Symmetric Anti-HCV Agents: Synthesis, Antiviral Properties, and Conformational Aspects of Core Scaffolds.

As hepatitis C virus (HCV) is one of the major health problems in many countries, interest has been aroused in the design, synthesis, and optimization of novel NS5A inhibitors, outside the chemical space of currently available direct acting antivirals (DAAs). Two series of symmetric molecules with core scaffold 3,3'-(buta-1,3-diyne-1,4-diyl)dianiline or 4,4'-(buta-1,3-diyne-1,4-diyl)dianiline, coupled on its nitrogen as amide with different end caps, were synthesized and tested for their activities against HCV by using cell-based antiviral assays. Molecules with the 3,3'-(buta-1,3-diyne-1,4-diyl)dianiline core were more active than their 4,4'-congeners. Only the 3,3'-derivatives showed noncoplanarity of core phenyls that mostly led to a better interaction with the target protein and appears to be a crucial element for efficient inhibition of HCV replication. Compounds 2f and 2q exhibited potent inhibition of genotype (GT) 1b HCV replication with EC50 values in the picomolar range and selectivity index greater than 6 orders of magnitude. The compounds seem more selective toward GT 1b and 4a. In conclusion, novel symmetric molecules with a 3,3'-(buta-1,3-diyne-1,4-diyl)dianiline core are potent and selective inhibitors that provide new extension to explore the structure-activity relationship of NS5A targeting DAAs.

Introduction

Hepatitis C virus infection (HCV) is a health issue known worldwide. It is estimated that more than 70 million people are currently infected.[1] It is a major causative agent of chronic liver illness and can prompt liver cirrhosis and hepatocellular carcinoma. HCV belongs to the Flaviviridae family, Hepacivirus genus.[2] The viral genome is a single-strand RNA of positive polarity and it is 9600 nucleotides in length. It possesses one large open reading frame (ORF) with untranslated regions (UTR) in both 5′ and 3′ ends. These UTR regions are well-conserved RNA structures essential for translation and viral genome replication.[3,4] A single polyprotein precursor is encoded by the ORF. After processing, the polyprotein gives the structural proteins core, E1 and E2, p7 needed for virus assembly and release, and the nonstructural proteins NS2, NS3, NS4A, NS4B, NS5A, and NS5B. Together with host cell factors, the NS proteins share in the formation of membrane-associated replication complex.[3,4]

There are eight major genotypes (GTs) of HCV and a minimum of 86 subtypes.[5] Genotype 1 is the world’s most prevalent and responsible for about 50% of HCV infections in Europe, North America, and Japan; genotype 2 is mainly found in Europe, North America, West Africa, and Japan; genotype 3 and 6 are mostly present in Southeast Asia genotype 4 has its highest prevalence in Egypt while genotype 5 predominates in South Africa.[6]

Several therapeutic options have been established for HCV-infected individuals. Not long ago, the standard-of-care for the HCV treatment was a dual therapy regimen consisting of ribavirin (RBV), an orally administered analogue of guanosine that is given twice daily, and pegylated-interferon alpha, administered as a subcutaneous injection once per week. However, because of several reasons including serious side effects, low sustained virologic response (SVR) rates, long treatment duration up to 48 weeks, and poor patient tolerance, more suitable treatment strategies were required.[7] In 2011, direct acting antivirals (DAAs) were introduced and revolutionized HCV treatment. Since then, DAAs were developed inhibiting the viral NS3/4A protease complex, the NS5B RNA polymerase, and the NS5A phosphoprotein important for genome replication and particle production. These DAAs allowed the implementation of interferon-free treatment schedules that are based on two or three DAAs with different modes of action combined and may include ribavirin.[8,9] Although DAAs are highly effective in most HCV-infected patients, especially in the case of NS5A inhibitors, a risk exists that resistance may develop, according to the genotype and the regimen.[10] Additionally, available DAAs are expensive (several thousand euros per treatment), which limits the access to therapy in low-income countries. Thus, there is a remaining and serious need for new effective NS5A inhibitors that will reduce the high cost of treatment.

