Epistatic interactions in NS5A from HCV genotypes 1a and 1b Olga - - PowerPoint PPT Presentation
Epistatic interactions in NS5A from HCV genotypes 1a and 1b Olga Kalinina Max Planck Institute for Informatics with: Eva Heger, Elena Knops, Saleta Sierra-Aragn, Rolf Kaiser Institute of Virology, University of Cologne AREVIR meeting
Max Planck Institute for Informatics with: Eva Heger, Elena Knops, Saleta Sierra-Aragón, Rolf Kaiser Institute of Virology, University of Cologne AREVIR meeting 06.05.2017
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2
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AUG C E1
*
E2 NS2 Protease Helicase NS4B NS5A NS5B 5NTR IRES
a b
Assembly module Replication module Structural proteins Non-structural proteins 3NTR p7 NS3 NS4A Stop Core E1 p7 NS2 NS3 NS4B NS5A NS5B Protease Helicase D1
D2D3
E2 Cofactor NS4A RNA-dependent RNA polymerase Phosphoprotein RNA replication Assembly Membrane reorganization Capsid Envelope glycoproteins Ion channel Protease assembly
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Bartenschlager et al., Nature Rev Microbiol, 2013
318 320 321
a b c
CYPA 90° CYPA–CsA D2 D1 AH D3 P58 P58 Y93 M28 P58 L31 Y93 M28 P58 M28 Y93 L31 L31 RNA- binding groove Daclatasvir Daclatasvir Y93 90° L31 M28
binding site
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Daclatasvir Elbasvir Ledipasvir Ombitasvir Velpatasvir
H O N H N N N N H N O H N O O N O O
H O N H N N N H O N N H N O H N O O N O O
H O N H N N F F N N H H H N O H N O O N O O
H O N H O N H H N N O H N O H N O O N O O H H N O H N O O N N O N N H H N O H N O O O
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Nettles et al., J Med Chem, 2014
(substitutions specific to genotype)
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models from Nettles et al., J Med Chem, 2014
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0.0 1.0 2.0 3.0 4.0
bits
AD
5
10
15
20
R25
30
H35
L
40
R
45
A
50
55
P
60
A
65
70
75
I TA
RT
80
K
T
85
GN
90
95
100
105
K
TFA
110
115
120
QV
125
130
I135
A
TDD
140
140
I
145
150
155
I
160
165
170
E
D175
180 N
Y
A
D
EY
L185
190
1a 1a 1a
0.0 1.0 2.0 3.0 4.0
bits
A5
I
10
15
S
TDF
20
25
T30
KQ
L
I
35
I
F
LSC
40
45
I
50
EH
Q
55
I
60
E
S
A
T
65
70
1b
75
T AI
K
A
80
M
85
R Y C90
V95
100
105
S110
115
120
I
125
130
I
I
V
135
AL
I
VK
140
140
145
150
155
160
P
165
S170
E
D
V
S
175
L
180
H
V
P
LV
185
190
1b 1b
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0.0 1.0 2.0 3.0 4.0
bits
AD
5
10
15
20
R25
30
H35
L
40
R
45
A
50
55
P
60
A
65
70
75
I TA
RT
80
K
T
85
GN
90
95
100
105
K
TFA
110
115
120
QV
125
130
I135
A
TDD
140
140
I
145
150
155
I
160
165
170
E
D175
180 N
Y
A
D
EY
L185
190
1a 1a 1a
0.0 1.0 2.0 3.0 4.0
bits
A5
I
10
15
S
TDF
20
25
T30
KQ
L
I
35
I
F
LSC
40
45
I
50
EH
Q
55
I
60
E
S
A
T
65
70
1b
75
T AI
K
A
80
M
85
R Y C90
V95
100
105
S110
115
120
I
125
130
I
I
V
135
AL
I
VK
140
140
145
150
155
160
P
165
S170
E
D
V
S
175
L
180
H
V
P
LV
185
190
1b 1b
elbasvir, ledipasvir, ombitasvir, daclatasvir
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10
