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Ординатура / Хирургия / Библиотека им академика М.И. Перельмана / Книга_5402_Библиотеки_им_академика_М_И_Перельмана

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(a) Regular (0 frame)
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translation
(b) –1 Frameshift translation
AAAAA
U
UUU UUU UGGG G
A A A A
90 − 95%
10.1 Introduction 255
3′
Gag
HIV-1
Structural
proteins
AAAAAA
A A A AUUU UUU UGGG G
3′
GagPol
HIV-1
structural proteins
5 − 10%
and enzymes
Figure 10.1 During translation of an mRNA containing a frameshift-stimulating element (FSE), the ribosome translates the transcript, reaches the FSE, overcomes its hindrance to translation and unwinds it, and terminates translation when it reaches the stop codon within the FSE (a, top). However, some of the time the ribosome is unable to easily overcome the hindrance to translation presented by the FSE, resulting in a shifting of the ribosome into the −1 open reading frame (b, bottom). Source: Anokhina and Miller [12]/with permission of Springer Nature. For HIV, a −1 frameshifting event is required for the production of viral enzymes (Gag and GagPol) essential for viral replication.
GTP
3
H
3ʹ
5ʹ
E P A EPA
FSS-mediated inhibition
of A-site tRNA binding
5ʹ
FSS-mediated inhibition
of tRNA/mRNA translocation
GTP
EF-Tu
EF-G
3ʹ
Cy3-labeled L9
Cy5-labeled S6
(a) (b)
Figure 10.2 Mechanisms of frameshifting, as described by Bao et al. [20] (a, left, Mechanism 1) Frameshift-stimulating stem loops can dock in the A-site of the ribosome, preventing the incoming tRNA from docking, resulting in the slippage of the tRNA in the P-site. (b, right, Mechanism 2) Alternatively, frameshift-stimulating elements can interact with the exterior of the ribosome, including the mRNA entry channel, preventing translocation of the ribosome and inducing frameshifting of the tRNAs in the P- and A-sites. In both cases, the ribosome must unfold the hindering RNA structure to continue translation. Source: Bao et al. [20]/Springer Nature/CC BY 4.0.
256 10 Approaches to the Identification of Molecules Altering Programmed Ribosomal Frameshifting
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Instead, it has been posited that a frameshift signal inhibits tRNA binding by interacting with the A-site. This was demonstrated using a construct that expanded the length of a hairpin frameshift-stimulating element (FSE) by six base pairs; this failed to inhibit tRNA binding to the A-site, pointing to the rst mechanism [20].
The human immunodeciency virus type 1 (HIV-1) is one of the more well-known examples of retroviruses employing frameshifting as a mechanism to produce and regulate the relative quantities of viral enzymes and structural proteins. The gag-pol HIV-1 mRNA codes for translation of two polyproteins: Gag (which is proteolytically processed to yield HIV matrix, capsid, and nucleocapsid) and Pol, which only forms as a Gag-Pol fusion polyprotein. Pol is proteolytically processed to yield protease, reverse transcriptase, and integrase enzymes. Gag-Pol forms when -1 PRF causes the ribosome to move in to a new reading frame, skipping the stop codon on the gag gene during translation [21, 23]. The frameshift eciency, resulting in the forma­tion of the Gag-Pol polyprotein, is approximately 5–10%, and this stoichiometry has been shown to be necessary for proper packaging of virus particles [21]. For example, mutants that result in Gag-Pol being produced 100% of the time were unable to make viral particles [23]. As discussed above in a general context, a frameshift stimulatory element (FSE, Figure 10.3) regulates the frequency of −1 PRF and hence the ratio of Gag and Gag-Pol. Therefore, we and others hypothesized several years ago that a compound that could bind to the FSE mRNA might modulate frameshifting, and consequently inhibit viral assembly and replication [23, 25].