NS5A is a zinc-binding phosphoprotein. It consists of 447 amino acid residues, with three domains separated by two linker regions having sequences of low complexity. Domains I (D1) and II (D2) are necessary for viral genome replication, whereas the assembly of virus particles requires domain III (D3). The first 31 amino acids of D1, which are conserved in all HCV GTs, contains an amphipathic α-helix, responsible for anchoring the protein to the endoplasmic reticulum (ER) and the surface of lipid droplets.[11] Amino acids 36–100 (subdomain 1a) coordinate a single zinc atom via four cysteine residues and can homodimerize, forming at least two unique dimeric complexes. The remaining amino acids 101–213 (subdomain 1b) participate in the formation of a putative RNA-binding domain at one of the homodimer interfaces.[12] NS5A’s D2 and D3 are inherently disordered and highly flexible, highlighting NS5A’s wide range of protein interactions.[11] For example, phosphatidylinositol 4-kinase IIIα (PI4KIIIa) interacts with the C-terminus of D1[13] and cyclophilin A with D2 and D3.[14,15] Several kinases, such as mitogen-activated protein kinase 1, casein kinase Iα and II, and AKT, appear to phosphoryle NS5A at multiple serine and threonine residues. As a result, NS5A exists as several phospho variants, appearing in a standard gel system as two major forms with 56 and 58 kDa apparent molecular weights. Available data suggest that the p56 form is primarily unphosphorylated or basally phosphorylated, while the p58 form is hyperphosphorylated. Phosphorylation of NS5A was shown to affect RNA replication, virus assembly, and innate antiviral defense.[11] However, the precise molecular mechanism underlying NS5A functions remains unknown, which is mainly due to the fact that the structure of membrane-bound NS5A has not been resolved, the nature of NS5A homooligomers in cells is unknown, and it is unclear how the phosphorylation status affects NS5A interaction with various viral and cellular proteins.

While the crystal structure of the N-terminal region of NS5A has been determined, the differences in the reported data concerning dimer orientation and the absence of a resolved structure for the inhibitor–protein complex renders structure-based rational drug design a difficult approach.[16,17] Because of this and the absence of a known enzymatic activity for NS5A, structure–activity relationships (SARs) for NS5A inhibitors have been mainly deduced by cell-based HCV replication assays, an often-used assay being HCV “mini-genomes”, also called replicons that are autonomously replicating in human hepatoma cells that are easy to culture.[18]

NS5A inhibitors block both viral RNA synthesis and virion assembly; however, the precise mechanism is unknown. Inhibition might be due to a block of the formation of the membrane-associated HCV replication complex, a perturbation of the interactions of NS5A with other viral/cellular proteins, redistributing NS5A from the ER to the lipid droplet surface, potentially modifying the active HCV replication complex, and/or a block of NS5A oligomerization.[19] Currently approved NS5A inhibitors are extremely potent, inhibiting viral replication with picomolar concentrations. However, the inhibitor efficiency can be drastically reduced because of the presence of NS5A resistance-associated mutations, which can exist already prior to treatment (baseline), and are rapidly selected during the NS5A-based DAA treatment.[20] Therefore, ongoing studies are aiming to discover next-generation RBV and interferon-free DAAs for once daily oral regimens, with pangenotypic and more potent activity, thus allowing to shorten treatment duration and to increase the genetic barrier to resistance.

Because of their high potency, NS5A inhibitors are included in all DAA-only cocktails used in clinical trials or approved for hepatitis C. Specifically, several combinations are currently available for genotype 1 HCV patients. For genotype 4, the regimens paritaprevir/ombitasvir/ritonavir and grazoprevir/elbasvir were approved and the sofosbuvir/ledipasvir combination obtained additional genotype approval 4–6. The next generation of DAAs aimed at achieving SVR in HCV GTs 1–6 and at inhibiting viral replication of strains resistant to first-generation treatments. Additionally, two next-generation treatments, sofosbuvir/velpatasvir and glecaprevir/pibrentasvir, for HCV GTs 1–6 and 1, 2, 5, 6, respectively, have been approved.[21,22]

Because of the fact that NS5A exists as a homodimer, the use of symmetric molecules is a rational approach for developing NS5A inhibitors.[23,24] In this work, we are interested in the design, synthesis, and optimization of novel NS5A inhibitors, outside of the chemical space covered by current patents and with pan-genotypic activity. Using the previously reported NS5A inhibitor ombitasvir,[25] a first generation NS5A inhibitor, as starting point, the following modifications were introduced: the 1-(4-tert-butyl-phenyl)-2,5-diphenyl-pyrrolidine core was replaced by either a 3,3′-(buta-1,3-diyne-1,4-diyl)dianiline or a 4-[4-(4-aminophenyl)buta-1,3-diyn-1-yl]aniline core, l-proline residue was kept or replaced by the unnatural d-proline amino acid, l-valine was retained or replaced by l-leucine, l-isoleucine, unnatural d-valine, or d-leucine, and the terminal methyl chain was kept or replaced by ethyl, butyl, isobutyl, or a benzyl group (Figure ).

