HIV Integrase inhibitor | BI 224436

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Target protein: 
HIV integrase
Probe Name: 
BI 224436
MOLECULAR WEIGHT [DA]: 
442.5
In stock: 
239

Chemical structure

Highlights

BI 224436 is the first non-catalytic-site integrase inhibitor (NCINI) reaching a clinical trial. It combines high solubility at all relevant physiological pH values with good cell permeability and good metabolic stability. BI 224436’s optimized in vitro ADME profile also translates into a good in vivo PK profile in preclinical animal species, with oral bioavailability ranging from 54-100%.

Worth noting is the excellent antiviral potency of BI 224436 in the presence of 50% human serum (ssEC95 22-75 nM). In addition, two-drug combination studies with other HIV-1 antiviral agents produced additive to synergistic effects. Thus BI 224436 could be a key component of new first-line cART regimen.

Wikipedia

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Target information

Following the reverse transcription of viral RNA into cDNA, HIV-Integrase (IN) is responsible to integrate newly synthesized viral cDNA into the host cell genome. IN fulfils this function via a two-steps process: a 3’-dinucleotide processing reaction and a strand transfer reaction. In the first step, IN binds to viral DNA as part of the pre-integration complex (PIC) in the cytoplasm and excises a dinucleotide from each 3’-end. Thereafter, the PIC is transported into the nucleus where the 3’-ends of the viral DNA are covalently linked to the 5’-ends of the host cell DNA in a process known as strand transfer. (1)

Currently approved IN inhibitors (raltegravir, elvitegravir, dolutegravir) are IN strand transfer inhibitors (INSTIs) binding to the IN active site. In contrast, BI 224436 binds to a conserved allosteric pocket at the dimer interface of the catalytic core domain (CCD) of IN and acts through a distinct mechanism. The term non-catalytic-site integrase inhibitors (NCINIs) is used to differentiate both series of compounds having different MOA.

BI 224436 is the first NCINI validated in a phase-1a clinical trial and differs from INSTIs in many regards: 1) BI 224436 binds to an allosteric pocket, which functional effect is to inhibit the 3’-processing step of IN. Additionally, binding to this allosteric pocket also prevents protein-protein interaction with the host cell Lens Epithelial Derived Growth Factor (LEDGF) required for HIV-1 viral replication; 2) BI 224436 shows a distinct resistancy profile against virus mutations and maintains its antiviral activity against a panel of mutants that emerge during treatment failure with other inhibitor classes (INSTIs and NNRTIs). (2)

HIV integrase in complex with an analog of BI 224436 (PDB code: 4NYF)

HIV integrase in complex with an analog of BI 224436 (PDB code: 4NYF)

In vitro Activity

BI 224436 displays an IC50 = 15 nM in a LTR-cleavage assay measuring the 3’-processing hydrolysis reaction of a dinucleotide from the DNA 3’-end of each viral long terminal repeat. Moreover, BI 224436 exhibits excellent antiviral potency (EC50 11-27 nM) in a panel of wild-type and recombinant viruses with different aa124/aa125 variants of IN.

A hallmark of BI 224436 is the low influence of human serum on antiviral potency (ssEC50 2.1-fold) which is the assay used for human dose predictions for HIV clinical candidates.

Probe name / Negative control

BI 224436

BI-0449

MW [Da]

442.5

311.8

LTR-cleavage assay (IC50) [nM]a

15

6,840

Luc-RGA (EC50) [nM]b

11-27

>40,000

ssEC50 (50% HS), fold-changec

2.1

-

MTT-C8166 (CC50) [nM]d

110,000

-

a Long Terminal Repeat (LTR) DNA 3’-processing assay measures the enzymatic activity of HIV-1 integrase to perform the essential 3’-processing reaction. Integrase binds to the viral DNA LTR ends at the CAGT-3’ sequence and catalyzes the removal of the two terminal nucleotides. In this homogeneous assay, the HIV-1 LTR DNA substrate consists of two annealed oligonucleotides, a 31-mer modified at the 3’ end with a black hole quencher (BHQ) and a 31-mer modified at the 5’ end with rhodamine red-X N-hydroxysuccinimide (NHS) ester (5RhoR-XN). Enzymatic cleavage by integrase releases the terminal dinucleotides and black hole quencher, which allows the rhodamine fluorescence to be detected.

