Resistance Characteristics of different Integrase...
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Resistance Characteristics of different Integrase Inhibitors Charles Boucher
Transcript of Resistance Characteristics of different Integrase...
Resistance Characteristics of different Integrase Inhibitors
Charles Boucher
Disclosure
Companies/funders
Research grants
Speakers fee
Other
Merck, Gilead, Roche
Viiv, Abvie
Co-owner/scientific director Virology Education
entry
reversetranscription integration
nuclearimport
transcriptionvirusproduction
The HIV life cycle
Hazuda 2012
Integration
• Insertion of the viral DNA into host chromosomal DNA, essential step in cycle
• Point of no return: cell becomes a permanent carrier
• Proviral persistence is the barrier to cure
(eg HCV)
Integration (two reactions)
• 3’ processing: 2/3 nucleotides are removed from the 3’ ends from the DNA strand at both sides of the proviral DNA
• Strand transfer reaction: the processed 3’ ends of viral DNA are covalently bound to the host chromosomal DNA
The mechanics of integration
Craigie and Bushman 2012
strand transfer inhibition
Hazuda 2012
unintegrated linear DNA
Dead end, two LTR circles
Integrase strand-transferinhibitors (INSTIs)
Métifiot, Marchand and Pommier 2013
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Integrase resistance in Benchmarks (raltegravir) studies
41 failures: 32 integrase mutations following “three patterns”
N155H (E92Q,V151I,T97A,G163R,L74M) Q148K/R/H (G140S,E138K)Y143R (L74A,E92Q,T97A,I203M,S230R)
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Resistance maps to the catalytic core
D64 D116 E152 SH3H H C C
1 50 212 288
Zinc Finger Catalytic Core DNA Binding
N155HQ148K/R
Key Raltegravir Mutations
Stanford HIV Data Base
Cross resistance elvitegravir and raltegravir
Fold change (IC50))
elvitegravir raltegravir
Q148K/R 67/118 34/30
N155H 38 23
N155H+E92Q 166 135
Q148H+G140S >1000 >1000
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- The selection of specific mutations is a composite of selection pressure and replication capacity
- Clinical resistance to raltegravir and elvitegravir requires one (to two) mutations (LOW GENETIC BARRIER)
- The resistant viruses selected by one will be resistant to the other inhibitor (cross resistance)
Raltegravir and elvitegravir (First generation)
IN VITRO, MOST RAL- AND EVG-RESISTANT SINGLE MUTANTS ARE SUSCEPTIBLE TO DTG
Mean FC
Viruses DTG RAL EVG
WT1,2 1 1 1
T66A1,2 0.26 0.61 4.1
T66I1,2 0.26 0.51 8.0
T66K1,2 2.3 9.6 84
E92I1,2 1.5 2.1 8.0
E92Q1,2 1.6 3.5 19
E92V1,2 1.3 1.4 8.3
G118S1,2 1.1 1.2 4.9
F121Y1,2 0.81 6.1 36
T124A1,2 0.95 0.82 1.2
E138K1,2 0.97 1 0.93
G140S1,2 0.86 1.1 2.7
Y143C1,2 0.95 3.2 1.5
Y143H1,2 0.89 1.8 1.5
Mean FC
Viruses DTG RAL EVG
Y143R1,2 1.4 16 1.8
P145S1,2 0.49 0.87 >350
Q146R1,2 1.6 1.2 2.8