10.2 Mechanisms of Frameshifting
To begin to understand how to target the FSE RNA, it is useful to understand what is necessary to facilitate a frameshifting event. Frameshifting can only occur when two elements are present: a highly conserved UUUUUUA sequence, known as the slippery sequence (Figure 10.3, boxed in blue), and a downstream frameshift stimu­latory stem–loop (Figure 10.3, upper stem) [23, 24]. The slippery sequence is where the shift of one nucleotide causes a change in reading frame during translation, while the stimulatory stem has been posited to pause the ribosome [24]. Studies elucidating the structure of the HIV-1 frameshift element mRNA determined that the slippery sequence is proceeded by the frameshift stimulatory signal, which is an irregular helix made up of an upper and lower stem [24, 25]. Of note, shortening or removing the stem–loop, along variations of the HIV FSE sequence do not aect tRNA binding to the A-site [20]. It has been posited that the interaction of the FSE stem–loop is not sequence-specic, most likely involving recognition of the RNA’s sugar-phosphate backbone [20].
A common method for investigating frameshifting that can also be employed to test the inuence of compounds is through use of a dual reporter assay. In the assay, the slippery sequence and FSE are sandwiched between two dierent reporters, typically Renilla luciferase (Rluc) and rey luciferase (Fluc) or other reporter genes. Rluc and Fluc yield enzymes acting on substrates to produce lumi­nescence at dierent wavelengths (colors) [26]. In cellular systems (or sometimes
1620
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10.3 Targeting Frameshifting in HIV 257
1660
C
AAA
C G
G
C C
G
UUA
C C
1650
G G U C
2
C
U
G
A
C
G
A
G
A
G
CU
G
A
AA
U
UUUUU
UU
A
G
U
1
G
A
GG
AA A A
GG
CC
A
U
AA
1600
1580
1560
U
A
G
A
A
A
C
A G G
A
3
A
G A A A G
G U
G
U
A
A
A
G U U
5 6
G U C G G G
Upper stem
A G G G C
1670
A G G
G A A
U U
Alternate lower
U U
stem
C U
U
CG
A
G
A
G
C
A
G
A
C C
1690
A
G
A
G
CG C
C G
C C C C CAAAAGAU AAG A A AG G GA AC
A A
A
Anchoring helix
1710
4
SHAPE-directed model
Figure 10.3 The SHAPE-determined model of the HIV gag-pol frameshift sequence RNA. Source: Low et al. [24]/with permission of American Chemical Society.
in a cellular lysate such as rabbit reticulocyte lysate), the downstream reporter is only expressed when frameshifting occurs while the upstream reporter is always expressed, allowing for an assay capable of measuring frameshifting eciency for a given FSE [26].
10.3 Targeting Frameshifting in HIV
Dual-reporter assays were employed extensively in analyzing one of the more prominent classes of compounds that bind the FSE mRNA: aminoglycosides. Guani­dinoneomycin B, an exhaustively guanidine-derivatized analog of neomycin B, is an example of this, and was studied extensively by Butcher and Tor [27]. However, aminoglycosides are generally regarded as binding to RNA targets in a non-selective
258 10 Approaches to the Identification of Molecules Altering Programmed Ribosomal Frameshifting
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manner [28]. The nature of aminoglycosides to bind indiscriminately to RNA has been attributed to their conformational exibility, which allows aminoglycosides to conform to varied RNA targets [28, 29]. Recently, nucleic acid dye tags were used to study the frameshifting event for HIV-1 [30]. Peptide-based and peptidomimetic compounds have been used with considerable success for targeting the HIV-1 FSE. These compounds were studied over a period of several years by the Miller group. Initial hit compounds were identied using a resin-bound variant of a library generation method called dynamic combinatorial chemistry. This uses reversible reactions to create dynamic combinatorial libraries, which can undergo evolution based on the selection pressure of library members binding preferentially to a nucleic acid (or other) target [31]. While many exchange chemistries are possible, here the reversible exchange was facilitated by the presence of cysteine residues present in each library member, allowing for the formation of resin-bound disuldes and subsequent reversible disulde exchange between resin-bound materials and solution-phase compounds [31]. In the screen targeting the HIV-1 FSE RNA, an 11,325 member Resin Bound Dynamic Combinatorial Library (RBDCL) was prepared. The equilibrium of the reversible exchange between the solid-phase and solution-phase monomers was altered when uorescently tagged RNA was intro­duced, allowing for the identication of an initial hit compound (Figure 10.4, 1)2via
C A
AA C-G C-G C-G U-A U-A C-G C-G G-G G-C
U-A C-G
G
A
U-A A-U G-U A-U A-U G-U
5ʹ-UUUUUUAG U-3ʹ
Slippery
sequence
G-U
stem-loop
Purine bulge
G
Upper
H2N
NH
3
O
HN
O
EtNN
O
O
NH
N
S
S
HN
O
O
N
Et
NH
O
HN
O
NH
2
3
1
Figure 10.4 The initial lead compound (right) determined via the RBDCL [32] for the HIV gag-pol FSE RNA (left) [33]. Source: (a) Palde et al. [33]/with permission of American Chemical Society; (b) McNaughton et al. [32]/with permission of American Chemical Society.