b Luciferase reporter gene assay (Luc-RGA): C8166 LTR-Luc cells infected with different HIV-1 viral strains was incubated at 37°C in presence of various concentration of inhibitors for 3 days. Viral strains used: HxB2 virus (A124/T125 IN variant); NL4.3 virus (T124/T125 IN variant); or recombinant NL4.3 virus (A124/T125, A124/A125, N124/T125, or N125/A125 IN variants)

c Determined by measurement of EC50 +50% human serum. C8166 LTR-luciferase reporter cells were infected with HIV-1 NL4.3 virus in presence of 50% human serum. After 3-days of cell incubation at 37°C, Steady Glo was added and luminescence was monitored as a measurement of the HIV replication in the presence of various concentrations of inhibitor.

d Cytotoxicity for C-8166 LTR-Luc cells was determined using the tetrazolium salt MTT metabolic assay after 3 days of incubation.

In vitro DMPK and CMC parameters

BI 224436 combines excellent solubility at all physiologically relevant pH values (Sol. pH 2.0-6.8 >0.84 mg/mL) with very good cell permeability as measured in the caco-2 assay (A-B: 14 x10-6 cm/s) and minimal cytochrome inhibition (CYP2C9 IC50: 20 μM). BI 224436’s optimized quinoline C4-aryl substituent improved metabolic stability in human hepatocytes (13% QH).

Probe name / Negative control

BI 224436

BI-0449

TPSA / cLogP / LogD7.4

82 / 4.7 / 0.44

50 / 4.1 / ---

Solubility @ pH 2.0 / 6.8 [µg/ml]

840 / >1,000

-

CACO permeability @ pH 7.4 [*10-6 cm/s]

14

-

CACO efflux ratio

0.3

-

Microsomal stability [% QH] (human/mouse/rat/monkey/dog)

14 / 6.4 / 7 / 11 / 16

-

Hepatocyte stability [% QH] (human/mouse/rat/monkey/dog)

13 / 12 / 9 / 13 / 32

-

Plasma protein binding [%] (human/mouse/rat/monkey/dog)

84.3 / 97.3 / 98.2 / 78.0 / 75.5

-

hERG [inh. % @ 100 µM]

5.8 %

-

CYP 3A4 (IC50) [µM]

23

>50

CYP 2C9 (IC50) [µM]

20

19

CYP 1A2 (IC50) [µM]

>30

-

CYP 2C19 (IC50) [µM]

>30

>50

CYP 2D6 (IC50) [µM]

>30

>50

 

In vivo DMPK parameters

BI 224436 combines excellent aqueous solubility across pH values (2.0 – 6.8) and good cellular permeability. In addition, BI 224436 displays a good PK profile in all investigated animal species with oral bioavailability typically ranging from 54-100%. For rodents and dogs, in vivo clearance (CL, % QH) is lower than values predicted by in vitro hepatocyte stability whereas monkey species is showing an opposite trend (i.e. higher in vivo clearance than anticipated). For rats, low in vivo clearance might be attributed to biliary enterohepatic recirculation of the parent compound/acyl glucuronide. (6, 7)

Given the overall favourable potency, in vitro ADME-CMC properties, in vivo PK profile, and clean animal toxicology studies, BI 224436 was advanced into phase-1a clinical development.