Figure 1

Structure of the clinically available ombitasvir and the scaffold of the newly synthesized compounds (1a–1p) and (2a–2q).

Results and Discussion

Chemistry

The reactions adopted in Scheme started with 3- or 4-ethynylaniline where Eglinton dimerization reaction was conducted using a stoichiometric amount of copper (II) salt in pyridine and afforded compounds (A1–A2). This step was followed by amide coupling with either N-boc-l-proline or N-boc-d-proline using HBTU as a coupling reagent to afford compounds (B1–B4). Then, deprotection of the boc protecting group using TFA led to compounds (C1–C4) as outlined in Scheme .

Scheme 1

Synthetic Route

Reagents and conditions: (i) Cu(OAc)2, pyridine/MeOH, 60 °C, 2 h. Yield: 84–100% (ii) HBTU, TEA, CH2Cl2, room temperatures, 2 h. Yield: 65–73% (iii) TFA/CH2Cl2, room temperature, 24 h. Yield: 49–67% (iv) HBTU, TEA, CH2Cl2, room temperature, 4 h. Yield: 6.5–88%.

Five series of terminal capping groups (Scheme ) were synthesized using different alkyl and benzyl carbamates of different d and l amino acids. The first series of capping groups were synthesized by reacting l-valine with methyl chloroformate, ethyl chloroformate, butyl chloroformate, isobutyl chloroformate, and benzyl chloroformate to yield the respective carbamate derivatives. The second series of capping groups were synthesized by reacting l-leucine with methyl, ethyl, butyl, and benzyl chloroformates to yield the respective carbamate derivatives. As for the third series of capping groups, they were synthesized by reacting l-isoleucine with ethyl, butyl, and benzyl chloroformates to yield the respective carbamate derivatives. d-Leucine was reacted with methyl and ethyl chloroformate to give the fourth series of capping groups. Finally, d-valine was reacted with ethyl chloroformate to yield the respective carbamate derivative. The carbamate derivatives were coupled with compounds (C1–C4) to afford compounds 1a–1p and 2a–2q, outlined in Scheme .

Scheme 2

Preparation of Amino Acid Carbamates

Reagents and conditions: (i) NaOH/1,4-dioxane, room temperature, overnight. Yield: 48–51%.

Biological Evaluation

Compound Screening Against HCV Genotype 1b Replicon

The synthesized compounds were evaluated for their activity against HCV RNA replication and their toxicity in the Huh5-2 stable cell line harboring a reporter HCV genotype 1b (strain Con1) replicon.[26] The firefly luciferase (F-Luc) expressed from the replicon is directly correlated with the viral replication levels. The median cytotoxic concentration (CC50) and the half maximum effective concentration (EC50) were obtained using serial dilutions of the compounds and by quantifying ATP levels inside the cells and HCV replication-driven luciferase activity, respectively (Table ). For the most potent analogues, the dose–response curve analysis is presented (Figure ). Selectivity indices (SI50) = CC50/EC50 were calculated for all compounds tested.

Table 1

Activity (EC50), Cytotoxicity (CC50), and Selectivity (SI) of The Synthesized Compounds Against Genotype 1b (Con1) in Replicon Assays