2 Reprinted (adapted) with permission from Palde, P.B., Ofori, L.O., Gareiss, P.C. et al. (2010). Strategies for recognition of stem-loop RNA structures by synthetic ligands: application to the HIV-1 frameshift stimulatory sequence. J. Med. Chem. 53 (16): 6018–6027. https://doi.org/10.1021/ jm100231t. Copyright 2010 American Chemical Society.
10.3 Targeting Frameshifting in HIV 259
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uorescence microscopy, followed by mass spectrometry [32]. The library members incorporated heterocyclic moieties to facilitate binding to the HIV-1 FSE RNA; the primary compound identied from the screen was symmetrical, with quinoline groups as the heterocycle [32, 33]. Post identication validation involved testing for anity and specicity via surface plasmon resonance (SPR). This yielded a K of 4.1± 2.4 μM and showed that the compound displayed no apparent anity to related RNA sequences [32].
Based on this initial hit, several structural hypotheses were tested to yield compounds with higher anity and selectivity for the FSE mRNA. One set of initial experiments focused on structure activity relationships of the 2-ethylquinoline 3-carboxamide moiety. Modifying the 2-ethyl to methyl or proton yielded insigni­cant
decreases in anity of the compound for the FSE RNA [33]. However, reducing the π-surface by replacing 2-ethylquinoline with 2-methyl-3-carboxypyridine resulted in ablation of binding to the FSE RNA [33]. Another point of modication on the lead compound was to test a suitable bioisostere for the disulde bridge of the compound, due to susceptibility of disuldes to reduction or exchange in a cellular environment [16, 33]. While disuldes have served a structural role in bioactive peptides, thioesters and carbon linkers have been demonstrated to enhance biostability without aecting function of the compound [33]. To that end, the Miller lab synthesized and tested the activity of olen and hydrocarbon analogs of the lead compound (Figure 10.5). It was found that the Z-isomer of the olen displayed greater anity for the FSE RNA over the E-isomer [33]. The Z-isomer olen analog displayed over fourfold increase of anity relative to the hydrocarbon analog; it was reasoned that this was due to the increased exibility and hydrophobicity of the fully saturated analog [33]. Further experi­ments demonstrated that analogs were selective for binding the stem–loop RNA. Interestingly, the monomeric compound, while able to bind to the FSE RNA, had binding ablated in the presence of yeast tRNA, showing that its binding to the FSE RNA was nonspecic [33]. Similar binding behavior was observed with 2-ethylquinoline 3-carboxylic acid, which binds to RNA non-specically, suggesting that the entire peptide and quinoline is necessary for selective binding to the FSE RNA [33].