PK profile of BI 224436a

BI 224436

mouseb

ratb

monkeyc

dogc

Clearance [% QH]

0.8

0.7

23

8

Vss [l/kg]

0.20

0.45

0.54

0.88

t1/2 [h]

2.6

8.8

1.4

5.9

Cmax [μM]

15 b

13 b

4.8

12

AUC [μM*h]

99 b

75 b

6.3

24

F [%]

100

54

82

81

a The oral formulation contained 1% MP, 0.3% Tween 80, 0.5% MC; the i.v. formulation contained 70% PEG, 30% water.

b Mouse and rat doses: 0.2 mg/kg i.v.; 0.4 mg/kg oral. The oral exposure was dose normalized to 2 mg/kg to allow for an appropriate comparison to monkey and dog PK studies.

c Monkey and dog doses: 1.0 mg/kg i.v.; 2.0 mg/kg oral

In vivo pharmacology

No HIV-1 animal model routinely available for PD testing.

Negative control

MOLECULAR WEIGHT OF NEGATIVE CONTROL [DA]: 
311.8

BI-0449 is a representative compound of the 3-acetic acid-4-aryl quinoline hit series discovered during HTS campaign. Compared to optimized BI 224436, it is ~450-fold less active in the biochemical LTR-cleavage assay. However BI-0449 is inactive in any HIV-1 replicon cellular assay up to the highest concentration tested (>40 μM).

BI-0449, which serves as a negative control.

BI-0449, which serves as a negative control.

Selectivity

No panel data available.

BI 224436

Selectivity data available

Cerep®

No

Panlabs®

No

Invitrogen®

No

DiscoverX®

No

Dundee

No

Co-crystal structure of the BI probe compound and the target protein

The Xray co-crystal structure of target in complex with BI 224436 is not available. However a closely related analog binding to a conserved allosteric pocket of the catalytic core domain of integrase has been reported (Figure 3, PDB code: 4NYF)1.

reference molecules

For a review on investigational HIV integrase inhibitors see reference 8.

Summary

BI 224436 is the first non-catalytic-site integrase inhibitor (NCINI) reaching a clinical trial. It combines high solubility at all relevant physiological pH values with good cell permeability and good metabolic stability.

BI 224436’s optimized in vitro ADME profile also translates into a good in vivo PK profile in preclinical animal species, with oral bioavailability ranging from 54-100%.

Worth noting is the excellent antiviral potency of BI 224436 in the presence of 50% human serum (ssEC95 22-75 nM). In addition, two-drug combination studies with other HIV-1 antiviral agents produced additive to synergistic effects. Thus, BI 224436 could be a key component of new first-line cART regimen.

The chemical structure of BI 224436 is also worth highlighting, since unsymmetrical C4-aryl substituent of the quinoline scaffold produced a stable chiral atropisomer that raised development complexity.(5)

Overall, as the first representative of a new class of HIV-1 integrase inhibitors tested in clinical trials, BI 224436’s attractiveness stems from its potent antiviral activity in addition to its good in vivo ADME-PK profile following oral (or i.v.) dosing.

Supplementary data

References

  1. Discovery of BI 224436, a Noncatalytic Site Integrase Inhibitor (NCINI) of HIV-1

    Lee D. Fader, Eric Malenfant, Mathieu Parisien, Rebekah Carson, François Bilodeau, Serge Landry, Marc Pesant, Christian Brochu, Sébastien Morin, Catherine Chabot, Ted Halmos, Yves Bousquet, Murray D. Bailey, Stephen H. Kawai, René Coulombe, Steven LaPlante, Araz Jakalian, Punit K. Bhardwaj, Dominik Wernic, Patricia Schroeder, Ma’an Amad, Paul Edwards, Michel Garneau, Jianmin Duan, Michael Cordingley, Richard Bethell, Stephen W. Mason, Michael Bös, Pierre Bonneau, Marc-André Poupart, Anne-Marie Faucher, Bruno Simoneau, Craig Fenwick, Christiane Yoakim, and Youla Tsantrizos

    Med. Chem. Lett. 2014, 5(4), 422-427.

