RESISTANCE CHARACTERISTICS

OF HIV INTEGRASE INHIBITORS

Roger Paredes, MD, PhD

Infectious Diseases & irsiCaixa AIDS Research Institute

Hospital Germans Trias i Pujol

Barcelona

HIV Clinical Fora Series Brazil: Integrase Inhibitors 2018

Integrase Inhibitors

Strand transfer Trans-esterification reaction direct nucleophilic attack of the

3´OH group on the phosphodiester backbone of the host target

DNA covalent insertion of viral DNA into the cell DNA

Integrase32 kDa

5 β-sheets + 6 α helices linked by

flexible loops allow conformational

changes required for 3´processing of

the viral DNA and strand transfer

https://en.wikipedia.org/wiki/Discovery_and_development_of_integrase_inhibitors

INSTIs: Mechanism of action

strand-transfer reaction, with no significant effect on the 3´-processing reaction.[9] INSTIs may therefore be more

specific and bind selectively to the target DNA binding site and hence be less toxic than bifunctional inhibitors that are

able to bind to both the donor and target binding sites.[12]

INBIs also bind to IN but the mechanism of action is unknown so the binding can not be detailed.[16]

Two structural components are necessary for integrase binding: a hydrophobic benzyl moiety that buries into a highly

hydrophobic pocket near the active site; and chelating triad that binds with two Mg2+ ions in a rather hydrophilic

region, anchoring the inhibitor onto the protein surface (see figure 3).[17] In fact, all potent integrase inhibitors

possess a substituted benzyl component that is critical for maintaining 3‘end joining potency. Removal of the benzyl

group prevents inhibitory function.[15] Lipophylic substituents are therefore beneficial for the strand transfer

inhibition, in particular the thiophenyl, furanyl and (thiophen-2-yl)phenyl substitutions. Heteroaromatic amine and

amide also cause increase in 3‘ processing inhibitory action.[6]

When catechol-based inhibitors of IN were researched it was observed that maintaining a planar relationship with the

bis-hydroxylated aryl ring increases potency. The inhibitory activity could be further optimized by including a meta-

chloro substituent, enhancing the interaction of the benzyl group with the adjacent hydrophobic pocket (see figure 4:

Structures A-G).[8]

Structure activity relationship (SAR)

Figure 3: Structure activity relationship of elvitegravir and raltegravir. A benzyl group in a hydrophobic

pocket and a triad to chelate the two Mg2+ ions.Two structural components are necessary for integrase binding:

• A hydrophobic benzyl moiety that buries into a highly hydrophobic pocket near the

active site

• A chelating triad that binds with two Mg2+ ions in a rather hydrophilic region

All potent integrase inhibitors possess a substituted benzyl component

that is critical for maintaining 3‘end joining potency.

https://en.wikipedia.org/wiki/Discovery_and_development_of_integrase_inhibitors

INSTIs: Mechanism of action

Mg2+ and Mn2+ are critical

cofactors in the integration

phase

INSTIs bind to the

active site of Mg2+ ions

Functional impairment

of integrase

Stanford HIVdb

By Andrea Low, MD and Mark Muesing, PhD. Understanding and

Inhibiting Integrase in the Treatment of HIV Disease Based on a

presentation at PRN by Mark Muesing, PhD and Martin Markowitz, MD

Integrase Inhibitors

First generation

• Raltegravir (RAL)

• Elvitegravir (EVG)

Second generation

RAL Resistance: Three Pathways

Witmer et al, ICAAC 2008

N155H Q148K/H/R Y143C

L74M L74M E92QE92Q E92Q T97AT97A T97A V151IV151I E138A G163RG163R E138K S230RG163K G140AS230R G140S

G163R

Key Raltegravir Mutations

Stanford HIV Data Base

Emerging RAL-resistant mutants

originate from pre-existing viruses

Codoñer et al, Antiv Res 2010; Armenia D et al., JID 2012

Genotype – Phenotype Correlations of RAL

Mutations

Q148 Pathway

0

100

200

300

400

500

600

Fo

ld-C

ha

ng

e I

C 50

Q148H

Q148H/G140S

Q148K

Q148K/E138A

Q148K/G140A

Q148K/E138A/G140A

Q148R

Q148R/G140S

Integrase Inhibitors

First generation

• Raltegravir (RAL)

• Elvitegravir (EVG)

Second generation

Integrase Inhibitors

First generation

• Raltegravir (RAL)

• Elvitegravir (EVG)

Second generation

• Dolutegravir (DTG)

• Bictarvy (BIC/FTC/TAF) –

FDA approved Feb 2018

• Cabotegravir - Advanced

development

DTG

BIC

DTG versus RAL alignment in active site

DTG

RAL

Bictegravir: Optimization of Structural A-and D-rings

Lazerwith et al. ASM Microbe 2016; June 16-20, 2016; Boston, MA. Poster 414.