Increasing the pi-surface area available for binding by replacing the 2-ethyl­quinoline with a benzo[g]quinoline enhanced anity (Figure 10.5, 2–8). These analogs were tested to determine binding kinetics, as the equilibrium dissociation constant K
on its own does not provide the full picture of the binding event. The
D
dissociation rate, kd, is regarded as an important determinant of selectivity for protein binders, and this represented an opportunity to test the idea in the context of RNA [34]. Slower dissociation rates indicate longer residence times and greater target selectivity [35]. With that in mind, binding experiments using SPR were carried out with immobilized biotinylated FSE RNA on the surface. The determined o-rates for compound 1, along with the analogs, were 10−2to 10−3s−1, which is a stark contrast to the fast on- and o-rate of a tested aminoglycoside, Neomycin [33]. With promising results, these analogs were tested in cells via a MTT assay, serving
D
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H2N
H2N
H2N
N
HN
O
N
O
OOHN
HN
O
NH
N
O
NH
O
NH
O
H2N
NH
2
N
HN
O
2
N
O
HN
O
N
HN
HN
O
O
O
N
N
N
O
NH
O
N
NH
NH
O
N
H2N
N
HN
NH
2
O
N
O
N
N
O
O
O
N
N
O
NH
O
N
O
N
NH
2
3
N
N
O
N
O
O
N
N
O
O
NH
NH
O
N
O
N
NH
N
NH
2
54
N
O
N
O
N
HN
HN
O
O
O
N
N
N
O
NH
O
N
NH
N
O
N
NH
H2N
N
HN
2
O
O
6
N
O
HN
O
N
O
N
N
N
O
N
NH
NH
O
O
N
N
NH
2
7
Figure 10.5 The N-methylation and triazole analogs of the olefin FSE RNA-binding compound. Source: Hilimire et al. [16]/with permission of American Chemical Society.
H2N
N
N
O
N
N
HN
O
O
O
N
N
O
O
NH
N
O
N
O
N
N
N
NH
2
8
10.3 Targeting Frameshifting in HIV 261
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as a reporter for mitochondrial activity, and found no statistically signicant cell toxicity with cells treated with compounds up to 1 mM [33].
Two further modications introduced were N-methylation and 1,4-triazole as an alternative disulde bioisotere to the olen. N-methylation was used to further enhance binding selectivity of the olen analog (Figure 10.5, 3), as this modication often improves anity, selectivity, and activity of peptides [36, 37]. Triazole was chosen as a bioisotere (Figure 10.5, 4–8) due to the robust metal-catalyzed Huisgen cycloaddition chemistry that was readily available, and that despite the precedent for triazole to be used in other targets, including RNA, they have not been used as a bioisostere for disuldes [16]. The structural similarities between disuldes, olens, and triazoles were clear, based on density functional theory (DFT) calculations, though the disulde torsional bond rotation is distinct from that of olens and triazoles [16]. What was found from these experiments is that inclusion of a triazole in the structure had no eect on anity, while N-methylation had a modest eect [16]. It was observed that N -methyl analog 3 had a dissociation constant (KD) for the FSE RNA of 13.0 ± 5.0 nM, a ve-fold increase in anity over the olen-containing compound [16]. Cell permeability and toxicity experiments revealed that compound 6 was non-toxic up to 110 μM, and compound 8 was the most cell permeable as determined via ow cytometry [16]. These N-methyl analogs were also studied for frameshift modulating and anti-HIV activity using pseudotyped HIV, and were found to enhance frameshifting at levels consistent with their relative potencies, and likewise to interfere with the infectivity of pseudotyped HIV. Finally, com­pounds were found to be active against both laboratory HIV-1 strains (HIV
IIIB
) and
a multi-drug-resistant patient isolate of HIV-1 [16, 36].
