Identification of broad-based HIV-1 protease inhibitors from combinatorial libraries

Chang, Max W.; Giffin, Michael J.; Müller, Rolf; Savage, Jeremiah; Lin, Y.-C.; Hong, Sukwon; Jin, Wei; Whitby, Landon R.; Elder, John H.; Boger, Dale L.; Torbett, Bruce E.

doi:10.1042/bj20091645

Cited by 19 publications

(16 citation statements)

References 35 publications

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“…Most proteases in vivo are thought to operate in an environment in which they are substrate saturated, and this will slow down and/or weaken competitive inhibitors by the factor of 1 + S/Σ K m , in which Σ K m is the sum of all values for all the substrates in a cell. In addition to the perennial problems of tissue penetration and pharmacokinetic considerations, this concept — backed up by a recent publication on HIV protease inhibitors that operate allosterically92 — could explain why the inhibitory concentration of a protease inhibitor drug in vivo is always several orders larger than in a purified system. By contrast, allosteric or exosite inhibitors need not be affected by substrate concentration.…”

Section: Discussionmentioning

confidence: 99%

Emerging principles in protease-based drug discovery

Drąg

Salvesen

2010

Nat Rev Drug Discov

507

458

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Proteases have an important role in many signalling pathways, and represent potential drug targets for diseases ranging from cardiovascular disorders to cancer, as well as for combating many parasites and viruses. Although inhibitors of well-established protease targets such as angiotensin-converting enzyme and HIV protease have shown substantial therapeutic success, developing drugs for new protease targets has proved challenging in recent years. This in part could be due to issues such as the difficulty of achieving selectivity when targeting protease active sites. This Perspective discusses the general principles in protease-based drug discovery, highlighting the lessons learned and the emerging strategies, such as targeting allosteric sites, which could help harness the therapeutic potential of new protease targets.Proteins are among the most stable biological polymers. Peptide bonds can withstand hours in boiling concentrated acid, yet they last no more than microseconds in the presence of a specific protease. The study of proteolysis goes back at least to the nineteenth century with the description of pepsin by Schwann in 1836 and of trypsin by Corvisart in 1856. Since then, proteases have been identified in almost every organism, have been discovered to play a part in most biological pathways 1 and have been implicated in almost every disease.Historically, much of the focus has been on the role of proteases in coagulopathies, inflammation, infectious diseases, cancer and degenerative diseases, and some protease inhibitors have been developed into highly successful drugs. For example, inhibitors of the human protease angiotensin-converting enzyme (ACE), such as captopril, have been used in the treatment of cardiovascular disorders, primarily hypertension and congestive heart failure, for several decades 2 . In addition, inhibitors of the HIV protease, such as ritonavir, atazananvir and tipranavir (Aptivus; Pfizer/Boehringer Ingelheim), have had a key role in transforming the treatment of HIV infection since their introduction in the mid-1990s 3 (see TABLE 1 Published in final edited form as:Nat Rev Drug Discov. 2010 September ; 9(9): 690-701. doi:10.1038/nrd3053. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript sales of US$1 billion, which is anticipated to rise to $3.5 billion by 2014 (REF. 4 ), whereas antihypertensive drugs that act on the proteases in the renin-angiotensin system currently have over $6 billion global sales 1 . Indeed, at present, we estimate that 5-10% of all pharmaceutical targets being pursued for drug development are proteases.The general strategy for therapeutically targeting proteases is to identify a specific inhibitor -generally a small molecule -that blocks the active site. As discussed below, discovery efforts for new inhibitors have typically been based on the structure of known protease substrates, presenting a substantial challenge for the development of peptidomimetic compounds that have the pharmacokinetic characteristics needed to be sui...

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Section: Discussionmentioning

confidence: 99%

Emerging principles in protease-based drug discovery

Drąg

Salvesen

2010

Nat Rev Drug Discov

507

458

View full text Add to dashboard Cite

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“…For example, angiotensin-converting enzyme (ACE) inhibitors are targeted to treat cardiovascular ailments (Smith and Vane, 2003). In addition, inhibitors of viral proteases, such as ritonavir, atazananvir tipranavir, Telaprevir and boceprevir (Chang et al, 2010; Flexner et al, 2005) have been used extensively in HIV and hepatitis C virus treatments (Pearlman, 2012). …”

Section: Discussionmentioning

confidence: 99%

High-throughput screening for the identification of small-molecule inhibitors of the flaviviral protease

et al. 2016

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The mosquito-borne dengue virus serotypes 1-4 (DENV1-4) and West Nile virus (WNV) cause serious illnesses worldwide associated with considerable morbidity and mortality. According to the World Health Organization (WHO) estimates, there are about 390 million infections every year leading to ~500,000 dengue haemorrhagic fever (DHF) cases and ~25,000 deaths, mostly among children. Antiviral therapies could reduce the morbidity and mortality associated with flaviviral infections, but currently there are no drugs available for treatment. In this study, a high-throughput screening assay for the Dengue protease was employed to screen ~120,000 small molecule compounds for identification of inhibitors. Eight of these inhibitors have been extensively analyzed for inhibition of the viral protease in vitro and cell-based viral replication using Renilla luciferase reporter replicon, infectivity (plaque) and cytotoxicity assays. Three of these compounds were identified as potent inhibitors of DENV and WNV proteases, and viral replication of DENV2 replicon and infectious RNA. Fluorescence quenching, kinetic analysis and molecular modeling of these inhibitors into the structure of NS2B-NS3 protease suggest a mode of inhibition for three compounds that they bind to the substrate binding pocket.

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“…PepA concentration varied from 0–300 nM in assay with WT HIV-1p and 0–400 nM with MDR HIV-1p. 44 The concentrations of substrate and protease were kept at 5 μM and 30 nM, respectively, while other experimental conditions were the same as above. The kinetic data was plotted as v 0 /v i versus [ PepA ] / IC 50PepA .…”

Section: Methodsmentioning

confidence: 99%

An Allosteric Modulator of HIV-1 Protease Shows Equipotent Inhibition of Wild-Type and Drug-Resistant Proteases

et al. 2014

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NMR and MD simulations have demonstrated that the flaps of HIV-1 protease (HIV-1p) adopt a range of conformations that are coupled with its enzymatic activity. Previously, a model was created for an allosteric site located between the flap and the core of HIV-1p, called the Eye site (18381626Biopolymers200889643652). Here, results from our first study were combined with a ligand-based, lead-hopping method to identify a novel compound (NIT). NIT inhibits HIV-1p, independent of the presence of an active-site inhibitor such as pepstatin A. Assays showed that NIT acts on an allosteric site other than the dimerization interface. MD simulations of the ligand–protein complex show that NIT stably binds in the Eye site and restricts the flaps. That bound state of NIT is consistent with a crystal structure of similar fragments bound in the Eye site (20659109Chem. Biol. Drug Des.201075257268). Most importantly, NIT is equally potent against wild-type and a multidrug-resistant mutant of HIV-1p, which highlights the promise of allosteric inhibitors circumventing existing clinical resistance.

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Identification of broad-based HIV-1 protease inhibitors from combinatorial libraries

Cited by 19 publications

References 35 publications

Emerging principles in protease-based drug discovery

Emerging principles in protease-based drug discovery

High-throughput screening for the identification of small-molecule inhibitors of the flaviviral protease

An Allosteric Modulator of HIV-1 Protease Shows Equipotent Inhibition of Wild-Type and Drug-Resistant Proteases

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