			2nd amino acid cap			genotype 1b (Con1)a
cpd #.	attachment to the core	proline*	cap*	X	Y	EC50 (nM)	CC50 (nM)	SI50
1a	para	S	S	–CH(CH3)2	–CH3	10	11 010	1101
1b	para	S	S	–CH(CH3)2	–C2H5	90	2580	29
1c	para	S	S	–CH(CH3)2	–C4H9	919	>20 000	>22
1d	para	S	S	–CH(CH3)2	–CH2CH(CH3)2	>10 000	>10 000
1e	para	S	S	–CH(CH3)2	–CH2C6H5	2560	>20 000	>8
1f	para	S	S	–CH2CH(CH3)2	–C2H5	3213	>10 000	>3
1g	para	S	S	–CH2CH(CH3)2	–C4H9	>10 000	>10 000
1h	para	S	S	–CH(CH3)C2H5	–C2H5	2010	>10 000	>4
1i	para	S	S	–CH(CH3)C2H5	–C4H9	>10 000	>10 000
1j	para	R	S	–CH(CH3)2	–C2H5	>10 000	>10 000
1k	para	R	R	–CH(CH3)2	–C2H5	>10 000	>10 000
1l	para	R	S	–CH2CH(CH3)2	–C2H5	5631	>10 000	>1
1m	para	R	R	–CH2CH(CH3)2	–C2H5	>10 000	>10 000
1n	para	S	R	–CH(CH3)2	–C2H5	267	70 620	265
1o	para	S	S	–CH2CH(CH3)2	–CH2C6H5	>10 000	>10 000
1p	para	S	S	–CH(CH3)C2H5	–CH2C6H5	>10 000	>10 000
2a	meta	S	S	–CH(CH3)2	–CH3	0.1208	>200 000	>1 655 629
2b	meta	S	S	–CH(CH3)2	–C2H5	451	>200 000	>443
2c	meta	S	S	–CH(CH3)2	–C4H9	>10 000	>10 000
2d	meta	S	S	–CH(CH3)2	–CH2CH(CH3)2	380	>20 000	>53
2e	meta	S	S	–CH(CH3)2	–CH2C6H5	>10 000	>10 000
2f	meta	S	S	–CH2CH(CH3)2	–C2H5	0.0399	>200 000	>5 010 020
2g	meta	S	S	–CH2CH(CH3)2	–C4H9	>10 000	>10 000
2h	meta	S	S	–CH(CH3)C2H5	–C2H5	392	>200 000	>510
2i	meta	S	S	–CH(CH3)C2H5	–C4H9	>10 000	>10 000
2j	meta	R	S	–CH(CH3)2	–C2H5	1776	>10 000	>5
2k	meta	R	R	–CH(CH3)2	–C2H5	>10 000	>10 000
2l	meta	R	S	–CH2CH(CH3)2	–C2H5	106.5	>10 000	>94
2m	meta	R	R	–CH2CH(CH3)2	–C2H5	410.3	>10 000	>24
2n	meta	S	R	–CH(CH3)2	–C2H5	70	>20 000	>277
2o	meta	S	S	–CH2CH(CH3)2	–CH3	>20 000	>20 000
2p	meta	S	R	–CH2CH(CH3)2	–CH3	0.0686	>200 000	>2 915 027
2q	meta	S	R	–CH2CH(CH3)2	–C2H5	0.0411	>200 000	>4 866 180
daclatasvir						0.0266	17 700	655 556

EC50 and CC50 were determined in Huh5-2 (Con1) replicon assays. Mean values from three independent experiments in triplicates are shown, SD ≤ 12%.

Figure 2

Dose–response curves for compounds 2a, 2f, 2p, and 2q against replication of HCV genotype 1b RNA. Huh5-2 replicon cells were seeded at a confluency of 30 percent and treated with compounds’ serial dilutions for 72 h. F-Luc activity was measured and expressed as relative light units (RLU) per μg of total protein. Values from compound-treated cells were expressed relatively to the ones from solvent-treated dimethyl sulfoxide (DMSO) (control) cells. Daclatasvir was used as a positive control. Bars represent mean values from three independent triplicate experiments. Error bars represent standard deviation (SD).

Structure–Activity Relationship

SARs was evaluated based on three key structural features, (i) the stereochemistry of the two chiral carbons of the amino acid proline (ii) the stereochemistry and the size of the terminal lipophilic amino acid cap and (iii) the nature and size of the terminal O-substituent: alkyl and arylalkyl carbamates.

Stereochemistry of 2 Chiral Carbons of the Amino Acid Proline

We compared the potency of the compounds with d-proline versus those with l-proline. Several 4-ethynylaniline-derived analogues containing l-proline showed EC50 values in the low micromolar and submicromolar range, while 3-ethynylaniline-derived analogues had EC50 values in the nanomolar and subnanomolar range. Meanwhile, their respective analogues having d-proline were of lower activity or inactive at the highest concentration tested (10 μM), as indicated by the comparison of compound 1b versus 1j, compound 1n versus 1k, and compound 1f versus 1l, as well as compound 2b versus 2j, compound 2n versus 2k, compound 2f versus 2l, and compound 2q versus 2m. The above comparison indicates that the proline moiety is involved in stereochemically dependent interactions with the target protein (Table ).