Success with replacing portions of the peptide with non-peptidic bioisosteres led to the question: could one incorporate other bioisosteric peptide mimics to further evolve these HIV-1 FSE binders to something entirely non-peptidic? To address that question, we hypothesized that the 2,5-diketopiperazine (DKP) could be integrated into FSE-binding molecules, and perhaps serve more broadly as desirable scaold for RNA-binding compounds. DKP is a considered a “privileged structure,” dened as a substructure exhibiting good drug-like properties and often molecules able to specically bind a broad range of biological targets [39]. DKPs are known to oer bioavailability and biostability advantages relative to simple peptides, due to improved stability, protease resistance, and conformational rigidity [40, 41]. The DKP has at least four points of functionality, making it a particularly diversiable scaold that can cover a great deal of chemical space. However, prior to our work, it had yet to be used as part of an RNA-binding compound. Thus a DKP-containing compound (10) was designed, synthesized, and tested alongside a non-DKP-containing compound (9) to determine the eects this new scaold has on binding to the FSE RNA (Figure 10.6). Initial DFT simulations suggested that the DKP and non-DKP analogs adopted similar orientations and distances, having only a 1 Å RMS dierence between the two [38]. Anity and selectivity experiments for both analogs determined that the incorporation of the DKP scaold did not impair binding, and competition with ve-fold excess yeast tRNA did not yield notable changes in binding constants [38]. In contrast, a DKP containing
262 10 Approaches to the Identification of Molecules Altering Programmed Ribosomal Frameshifting
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NH
2
HN
O
NH
N
O
N
H2N
HN
O
O
NH
N
HN
O
N
O
NH
HN
O
O
H2N
O
N
N
N
N
O NH
O
HNH2N
NN
NN
NH
NN
O
OO
NN
H2N
O
O
NH
HN
O
O
N
HN
O
N
HN
N
N
109
Figure 10.6 The DKP (10) and non-DKP (9) containing analogs. They both adopt similar structural and 3D space. Source: Arévalo et al. [38]/with permission of Royal Society of Chemistry.
half-compound displayed no binding to the RNA, demonstrating the necessity of the entire compound [38].
To determine where the DKP-containing compound was binding onto the FSE RNA, a series of surface plasmon resonance (SPR) competition experiments were performed by co-injecting the DKP compound with ve-fold excess of stem and loop swapped FSE RNA mutants, along with FSE RNA (Figure 10.7). The competition experiment revealed that WT HIV-1 FSE RNA had ablated approximately 40% of total binding based on R
value, suggesting that the anity of the DKP-containing
max
compound is impacted by whether the RNA is immobilized or in solution [38]. Of
NH
2
O
A
C
A A
C C C U U C C G
G
HIV-1 FSS
5 µM 10 + 25 µM “stem-swapped” RNA
5 µM 10 + 25 µM “loop mutant”
Figure 10.7 DKP containing compound co-inject competition experiments with WT HIV-1 FSE RNA, “stem-swapped” and “loop” mutant RNAs via SPR. Source: Arévalo et al. [38]/with permission of Royal Society of Chemistry.
G G G A A G G C
C
“stem-swapped” RNA “loop mutant” RNA
Conditions
5 µM 10
5 µM 10 + 25 µM HIV − 1 FSS
C
A A
G
G G A A G G
C
C
A
C
C C U U C C G
G
K
D
5.04×e
6.5×e
6.4×e
6.3×e
R(max)
–7
15.9 0
–7
9.6
–7 –7
15.2
Δ[R(max)], %
13
C C
C C U U C C G
G
40 18
4
C
GAC
G G A A G G
C
C
10.4 Targeting Frameshifting in SARS-CoV-1 and SARS-CoV-2 263
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p = 0.046
7
3×10
7
2×10
7
1×10
Fluorescence intensity
0
0
25
μM
100 150
10 9
P24, pg/mL
800,000
600,000
400,000
200,000
Mock
0
0
Media μM
p = 0.067 p = 0.007
15 25 100
p = 0.022
10 9
8
150
(b)(a)
Figure 10.8 The toxicity and anti-HIV activity assays, from left to right. Both analogs are non-toxic up to 150 μM in MT-2 cells and display modest anti-HIV activity. Source: Arévalo et al. [38]/with permission of Royal Society of Chemistry.
the two mutant RNA that were co-injected, the stem-swapped RNA sequence caused an 18% decrease in R
, while the loop-swapped mutant only competed o 4%
max
(Figure 10.7). This nding suggests that most of the interactions of DKP analog to the FSE RNA is at the loop region [38]. Toxicity assays performed with MT-2 cells treated with both analogs have shown that they both do not show any notable tox­icity up to 150 μM (Figure 10.8). The anti-HIV activity was not impacted with the inclusion of the DKP scaold, though there was a loss of activity compared to the control [38].