Structure of Bictegravir

A-Ring D-Ring

RAL EVG DTG BIC

EC50 (nM, MT4)

Plasma Adjusted

EC50 (nM, MT4)

8.9

21

1.8

43

1.7

47

1.9

83

human liver microsomal

Cl (L/h/kg) 0.24 0.43 0.16 0.17

%free human plasma 12.2 0.5 0.7 0.30

OCT-2 IC50 (µM) 0.13 0.49

PXR %Emax@ 15 µM 51 18

Solubility (pH = 7, µg/mL) 1906 2 53 119

G140S/Q148R fold shift 249 297 4.8 2.0

Lazerwith et al. ASM Microbe 2016; June 16-20, 2016; Boston, MA. Poster 414.

Bictegravir Characteristics After Optimizing Both

the A & D-ring

Integrase Inhibitor Resistance to Mutations and

Combinations

160

140

120

100

80

60

40

20

RAL

EVG

DTG

BIC

Adapted from White K et al, 14th Euro Workshop, May 2016, Rome

BIC vs. DTG: clinically meaningful?

4th European Workshop on HIV & Hepatitis May 25-27, 2016.

BIC resistance ex vivo

Two patterns of resistance substitutions in IN

after extended culture with BIC

• R263K ± M50I (<3-fold reduced susceptibility)

• S153F or S153Y (≤2-fold reduced susceptibility)

Selected variants remained sensitive or had

low-level reduced susceptibility to BIC

Selecting

Drug

Key IN Substitutions at Select Passages by Deep Sequencing (Frequency)a

IN Genotype of

Representative SDM

EC50 Fold Change Compared to

HIV-1 xxLAI WTRC

P4

(48 days)

P6

(66-87 days)b

P8 – P9

(80-131 days)c

P10 – P12

(113-191 days)d

P13

(138-229 days)e BIC DTG EVG RAL

BIC None T66I (8.0%)

S153F (2.4%)

T66I (3.1%)

S153F (38%)

E157K (3.4%)

S153F (97%)

E157K (3.2%)

S24G (32%)

S153F (>99%)

S24G (11%)

T66I 0.4 0.4 8.6 0.8 76%

S153F 1.4 1.1 2.2 1.4 52%

T66I/S153F 0.6 0.6 30 0.6 12%

E157K 1.0 0.8 0.8 1.3 16%

DTG None S153Y (34%) S153Y (87%)

L234F (72%)

S153Y (90%)

L234F (87%)

S153Y (>99%)

L234F (>99%)

S153Y 2.0 1.7 2.4 1.1 45%

L234F 1.2 1.2 1.3 0.6 120%

S153Y/L234F 2.2 1.9 3.0 0.7 33%

D a y s i n c u l t u r e

Dr

ug

Co

nc

en

tr

atio

n (

nM

)

0 5 0 1 0 0 1 5 0 2 0 0 2 5 0

0 . 1

1

1 0

1 0 0

1 0 0 0

1 0 0 0 0

1 0 0 0 0 0

W i l d - t y p e

B I C ( F i n a l = P 1 3 , 2 0 7 d a y s )

D T G ( F i n a l = P 1 3 , 2 2 9 d a y s )

E V G ( F i n a l = P 1 3 , 1 3 8 d a y s )

R A L ( F i n a l = P 1 3 , 1 6 6 d a y s )

K Andreatta, et al. CROI 2018

No DTG resistance after 1st-line DTG

VF in RCTs

Study Summary

efficacy

PDVF in

DTG arm

INSTI resistance

FLAMINGO DTG > DRV/r 2 / 242 0

ARIA DTG > ATV/r 1/ 248 0 (1 K219K/Q + E138E/G)

SINGLE DTG > EFV 18 / 422 1 E157Q/P (no emergent INSTI DR)

SPRING-2 DTG = RAL 16 / 411 0

• DTG better than non-INSTIs, non-inferior to RAL

• No INSTI resistance emergence in ideal conditions

• ART-naive

• WT virus Active backbone

• Early ART switch after PDFV

Figure 1: B/F/TAF Treatment-Naive Study Designs

▪ Randomized, double-blind, multicenter, active-controlled, Phase 3 studies of treatment-naïve HIV-1 infected participants: GS-US-380-1489 (NCT02607930) and GS-US-380-1490 (NCT02607956)

▪ Primary endpoint: proportion with HIV-1 RNA < 50 copies/mL at Week 48 by US FDA-defined Snapshot Algorithm2,3

White K, CROI, 2018, #532 23

2. Gallant J, et al., The Lancet (2017) 390:10107.

3. Sax PE, et al., The Lancet (2017) 390:10107.

00

10

20

30

40

50

60

70

80

90

100

Week

Pro

po

rtio

nw

ith

HIV

-1R

NA

<5

0c

op

ies

/mL

(%)

B/F/TAF

DTG/ABC/3TC

DTG+F/TAF

4 8 12 24 36 48

Figure 2. Rapid Suppression of HIV-1 RNA to < 50 copies/mL through Week 48 (Missing = Excluded Approach)

White K, CROI, 2018, #532 24

AE=adverse event; DC=discontinuation; Other reasons= lost to follow-up, withdrew consent, investigator discretion, noncompliance, etc.)