Role of the Size and Stereochemistry of the Terminal Amino Acid (Cap)

Three aliphatic lipophilic amino acids (valine, leucine, or isoleucine) were included for comparisons: in the case of 4-ethynylaniline-derived analogues, compound 1b is 3-fold more active than compound 1n, which indicates that the (S) configuration is preferred over (R). In the case of 3-ethynylanilin-derived analogues, comparing compounds 2b versus 2n, 2o versus 2p, and 2f versus 2q, we observed the following: 2n (d-valine ethyl analogue) is more active than 2b (l-valine ethyl analogue) by about 6 fold and 2p (d-leucine methyl analogue) is more active than 2o (l-leucine methyl analogue) by about 3 × 105 fold. However, compounds 2f (l-leucine ethyl analogue) and 2q (d-leucine ethyl analogue) were observed to be equipotent. In conclusion, d-amino acid analogues are more active than those containing l-amino acids with only one exception, compound 2f (l-leucine ethyl analogue). All of the above indicate that the terminal capping residue does not appear to have stereoselective interactions with the binding site of NS5A. These results are important for the development of new peptidic lead compounds and add a new dimension to studies of peptidic molecules and their functions. Moreover, this confirms the usefulness of the peptidomimetic approach for the molecular characterization and the structural modification of the drugs in order to improve their physicochemical properties.

Next, the preferred size (valine, leucine, or isoleucine) of the terminal amino acid for the potency of the compounds is explored. To this end, in the case of 4-ethynylaniline-derived analogues, when comparing the EC50 values of compound 1b versus compounds 1f and 1h, the less bulky valine showed to confer higher activity than isoleucine and leucine. This pattern is confirmed by the relative potency of compounds 1e versus 1o and 1p. Interestingly, for 3-ethynylaniline-derived analogues, comparing the activities of compound 2f versus 2b and 2h showed significantly higher potency in the presence of leucine, as compared to isoleucine and valine. Thus, unlike most of the clinically used NS5A inhibitors, in which the capping residue is l-valine, herein, we introduce other lipophilic amino acids as valuable substitutes for valine. This expands the chemical space for the discovery of novel NS5A inhibitors.

Size of the Terminal O-Substituent (Alkyl Carbamate) for the Capping Group

In 4-ethynylaniline-derived analogues, activity data for compounds 1b, 1c, 1d, and 1a, have clearly shown that the less-bulky, less-branched methyl substituent gives the highest activity followed by ethyl, butyl, and then the isobutyl substituent. Similarly, for 3-ethynylaniline-derived analogues 2a, 2b, 2c, and 2d containing l-valine, the less-bulky, less-branched methyl substituent also gives the highest activity followed by isobutyl, ethyl, and then butyl. However, the situation is almost reversed in the case of compounds having the l-leucine capping group 2o, 2f, and 2g, where the ethyl substituent gives the highest activity, whereas methyl and butyl show no activity at the highest concentration used. Similarly, for d-leucine capping containing compounds 2p and 2q, the ethyl substituent showed higher activity than the methyl derivative. In conclusion, it was found that for l-valine capping, the order of activity from highest to lowest is methyl > isobutyl > ethyl > butyl. However, in the case of l- and d-leucine capping, the order of activity from highest to lowest is ethyl > methyl. Thus, the size of terminal amino acid and the size of the substituent in the terminal oxygen have interdependent roles and should be viewed in the context of the properties of the whole capping group (Table ).

Studying the implication of the size and nature of the terminal O-substituent (alkyl vs aryl), in the case of 4-ethynylaniline-derived analogues, the benzyl derivative compound 1e is found to be 28-fold less active than the ethyl derivative compound 1b. This indicates a potential steric clash of benzyl carbamate at the two terminals of the compound with the binding sites of NS5A. The same indication also exists for 3-ethynylaniline-derived analogues, as the benzyl-substituted derivative 2e (l-valine benzyl derivative) is 22-fold less active than ethyl-substituted 2b.

Comparison of the clinically used NS5A inhibitor daclatasvir with the most active compound 2f (l-leucine ethyl analogue) shows that they are almost equipotent, indicating the value of our approach in developing new anti-HCV agents.

