HIV NNRTI | BI-2540

Write a review / see user reviews
Target protein: 
HIV NNRT
Probe Name: 
BI-2540
MOLECULAR WEIGHT [DA]: 
442.5
In stock: 
84

Chemical structure

Highlights

BI-2540 is a potent inhibitor of HIV non-nucleoside reverse transcriptase (NNRT) and cross-reactive against clinically relevant mutants of reverse transcriptase. BI-2540 shows low clearance and good bioavailability upon p.o. dosing in rats. With BI-2439, a relatively close analog of BI-2540 with significantly lower activity (420-fold) is available as negative control for in vitro experiments.

Collapse AllExpand All

Target information

Description of the protein: The human immunodeficiency virus (HIV-1) reverse transcriptase (RT) enzyme performs the retrotranscription of the viral single-stranded RNA into double-stranded linear DNA. The viral genomic retrotranscription arises from the cooperative effect of two enzymatic functions of RT: a DNA polymerase activity (copy of the RNA/DNA template) and ribonuclease H activity (cleavage of RNA when part of a RNA/DNA duplex).

Protein domain structure: RT of HIV-1 is a heterodimer composed of subunit p66 (560 AA) and p51 (440 AA). The larger subunit p66 contains both active sites responsible for RT enzymatic functions (DNA polymerase and RNase H activities).1

Molecular mechanism: there are two different classes for RT inhibitors: nucleoside RT inhibitors (NRTI) and non-nucleoside RT inhibitors (NNRTI). NNRTI bind to an allosteric site adjacent to the polymerase active site (~10 Å). Binding of NNRTI interferes with the chemical step of DNA synthesis by affecting the alignment of the primer terminus with the polymerase active site. Thus, NNRTIs efficacy stems from the structural rearrangement in the p66 subunit which precludes viral DNA synthesis.

Biology: HIV-1 largely infects CD4-positive T lymphocytes and macrophage cells, thus destroying the immune system. Lymphoid organs are a major reservoir of ongoing HIV-1 replication. HIV life cycle consists of seven steps: 1) binding, 2) fusion, 3) reverse transcription, 4) integration, 5) replication, 6) assembly, and 7) budding.

Disease link: HIV-1 infects >30 million people worldwide. Infected patients cannot be cured; therefore a “triple drug cocktail” of antiretroviral therapy (ART) must be continuously administered. Combination drug therapies suppress viral load by blocking viral replication and improving efficacy to overcome resistant variants.1,2

HIV NNRTI in complex with related structure GW564511 (PDB code: 3DLG)

HIV NNRTI in complex with related structure GW564511 (PDB code: 3DLG)

In vitro Activity

BI-2540 is a potent HIV non-nucleoside reverse transcriptase (NNRT) inhibitor. For cellular efficacy against RT mutants please refer to the selectivity section.

Probe name / Negative control

BI-2540

BI-2439

MW [Da]

528

476

HIV1-RT Pico, WT (IC50)* [nM]

12

5053

HIV replicon ELISA, WT (EC50) § [nM]

0.76

n.d.

HIV replicon LUC, WT (EC50) ς [nM]

2.6

n.d.

* Enzymatic assay: HIV-1 reverse transcriptase (Picogreen Fluorescence Assay); 15 min pre-incubation before adding substrate solution, 50 min incubation at 37°C, PicoGreen as a fluorescent intercalator.

§ HIV viral replication assay: C8166 cells, 72 h incubation at 37°C, readout: ELISA quantification of p24

ς HIV-1 luciferase assay: C8166 cells, 72 h incubation at 37°C, readout: RLU of luciferase, Steady Glo.

In vitro DMPK and CMC parameters

Probe name / Negative control

BI-2540

BI-2439

cLogP

5.7

4.2

Solubility @ pH 7.0 [µg/ml]

>52

n.d.

CACO permeability @pH 4 / 7.4 [*10-6 cm/s]

0.2 / 23

n.d. / 12

CACO efflux ratio

0.1

1.4

Microsomal stability [% QH] (human)

<24

n.d.

Plasma protein binding [%] (human)

99.5

n.d.