11
0.0 1.0 2.0 3.0 4.0
bits
A5
I
10
15
S
TDF
20
25
T30
KQ
L
I
35
I
F
LSC
40
45
I
50
EH
Q
55
I
60
E
S
A
T
65
70
1b
75
T AI
K
A
80
M
85
R Y C90
V95
100
105
S110
115
120
I
125
130
I
I
V
135
AL
I
VK
140
140
145
150
155
160
P
165
S170
E
D
V
S
175
L
180
H
V
P
LV
185
190
1b 1b 703 sequences 45 sequences
0.0 1.0 2.0 3.0 4.0
bits
5
I
10
15
A
S
TDF
20
RR
K
Q
25
M
30
L
I
V
35
L
40
45
I
50
H
Q
55
60
K
A
T
65
70
R30Q R30Q R30Q
70
75 I A
KT
80
M
85
Y QR
90
95
100
105
110
115
120
I
125
130
I
V
135
V S AL
I
VK
140
140
145
150
VD
155
160
A
165
KPLL
170
E
D
V
T
175
L
Q
I
180
H
P V
L
L185
190
11
0.0 1.0 2.0 3.0 4.0
bits
A5
I
10
15
S
TDF
20
25
T30
KQ
L
I
35
I
F
LSC
40
45
I
50
EH
Q
55
I
60
E
S
A
T
65
70
1b
75
T AI
K
A
80
M
85
R Y C90
V95
100
105
S110
115
120
I
125
130
I
I
V
135
AL
I
VK
140
140
145
150
155
160
P
165
S170
E
D
V
S
175
L
180
H
V
P
LV
185
190
1b 1b 703 sequences 45 sequences
0.0 1.0 2.0 3.0 4.0
bits
5
I
10
15
A
S
TDF
20
RR
K
Q
25
M
30
L
I
V
35
L
40
45
I
50
H
Q
55
60
K
A
T
65
70
R30Q R30Q R30Q
70
75 I A
KT
80
M
85
Y QR
90
95
100
105
110
115
120
I
125
130
I
V
135
V S AL
I
VK
140
140
145
150
VD
155
160
A
165
KPLL
170
E
D
V
T
175
L
Q
I
180
H
P V
L
L185
190
11
0.0 1.0 2.0 3.0 4.0
bits
A5
I
10
15
S
TDF
20
25
T30
KQ
L
I
35
I
F
LSC
40
45
I
50
EH
Q
55
I
60
E
S
A
T
65
70
1b
75
T AI
K
A
80
M
85
R Y C90
V95
100
105
S110
115
120
I
125
130
I
I
V
135
AL
I
VK
140
140
145
150
155
160
P
165
S170
E
D
V
S
175
L
180
H
V
P
LV
185
190
1b 1b 703 sequences 45 sequences
0.0 1.0 2.0 3.0 4.0
bits
5
I
10
15
A
S
TDF
20
RR
K
Q
25
M
30
L
I
V
35
L
40
45
I
50
H
Q
55
60
K
A
T
65
70
R30Q R30Q R30Q
70
75 I A
KT
80
M
85
Y QR
90
95
100
105
110
115
120
I
125
130
I
V
135
V S AL
I
VK
140
140
145
150
VD
155
160
A
165
KPLL
170
E
D
V
T
175
L
Q
I
180
H
P V
L
L185
190
(‘alternative’) coincides with 1a consensus, are these mutations significantly overrepresented?
coincides with 1a consensus — ‘diagnostic’ positions
and ‘1b typical’ in diagnostic positions
alternative residues in both positions with expected frequency (= product of frequencies in individual positions)
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1b R30QL
R
K
1b R30Q
R
K
M
13 0.125 0.25 0.375 0.5 V8I T17S Q24K L28M V34I K44R Q54H K78R T83M V121I T122R V153L N180H
1b typical 1b atypical Q
p = 2.28e-07 *** p = 0.003978 *** p = 0.04645 ** p = 0.0396 ** p = 0.06442 * p = 0.05955 *
***: p < 0.01; **: p < 0.05; *: p < 0.1
14 V8I T17S Q24K L28M V34I K44R Q54H K78R T83M V121I T122R V153L N180H V8I n/a
0.06 0.04
0.02
T17S n/a
0.00 0.00
0.00 0.01
Q24K *** n/a 0.08 0.01
0.03
L28M * *** n/a 0.01
0.04
V34I n/a
0.01
K44R n/a 0.05 0.01
0.00 0.00 Q54H *** n/a 0.04
K78R n/a
0.02
0.02 T83M * *** n/a 0.01
0.01
V121I n/a
0.01
T122R n/a 0.01 0.03 V153L * n/a 0.04 N180H * n/a
freq(alt1 & alt2) − freq(alt1) × freq(alt2) ***: p < 0.05 *: p < 0.1
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model 1
models from Nettles et al., J Med Chem, 2014 daclatasvir R30 L28 V8 T83 T122 N180 Q24
model 2
daclatasvir R30 L28 V8 T83 T122 N180 Q24
maybe not so resistant after all?