Cytotoxicity and Selectivity of the Synthesized Compounds

Concerning the cytotoxicity (CC50) and selectivity (SI50) of the analogues in Huh5-2 replicon cells (Table ), we observed that all the 4-ethynylaniline-derived compounds (1a–1p) showed high selectivity to inhibit virus replication. The most potent of them, 1a, is also the one with the highest selectivity index, as it shows SI50 of 1101. Moreover, for the most active 3-ethynylaniline-derived compounds that were tested up to 200 μM concentration, we observed very high selectivity indices with SI50s ranging from 1.5 × 106 to 5 × 106. The most potent compound, 2f (l-leucine ethyl analogue), showed the highest SI50 (>5 010 020), which might give a preliminary indication about safety and the suitability of the developed scaffold for further drug development.

Compound Activity Against HCV 3a and 4a Replicon Cells

For the most potent anti-HCV 1b 3-ethynylaniline-derived analogues, 2a, 2f, 2p, and 2q, their activity against other GTs was also tested. In detail, we measured viral replication-driven F-Luc activity in Huh7.5-3a and Huh7.5-4a stable cell lines harboring HCV genotype 3a (strain S52) and 4a (strain ED43) replicons, respectively. All four compounds had significant activity against genotype 4a, with 2a (l-valine methyl derivative) being the most active, with EC50 = 6.11 nM, and the safest, with SI50 > 32 733 (Table ). This confirms that analogues 2a, 2f, 2p, and 2q have activity against 1b and 4a like daclatasvir and ombitasvir. However, their potency was higher against genotype 1b by 50–2440-fold. Nevertheless, they exhibited marginal activity against genotype 3a.

Table 2

Activity (EC50), Cytotoxicity (CC50), and Selectivity (SI) of the Synthesized Compounds Against Genotype 3a (S52) and 4a (ED43) Replicon Assays

		2nd amino acid cap			genotype 3a (S52)a			genotype 4a (ED43)a
cpd #	proline*	cap*	X	Y	EC50 (nM)	CC50 (nM)	SI	EC50 (nM)	CC50 (nM)	SI50
2a	S	S	–CH(CH3)2	–CH3	9500	>200 000	>21	6.11	>200 000	>32 733
2f	S	S	–CH2CH(CH3)2	–C2H5	>10 000	>200 000		40.94	>200 000	>4885
2p	S	R	–CH2CH(CH3)2	–CH3	4668	>200 000	>43	18.62	>200 000	>10 741
2q	S	R	–CH2CH(CH3)2	–C2H5	>10 000	>200 000		100.3	>200 000	>1994
daclatasvir					8.348	17 700	2120	0.021	17 700	842 857

EC50 and CC50 values were determined in Huh7.5-3a (S52) and Huh7.5-4a (ED43) replicon cells. Mean values from three independent experiments in triplicates are shown, SD ≤ 12%.

Validation of Compounds’ Activity with Other Methods

By determining the levels of viral RNA and NS5A proteins, we validated the inhibition potency of the compounds observed in luciferase activity assays against HCV genotype 1b. Huh5-2 cells were mock-treated (control) or incubated with compounds 2f and 2q at 0.5 and 0.05 nM. Total RNA was extracted from cells and HCV RNA was quantified by reverse transcription–quantitative polymerase chain reaction (RT–qPCR), while NS5A levels were examined in paraformaldehyde-fixed cells by indirect immunofluorescence/confocal microscopy analysis (Figure A). We found that 0.05 nM of compound 2q reduced HCV RNA replication to 56%, whereas the same concentration of compound 2f reduced HCV RNA to ∼90% arguing for higher potency of compound 2f. In agreement, indirect immunofluorescence analysis of HCV NS5A in Huh5-2 cells showed almost undetectable levels of the viral protein at the highest compound concentration used (Figure B). Note that cell viability was not affected, as shown by nuclei staining with propidium iodide (PI). This result corroborates that compound 2f is a more potent NS5A inhibitor than 2q against the HCV genotype 1b replicon.

Figure 3

Activity of compounds 2q and 2f against HCV RNA and protein expression in Huh5-2 replicon cells. (A) Levels of (+) strand HCV RNA as determined by RT-qPCR in cells treated with 0.5 and 0.05 nM of compound 2q or 2f or mock-treated with DMSO (control). Values from compound-treated cells are expressed relative to those from control cells and normalized to the mRNA levels of the housekeeping gene YWHAZ. p < 0.001 vs control cells, p < 0.001 2q 0.5 nM vs 0.05 nM (Student’s t-test). (B) Middle panels: indirect immunofluorescence analysis for NS5A in cells treated as in (A). Left panels: nuclei staining with PI. Right panels: merged images. Bar, 100 μm.