Q148H1,2 0.97 13 7.3
Q148K1,2 1.1 83 >1700
Q148R1,2 1.2 47 240
I151L1,2 3.6 8.4 29
S153F1,2 1.6 1.3 2.8
S153Y1,2 2.5 1.3 2.3
M154I ,2 0.93 0.82 1.1
N155H1,2 1.2 11 25
N155S1,2 1.4 6.2 68
N155T1,2 1.9 5.2 39
G193E2 1.3 1.3 1.3
3 ≤ FC < 5 5 ≤ FC < 10 10 ≤ FC
RAL and EVG-related single mutation SDMs (site directed mutants)
1. Adapted from Kobayashi M, et al. Antimicrob Agents Chemother 2011;55:813–212. Adapted from Seki T, et al. CROI 2010. Abstract 555
COMBINATIONS WHICH INCLUDE 148 MUTANTS CAN BE RESISTANT TO DTG
3 ≤ FC < 5 5 ≤ FC < 10 10 ≤ FC
Adapted from Kobayashi M, et al. Antimicrob Agents Chemother 2011;55:813–21
Mean FC
Viruses DTG RAL EVG
WT 1 1 1
T66I/L74M 0.35 2.0 14
T66I/E92Q 1.2 18 190
T66K/L74M 3.5 40 120
L74M/N155H 0.91 28 42
E92Q/N155H 2.5 >130 320
T97A/N155H 1.1 26 37
L101I/S153F 2.0 1.3 2.6
F121Y/T125K 0.98 11 34
E138A/Q148R 2.6 110 260
E138K/Q148H 0.89 17 6.7
E138K/Q148K 19 330 371
E138K/Q148R 4.0 110 460
Mean FC
Viruses DTG RAL EVG
G140C/Q148R 4.9 200 485
G140S/Q148H 2.6 >130 >890
G140S/Q148K 1.5 3.7 94
G140S/Q148R 8.4 200 267
Y143H/N155H 1.7 38 16
Q148R/N155H 10 >140 390
N155H/G163K 1.4 23 35
N155H/G163R 1.1 17 35
N155H/D232N 1.4 20 36
V72I/F121Y/T125K 1.3 13 58
L101I/T124A/S153F 1.9 1.4 2.0
E138A/S147G/Q148R 1.9 27 130
V72I/F121Y/T125K/I151V 1.2 7.0 37
RAL and EVG-related single mutation SDMs (site directed mutants)
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
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
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Week
Pro
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rtio
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HIV
-1R
NA
<5
0c
op
ies
/mL
(%)
B/F/TAF
DTG/ABC/3TC
DTG+F/TAF
4 8 12 24 36 48
Rapid Suppression of HIV-1 RNA to < 50 copies/mL through Week 48 (Missing =
Excluded Approach)
White K, CROI, 2018, #532 19AE=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
Resistance Analysis Population through Week 48 and Resistance Summary
White K, CROI, 2018, #532 20
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 Drugs
0 0 0
Number of Participants, n (%)
PI = protease inhibitor; PR = protease; R = resistance
Genetic barrier to resistance of DTG
• High genetic barrier to resistance observed in patients
– Clinical studies using DTG containing cART and dual therapy (3TC/rilpivirine)
– Clinical practice
– Only one case report of INSTI naive patient failing on cART containing DTG
• High genetic barrier to resistance observed in vitro
– Classical single INSTI-Resistance Associated Mutations (RAM) confer only small changes changes in IC50
• We performed a randomised clinical study to evaluate the efficacy of DTG monotherapyas maintenance in patients with well controlled HIV infection during previous cARTcomparing efficacy of DTG monotherapy to continuation of cART.