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0.125 0.25 0.375 0.5 V8I T17S Q24K L28M V34I K44R Q54H K78R T83M V121I T122R V153L N180H
1b typical 1b atypical Q
daclatasvir R30 L28 V8 T83 T122 N180 Q24
Position all 1a 1a with Q30R p-value *** K24Q 335 K, 4Q 5 K, 3 Q 0.0002717 *** M28L 321 M, 4 L 5 M, 2 L 0.005504 ** R122T 352 R, 3 T 8 R, 2 T 0.00648 ** H180N 321 H, 20 N 6 H, 3 N 0.01612 I8V 313 I, 13 V 7 I, 2 V 0.05621 M83T 309 M, 34 T 8 M, 1 T
with Q30R RAV and therapy success
Q24K and L28M that are overrepresented in 1b strains with R30Q present
pocket, but do not contact inhibitor in the models
1a background renders NS5A susceptible?
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1 K-0539 SGSWLRDVWX WIXTVXTDXK SWLQSKLLXQ XPGVXFFSCQ RGYXGVWXXD GIMXTTCPCG AQITGHVKNG K-2264n SGSWLRDVWD WICTVLTDFK TWLQSKLLPQ LPGVPFFSCQ RGYKGVWRGD GIMHTTCPCG ARITGHVKNG K-0393 SGSWLRDVWD WICTVLTDFK TWLQSKLLPQ LPGVPFLSCQ RXYKGVWRGD GVMQTXCPCG AQITGHVKNG K-1389 SGSWLRDVWD WICTVLTDFK XWLQSKLLPQ LPGVPFLSCQ RGYKGVWXGD GIMHTTCPCG AQITGHVKNG K-1595 SGSWLRDVWD WICTVLADFK TWLQSKLLPQ LPGVPFFSCQ RGYKGVWRGD GIMQTTCPCG AQITGHVKNG K-1175 SGSWLRDVWD WICTVLTDFK TWLQSKLLPQ XPGVPFFXCQ RGYKGVWRGD GIMQTTCPCG XQXTGHVKNG K-1253 SGSWLRDVWD WICTVLTDFK TWLQSKLLPQ IPGVPFFSCQ RGYRGVWRGD GIMQTTCPCG AQITGHVKNG K-2189 SGSWLRDVWD WICTVLTDFK TWLQSKLLPQ MPGIPFLSCQ RGYKGVWRGD GIMQTTCPCG AQISGHVKNG 11643_260214 ---------- -ICTVLTDFK XWLQSKLLPQ LPGXPFXSCQ RGYKGVWRGD GIMNTTCTCG AXXTGHVKNG K-2473 AGSWLRDVWD WICTVLTDFK TWLQSKLLPQ FPGVPFLSCQ RGYKGIWRGD GIMHTTCPCG AQITGHVKNG K-0882 SGSWLRDIWD WICEVLSDFK TWLKAKLMPQ LPGIPFVSCQ RGYRGVWQGD GIMHTRCHCG AEITGHVKNG K-0849 SGSWLRDXWD WICTVLTDFK TWLQSKLLPQ LPGVPFLSCQ RGYRGVWRGD GIMQTTCPCG AQIAGHVKNG K-1861 SGSWLRDVWE WICTVLSDFK TWLRSKLLPQ MPGVPFISCQ RGYKGVWRGD GIMQTTCPCG AQITGHVKNG 71 K-0539 SMXIVGPXTC SXTWHGTFPI NAYTTGPXTP TXAPNYSRAL WRXAAXEYVE VTRVGDFXYV TGMTTDNVKC K-2264n SMRIFGPKTC SNTWHGTFPI NAYTTGPCTP SPAPNYTRAL WRVAAEEYVE VTRVGDFHYV TGMTTDNVKC K-0393 SMRIVGPRTC SNTWHGTFPI NAYTTXPCTP SPAPNYSRAL WRVAAEEYVE ITRVGDFHYV TGMTTDNVKC K-1389 