  2. Preclinical Profile of BI 224436, a Novel HIV-1 Non-Catalytic Site Integrase Inhibitor

    Craig Fenwick, Ma'an Amad, Murray D. Bailey, Richard Bethell, Michael Bös, Pierre Bonneau, Michael Cordingley, René Coulombe, Jianmin Duan, Paul Edwards, Lee D. Fader, Anne-Marie Faucher, Michel Garneau, Araz Jakalian, Stephen Kawai, Louie Lamorte, Steven LaPlante, Laibin Luo, Steve Mason, Marc-André Poupart, Nathalie Rioux, Patricia Schroeder, Bruno Simoneau, Sonia Tremblay, Youla Tsantrizos, Myriam Witvrouw and Christiane Yoakim

    Antimicrobial Agents and Chemotherapy 2014, 58(6), 3233-3244

  3. Aligning Potency and Pharmacokinetic Properties for Pyridine-Based NCINIs

    Lee D. Fader, Murray Bailey, Eric Beaulieu, François Bilodeau, Pierre Bonneau, Yves Bousquet, Rebekah J. Carson, Catherine Chabot, René Coulombe, Jianmin Duan, Craig Fenwick, Michel Garneau, Ted Halmos, Araz Jakalian, Clint James, Stephen H. Kawai, Serge Landry, Steven R. LaPlante, Stephen W. Mason, Sebastien Morin, Nathalie Rioux, Bruno Simoneau, Simon Surprenant, Bounkham Thavonekham, Carl Thibeault, Thao Trinh, Youla Tsantrizos, Jennifer Tsoung, Christiane Yoakim, and Dominik Wernic

    Med. Chem. Lett. 2016, 7(8), 797-801

  4. Inhibitors of human immunodeficiency virus replication

    Y. S. Tsantrizos et al.

    2009, patent application WO 2009/062285.

  5. Concise and Practical Asymmetric Synthesis of a Challenging Atropisomeric HIV Integrase Inhibitor

    Keith R. Fandrick , Wenjie Li , Yongda Zhang , Wenjun Tang ,Joe Gao , Sonia Rodriguez ,Nitinchandra D. Patel , Diana C. Reeves , Jiang‐Ping Wu ,Sanjit Sanyal , Nina Gonnella , Bo Qu ,Dr. Nizar Haddad , Jon C. Lorenz ,Kanwar Sidhu ,June Wang , Shengli Ma , Nelu Grinberg , Heewon Lee , Youla Tsantrizos , Marc‐André Poupart , Carl A. Busacca , Nathan K. Yee , Bruce Z. Lu , Chris H. Senanayake

    Angew. Chem. Int. Ed. 2015 54, 7144-7148

  6. Minimizing the Contribution of Enterohepatic Recirculation to Clearance in Rat for the NCINI Class of Inhibitors of HIV

    Lee D. Fader, Rebekah Carson, Sébastien Morin, François Bilodeau, Catherine Chabot, Ted Halmos, Murray D. Bailey, Stephen H. Kawai, René Coulombe, Steven Laplante, Kevork Mekhssian, Araz Jakalian, Michel Garneau, Jianmin Duan, Stephen W. Mason, Bruno Simoneau, Craig Fenwick, Youla Tsantrizos, and Christiane Yoakim

    Med. Chem. Lett. 2014, 5(6), 711-716

  7. Aligning Potency and Pharmacokinetic Properties for Pyridine-Based NCINIs

    Lee D. Fader, Murray Bailey, Eric Beaulieu, François Bilodeau, Pierre Bonneau, Yves Bousquet, Rebekah J. Carson, Catherine Chabot, René Coulombe, Jianmin Duan, Craig Fenwick, Michel Garneau, Ted Halmos, Araz Jakalian, Clint James, Stephen H. Kawai, Serge Landry, Steven R. LaPlante, Stephen W. Mason, Sebastien Morin, Nathalie Rioux, Bruno Simoneau, Simon Surprenant, Bounkham Thavonekham, Carl Thibeault, Thao Trinh, Youla Tsantrizos, Jennifer Tsoung, Christiane Yoakim, and Dominik Wernic

    Med. Chem. Lett. 2016, 7(8), 797-801

  8. Investigational HIV integrase inhibitors in phase I and phase II clinical trials

    Yingshan Han, Thibault Mesplède and Mark A. Wainberg

    Expert Opinion on Investigational Drugs 2017, 26, 1207-1013

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