CYP 3A4 (IC50) [µM]

18

>50

CYP 2C9 (IC50) [µM]

>30

8.5

CYP 1A2 (IC50) [µM]

>30

>50

CYP 2C19 (IC50) [µM]

>30

>50

CYP 2D6 (IC50) [µM]

>30

>50

In vivo DMPK parameters

BI-2540 shows a low clearance and good bioavailability upon p.o. dosing in rats.

BI-2540

Rat

Clearance [% QH]a

2.9

Vss [l/kg]a

2.26

MRT [h]a

12.8

tmax [h]b

1.0

Cmax [μM]b

11860

AUC [μM*h]b

125620

F [%]b

53

a i.v. (2 mg/kg)

b p.o. (10 mg/kg)

Negative control

MOLECULAR WEIGHT OF NEGATIVE CONTROL [DA]: 
311.8

BI-2439 is a relatively close analog of BI-2540 with significantly lower activity (420-fold) in the HIV-RT Picogreen Fluorescence assay (IC50 = 5 µM) and is therefore offered as an in vitro negative control.

BI-2439 which serves as a negative control

BI-2439 which serves as a negative control

Selectivity

Cellular efficacy against RT mutants: HIV-1 luciferase assays: C8166 cells, 72 h incubation at 37°C; readout: RLU of luciferase, Steady Glo

Mutations

BI-2549

X-fold vs. wt

Wild type (WT) EC50 [nM]

2.58

--

A98G EC50 [nM]

3.94

1.5

K103N EC50 [nM]

2.36

0.9

V106A EC50 [nM]

12.8

5.0

V106I EC50 [nM]

4.19

1.6

E138K EC50 [nM]

15.0

5.8

Y181C EC50 [nM]

2.44

0.9

Y188C EC50 [nM]

0.38

0.1

Y188L EC50 [nM]

39.1

15

G190A EC50 [nM]

3.10

1.2

P236L EC50 [nM]

7.53

2.9

L100I/K103N EC50 [nM]

3.18

1.2

K103N/G190A EC50 [nM]

8.16

3.2

K103N/V108I EC50 [nM]

4.82

1.9

K103N/Y181C EC50 [nM]

6.54

2.5

K103N/P225H EC50 [nM]

4.77

1.8

V106A/E138K EC50 [nM]

119

46

V106A/P236L EC50 [nM]

199

77

V106I/E138K EC50 [nM]

38.1

15

V106I/P236L EC50 [nM]

36.1

14

E138K/P236L EC50 [nM]

60.3

23

 

No data panel available

BI-2540

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

No X-ray available.

reference molecules

Commercially available NNRTIs: Nevirapine, Delavirdine, Efavirenz, Dapivirine, Etravirine, Rilpivirine.2

Summary

BI-2540 is a potent inhibitor of HIV non-nucleoside reverse transcriptase (NNRT) and cross-reactive against clinically relevant mutants of reverse transcriptase. BI-2540 shows low clearance and good bioavailability upon p.o. dosing in rats. With BI-2439, a relatively close analog of BI-2540 with significantly lower activity (420-fold) is available as negative control for in vitro experiments.

A practical synthesis for BI-2540 was reported.3

Supplementary data

References

  1. Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition

    Sarafianos S. G., Marchand B., Das K., Himmel D. M., Parniak M. A., Hughes S. H., Arnold E.

    J. Mol Biol. 2009, 385, 693-713.

  2. Peris Non-nucleoside reverse transcriptase inhibitors: a review on pharmacokinetics, pharmacodynamics, safety and tolerability

    Usach I., Melis V., Peris J.-E.

    J. Int AIDS Soc. 2013, 16, 1-14.

  3. Practical Synthesis of A Benzophenone-Based NNRT Inhibitor of HIV-1

    Wang X.-J., Zhang L., Sun X., Lee H., Krishnamurthy D., O’Meara J. A., Landry S., Yoakim C., Simoneau B., Yee N. K., Senanayake C. H.

    Org. Process Res. Dev. 2012, 16, 561-566.

0 Reviews

No reviews have been posted yet. Add yours below!

Write a review