyking met die oorspronklike aktiewe molekuul.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/105138
This item appears in the following collections: