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
-se
pt-
06
19
-de
s-0
6
30
-ma
y-0
7
7-s
ep
t-0
7
30
-ja
n-0
8
16
-ma
y-0
8
17
-se
pt-
08
19
-de
s-0
8
3-a
pr-
09
19
-oct-
09
15
-ma
rch
-10
2-j
ul-
10
2-n
ov
-10
6-a
pr-
11
19
-ma
y-1
1
2-s
ep
t-1
1
11
-ja
n-1
2
20
-ju
ne
-12
26
-oct-
12
30
-ap
r-1
3
5-n
ov
-13
15
-ap
r-1
4
14
-oct-
14
9-f
eb
r-1
5
12
-ju
ne
-15
2-d
es
-15
21
-de
s-1
51
8-j
an
-16
10
-ma
r-1
6
6-j
un
e-1
63
0-j
un
e-1
64
-ju
l-1
65
-au
g-1
62
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