10.4 Targeting Frameshifting in SARS-CoV-1 and SARS-CoV-2
Much like HIV-1, frameshifting in coronaviruses such as SARS-Cov-1 and -Cov-2 acts as a regulatory mechanism that controls the ratio of the production of non-structural proteins and enzymes. Specically, genes orf1a and orf1b have an overlap in reading frames in the genome, requiring a frameshifting event during translation to produce the out-of-frame downstream polyprotein pp1ab in addition to the in-frame upstream polyprotein pp1a [42]. These polyproteins are further processed into nonstructural viral proteins such as proteases for viral protein processing (part of pp1a) and replication enzymes, including the RNA-dependent RNA polymerase (in pp1ab) [42].
While disrupting frameshifting of the HIV gag-pol polyprotein can abolish viral reproduction, changing the frameshift eciency of beta coronaviruses such as SARS-CoV-1 and 2 impacts early viral growth kinetics, viral infectivity, and viral replication (Figure 10.9) [13, 14].
As previously stated, frameshifting requires an upstream slippery sequence and downstream frameshift-stimulating structure. In the case of beta coronaviruses, the canonical FSE is a three-stem, three-loop H-type pseudoknot [43, 44] capable of forming upstream and downstream interactions with neighboring RNA [45, 46] and dimerizing with another FSE [47]. This structure is conserved in coronaviruses, and
264 10 Approaches to the Identification of Molecules Altering Programmed Ribosomal Frameshifting
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Slippery site sequence U UUA AAC (WT)
U UUU UUU A AAA AAU
U UUG AAC
% –1 PRF Standard deviation Plaque size
14.4
4.88
2.33
0.15
2.35 4.53+ + +
1.31
0.55
0.03
+ +
+ –
TCID
<1 <1
ND
50
Figure 10.9 Mutating the SARS-CoV-1 slippery sequence reduces frameshift efficiency, which negatively impacts viral plaque size and infectivity. Source: Plant et al. [13]/with permission of American Society for Microbiology. Frameshift efficiency was measured in Vero E6 cells by incorporating either a wild-type or mutant slippery sequence and the FSE into a dual luciferase reporter plasmid. Clones of the SARS-CoV-1 genome were transfected into Vero E6 cells to measure infectivity of transcripts.
Loop 1
Slippery site
Stem 2
Stem 1
Stem 3
Loop 2
Loop 3
pseudoknot
mRNA
Pseudoknot
tRNA
LSU
Stem 3
Head
h16
Stem 2
Stem 1
Shoulder
Beak
Body
Attenuator
loop
Figure 10.10 SARS-CoV-2 orf1ab FSE (green, purple, and blue) and ribosome (large subunit, light blue; small subunit, light green) captured together prior to a frameshifting event. The viral RNA is in the 0 frame, with a stop codon incorporated in the upstream slippery sequence. The presence of a mutant eRF1 prevents the release of the nascent polypeptide. The experiment was performed in rabbit reticulocyte lysate. Cryo-EM resolution ranged from 2.2 to 7. 4 Å. Source: Bhatt et al. [18]/American Association for the Advancement of Science/CC BY 4.0.
changing the structure results in a corresponding change in frameshift eciency [13]. An upstream hairpin stem loop, known as the attenuator stem loop, adds addi­tional regulation to frameshift eciency [44, 48].
The mechanism of frameshifting in coronaviruses is still under investigation, but cryo-EM and crystallography data from the Ban Lab shows the FSE wedged into the mRNA entry channel during translation (Figure 10.10) [18], providing evidence of a mechanism for inhibiting ribosomal translocation and causing ribosomal stalling required for a frameshifting event to occur.
One of the challenges of targeting frameshifting in SARS-CoV-2 is the com­plexity of the frameshift-stimulating element (FSE). Originally believed to be a three-stemmed, three-looped H-type pseudoknot, research by the Woodside group and others have shown that while this conformation occurs in isolation (Figure 10.11), the RNA element is context-dependent and can assume multiple conformations and associations with upstream and downstream RNA sequences, especially in a cellular environment (Figures 10.12 and 10.13) [18, 45, 49].
Initial structural data was obtained based on the canonical pseudoknot structure located at the 3′end of orf1a. Composed of three stems and three loops, this