DOMONO study (NTC02401828) –randomized clinical trial on DTG
maintenance monotherapy
• Inclusion criteria:
– CD4 nadir > 200 cells/mm3, and HIV1-RNA zenith < 100.000 copy/mL
– Self reported therapy adherence > 95%
– HIV1-RNA < 50 copy/mL, > 6 months
• Exclusion criteria:
– Documented virological failure on any cART
– Documented RAMs
• Virological failure (VF):
– Defined as 2 consecutive plasma HIV1-RNA > 200 copy/mL
Wijting et al., CROI, 2017. Wijting et al. In press
Results of DOMONO study
• At week 48:
– DTG maintenance monotherapy: viral suppression 87/95 (92%)
– Concurrent control group: viral suppression 149/152 (98%)
– DTG monotherapy inferior
– Premature stop of study
Wijting et al., CROI, 2017. Wijting et al. The lancet HIV 2017
Age (median, Q1 - Q3) 47 years (41 – 53)
HIV1-RNA zenith (median, Q1 - Q3) 56.300 copy/mL (19.300 – 99.635)
CD4 nadir (median, Q1 - Q3) 230 cells/mm3 (85 – 310)
HIV-1 subtype B (12/13), CRF02_AG (1/13)
INST-naive 9/10 (69%)
Time between diagnosis and start cART(median, Q1 - Q3)
47 months (4 – 85)
Time on cART (median, Q1 - Q3) 72 months (39 – 132)
Time suppressed on cART (plasma HIV1 RNA < 50 cop/mL (median, Q1 - Q3)
59 months (21 – 101)
Baseline characteristics of all patients with viral Failure
1 Kobayashi et al., Antimicrob Agents Chemother, 2011. 2 Wainberg et al., J Virus Erad, 2015. 3 Underwood et al., J Acquir Immune Defic Syndr , 2012. 4 Pham et al., JID in tress
patient 4 6 10 1 2 3 9 8 5 7
HIV-RNA zenith (c/mL) 18.500 7.420 66.500 17.500 99.270 56.300 24.900 67.000 34.600 20.100
DTG plasma level at VF (mg/L)
1.29 (+14h) 2.00 (+19h) 5.31 (+19h) 2.59 (+16h) 2.96 (+22h) 1.00 (+24h) 0.86 (+16) 1.44 (+24h) 0.70 (+13h) 2.15 (+9h)
adherence >95% >95% >95% >95% >95% >95% >95% >95% >95% >95%
INSTI-RAM at VF No - No No S230R - E92Q + N155H No R263K N155H
Fold change IC50 DTG(1-4)
- - - - 4 - 2.5 - 2 - 4 1 - 2
Genetic barrier to DTG resistance
• N155H, E92Q + N155H, R263K, S230R → 1-4 fold change in IC50 of DTG in vitro
• Single INSTI-RAMs conferring low level resistance in vitro are sufficient to cause
virological failure in 50 mg once daily DTG maintenance monotherapy
• Genetic barrier to DTG resistance too low to justify maintenance monotherapy
• Cross resistance with other INSTIs
EXTRA – paper Malet
EXTRA – paper Malet
Large variation in time to virological failure
3' polypurine tract (PPT) LTR
HXB2_ref A A A A G A A A A G G G G G G A C T G
9053 Lai* A A A A G A A A A G C A G T - A C T G
Pat 1 A A A A G A A A A G G G G G G A C T G
Pat 3 A A A A G A A A A G G G G G G A C T G
Pat 4 A A A A G A A A A G G G G G G A C T G
Pat 6 A A A A G A A A A G G G G G G A C T G
Pat 8 A A A A G A A A A G G G G G G A C T G
Pat 10 A A A A G A A A A G G G A G C A C T G
First patient failing on INSTI with emergence of changes in 3’-PPT
The mechanics of integration
Craigie and Bushman 2012
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1000000
0 12 24 36 48 60 72 84 96
SAILING: TREATMENT EXPERIENCED
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
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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
Conclusions
• Genetic barrier to resistance of DTG with 50 mg dose is too low to justify
maintenance monotherapy. DTG monotherapy failure caused by viruses with
single INSTI-RAMs that confer crossresistance to INSTIs. To rule out INSTI
resistance sequencing outside integrase may be needed
• Second generation has a higher genetic barrier ( cave drug levels!) Selection of
INSTI drug resistance in naive individuals using triple therapy is extremely rare
• Dual therapy (DTG or carbotegravir) with 3TC or rilpivirine trials are underway.
• In patients failing first generation INSTI resistance testing can evaluate the
possibility of switching to second generation.
• Baseline resistance testing is not needed for care, surveillance is warranted
• All patients included
• Viroscience, Erasmus MC
• Charles Boucher
• Rob Gruters
• Cynthia Lungu
• David van der Vijver
• Patrick Boers
• Suzan Pas
• Jolanda Voermans
• Internal Medicine, Erasmus MC
• Bart Rijnders
• Ingeborg Wijting
• Ineke van der Ende
Acknowledgements
▪ McGill University AIDS Centre, Canada
▪ Mark Wainberg
▪ Thibault Mesplede
▪ Hanh Pham
▪ Virology, UMC Utrecht
▪ Rob Schuurman