Week 4

76%

76%

80%

Week 8

91%

92%

90%

Week 12

96%

96%

95%

Week 48

99% B/F/TAF

98% DTG/ABC/3TC

99% DTG+F/TAF

B/F/TAF vs. DTG/ABC/3TC or vs. DTG + F/TAF:

displayed rapid viral suppression and non-inferior efficacy at Week 48

Figure 4. Week 48 Virologic Outcome of B/F/TAF-treated Participants Stratified by Baseline Resistance Category

White K, CROI, 2018, #532 25

1º=Primary Resistance Substitution; 2º=Secondary Resistance Substitution

Table 7. Resistance Analysis Population through Week 48 and Resistance Summary

White K, CROI, 2018, #532 26

Resistance Category

B/F/TAF

(N=634)

DTG/ABC/3TC

(N=315)

DTG + F/TAF

(N=325)

Resistance Analysis Population (RAP)

(% of FAS)8 (1.3%) 4 (1.3%) 5 (1.5%)

Subjects with Data for Any Gene (% of RAP) 8 (100%) 3 (75%) 5 (100%)

Subjects with RT Data 8 (100%) 3 (75%) 5 (100%)

Subjects with IN Data 8 (100%) 2 (50%) 3 (60%)

Developed Resistance Substitutions to

Study Drugs0 0 0

Number of Participants, n (%)

PI = protease inhibitor; PR = protease; R = resistance

Slow resistance development and

transmission in resource-rich settings

Scherrer A, et al. J Infect Dis 2017

10

100

1000

10000

100000

1000000

0 12 24 36 48 60 72 84 96

SAILING: Subjects 4 & 3

Day 1 PDVF

HIV-1 RNA 84313 27050

IN mutation - I60L, T97A, N155H

DTG FC 0.66 2.4

RAL FC 0.52 113

IN RC NRb NR

PDVF BR: No emergent resistance, loss of RT

M184V and PI L10F, M36I, M46I, I54V, V82A.

Underwood, et al. Abs#85. IDRW June 4-8, 2013. Toronto, Canada

10

100

1000

10000

0 12 24 36 48 60 72 84 96 108 120 132 144

Day 1 PDVF Confirm.

HIV-1

RNA

733 622 1054

IN

mutation

- A49G,

S230R,

R263K

A49G,

S230R,

R263K

DTG FC 0.73 3.82 5.77

RAL FC 0.54 2.39 2.62

IN RC* 20% 7.1% 12%

PDVF BR: No emergent resistance, and no NRTI

resistance at any time points

HIV

-1 R

NA

c/m

L

19

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pt-

06

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-au

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9-a

ug

-16

20

40

60

80

100

800

1000

1200

1400

HVG

TDF/FTC

EFV

NVP

DTG

RPV

DRV/COBI

TDF/FTC

EFV

NVP

DTG

RPV

DRV/COBI

VL

(co

pie

s/m

l)

DTG monotherapy

10 years on NNRTI 3-drug ART

Blanco JL, et al EACS 2017

Viral dynamics during DTG monotherapy maintenance failure

Slide Courtesy of Charles Boucher, Erasmus University

Conclusions

• INSTIs are the current mainstay of ART

• Genetic barrier

• RAL, ELV: Low

• DTG, BIC: Higher (but not as high as boosted PIs)

• Failure to DTG monotherapy with “RAL-like” resistance profiles

• Currently no need for pre-ART genotyping for clinical

management

• Surveillance is warranted

• NEVER monotherapy

FLSida: Isabel Bravo, Pep Coll, Carla Estany, Cristina HerreroBCN Checkpoint: Jorge SazIrsiCaixa: Bea Mothe, Jorge Carrillo, Christian Brander, Julià Blanco,

Bonaventura ClotetVall d’Hebron: Manel Crespo, Jordi Navarro, Ariadna Torrela

UVIC-UCC: Malu Calle

This study is supported by the University and Resear ch Secretary - Department of Economy and Knowledge of the Government of Catalonia and the European Social Fund (Ref. 2015 FI_B 00184) and the Fondo de Investigaciones Sanitarias (PI13/02514) & Fondos FEDER & the RED de SIDA RD16/0025/0041

Marc Noguera

Yolanda Guillén

Cristina Rodríguez

Chiara Mancuso

Muntsa Rocafort

Maria Casadellà Mariona

Parera

Javier Rivera

Gràcies!

Jonathan Shapiro, Slides