SMRIVGXKTC SNTWHGTFPI NAHTTGPCTX SPAPNYSRAL WRVAAEEYVE VTQVGDFHYV TGMTTDNIKC K-1595 SMRIVGPKTC SNTWHGTFPI NAXTTGPCTP SPAPNYSRAL WRVAAEEYVE ITRVGDFHYV TGMTTDNVKC K-1175 SMXIVGPXTC SNTWHXTFPI NAYTTGXXTP SPAPNYSRAL WRVAAEEYVE VTRVGDFHYV TGITNDNIKC K-1253 SMRIVGPRTC SNTWHGTFPI NAHTTGPCTP SPAPNYSRAL WRVAAEEYVE VTRVGDFHYV TGMTTDNVKC K-2189 SMRIVGPKTC SNTWHGTFPI NAYTTGPCSP SPAPNYSRAL WRVAAEEYVE VTRVGDFHYV TGMTADNIKC 11643_260214 SMRIVGPXTC SNTWXGTFPI NAYTTGPCTP SPAXXYXRAL WRVSAEEYVE VTRVGDFHXV TGMXTDNXKC K-2473 SMRIVGPRTC SNTWHGTFPI NAYTTGPCTP SPAPNYSRAL WRVAAEEYVE VTRVGDFHYV TGMTTDNVKC K-0882 TMRIVGPKTC RNMWSGTFPI NAYTTGPCSP LPAPNYTFAL WRVSAEEYVE IRRVGDFHYV TGMTTDNLKC K-0849 SMRIVGPRTC SNTWHGTFPI NXYTTGSCSP SPAPNYSKAL WRVAAEEYVE VTRVGDFHYV TGVTTDNVKC K-1861 SMRIVGPKTC SNTWHGTFPI NAYTTGPCVP SPAPNYSRAL WRVAAEEYVE VTRVGDFHYV TGMTTDNVKC 141 K-0539 PCQVPAPEFF TEVDGVRXHX YAPXXKPLLR XEXTFXVGLN QYVVGSQLPC EP K-2264n PCQVPAPEFF TEVDGVRLHR YAPACKPLLR EEVTFQVGLN QYLVGSQLPC EP K-0393 PCQVPAPEFF TEVDGVRLHR YAPACRPLLR DEVTFQVGLN QYVVGSQLPC EP K-1389 PCQVPAPEFF TEVDGVRLXR YAPACKPLLR DEVTFQVGLN QYLVGSQLPC EP K-1595 PCQVPAPEFF TELDGVRLHR YAPACRPLLR DEVTFQVGLN QYPVGSQLPC EP K-1175 XCQVPXPEFF TEVDGVRLHR YAPACKPLLR EEVTFQVGLN QYLVGSQLPC EP K-1253 PCQVPAPEFF TEVDGVRLHR YAPACKPLLR EEVCFQVGLN QYPVGSQLPC EP K-2189 PCQVPTPEFF TEVDGVRLHR YAPACKPLLR DEVTFQVGLN QYLVGSQLPC EP 11643_260214 PCQVPAPEFF XEVDXVRLHR YAPACKPXLR EEVTFQVGXH QYLVGSQXPC EP K-2473 PCQVPAPEFF TEVDGVRLHR YAPACKPLLR DEVTFQVGLN QYVVGSQLPC EP K-0882 XCQVPSPEFF TXLDGVRLHR FAPPCKPLLR DEVSFRVGLH DYPVGSQLXC EP K-0849 PCQVPAPEXF TEVDGVRLHR YAPACXPLXR EEVSFQVGLN QYLXGSQLPC EP K-1861 PCQVPAPEFF TEVDGVRLHR YAPACRPLLR EEVTFQVGLN QYLVGSQLPC EP
sequence name drugs therapy
K-0539 ??? success K-2264 ledipasvir +sofosbuvirosbuvir +ribavirin failure K-0393 ledipasvir +sofosbuvirosbuvir success K-1389 ??? success K-1595 ??? success K-1175 ??? success K-1253 ??? success K-2189 ??? success 11643_260214 _NS5A ??? success K-2473 ??? success K-0882 paritaprevir +ombitasvir +dasabuvir success K-0849 ??? success K-1861 ??? failure