Molecular Modelling

We adopted a computational approach to explain the higher activity of compound 2f relative to its analogue with the 4,4′-(buta-1,3-diyne-1,4-diyl)dianiline core 1f (EC50 = 4.3 μM). Interestingly, the energy minimized form of the much less-active analogue 1f showed planarity of the core scaffold and a relatively extended structure of the whole molecule (Figure ); this is expected because of the extended conjugation present in the p,p′-disubstituted core. In contrast, compound 2f showed a clear noncoplanarity between the two core aniline rings, Figure . It is worth mentioning that the conjugation in this molecule cannot include the amide moieties as they are meta-oriented relative to the diphenyldiyne central core. This m-orientation causes proline and capping residue carbamate to be less extended and to be in spatial projection that leads to better interaction with the binding site of NS5A.

Figure 4

Energy minimized form of compound 1f (A) with the 4,4′-(buta-1,3-diyne-1,4-diyl)dianiline core showing coplanarity between the two core aniline rings and compound 2f (B) with the 3,3′-(buta-1,3-diyne-1,4-diyl)dianiline core showing different spatial projection and non co-orientation of the two core aniline rings and their capping groups, (C) the energy minimized form of ombitasvir showing noncoplanarity of two phenyls and different spatial orientations of the two capping groups (D) an overlay of 1f and 2f showing different orientations of the two capping groups at one end. Energy minimization was done by MMFF94x forcefield and followed by automatic overlaying using MOE software.

Conclusions

Novel NS5A inhibitors of the core scaffolds 3,3′-(buta-1,3-diyne-1,4-diyl)dianiline and 4,4′-(buta-1,3-diyne-1,4-diyl)dianiline with different capping groups are presented. Our results showed that the 3,3′-disubstituted core has a superior activity over the 4,4′-disubstituted core which can be attributed to the difference in the adopted conformation and relative orientation of the key binding groups in the binding site. Additionally, using l-leucine in the end-capping group with the 3,3′-disubstituted core can show higher potency (in the picomolar range) than the frequently used l-valine, adding new insight to the possible diversity of the designed inhibitors. New structural analogues will be generated in order to investigate the conformational aspects of the core scaffold and acquire more SAR information to help refine the requirements for optimal activity.

Experimental Section

Solvents and reagents were obtained from commercial suppliers and were used without further purification. All organic solvents used were of pure analytical grade. Column chromatography was carried out using silica-gel 70–230 μm mesh. Reaction progress was monitored by TLC using fluorescent precoated silica gel plates and detection of the components was made by short UV light (λ = 254 nm). Carbamates were detected using the furfural/sulphuric acid detection reagent. 1H NMR spectra were run at either 300 or 500 MHz and 13C NMR spectra were run at 75 or 101 or 126 MHz in the deuterated solvent (DMSO-d6). Chemical shift (δ) were reported in parts per million (ppm) downfield from TMS, and all coupling constants (J) are given in Hz. Multiplicities are abbreviated as s: singlet; d: doublet; t: triplet; q: quartet; m: multiplet; dd: doublet of doublet; dt: doublet of triplet; and brs: broad singlet. The purities of the tested compounds were determined by high-performance liquid chromatography (HPLC) coupled with a mass spectrometer and were higher than 90% for all compounds. Mass spectra were obtained on the (HPLC–ESI-MS) instrument equipped with an ESI source and a triple quadrupole mass detector (Thermo Finnigan). MS detection was carried out at a spray voltage of 4.2 kV, a nitrogen sheath gas pressure of 4 × 105 Pa, an auxiliary gas pressure of 1 × 105 Pa, a capillary temperature of 400 °C, a capillary voltage of 35 V, and a source CID of 10 V. All samples were injected by autosampler (Surveyor, Thermo Finnigan) with an injection volume of 10 μL. A RP C18 NUCLEODUR 100–3 (125 mm × 3 mm) column (Macherey-Nagel) was used as the stationary phase. The solvent system consisted of water containing 0.1% TFA (A) and 0.1% TFA in acetonitrile (B). HPLC method: flow rate 400 μL/min. The percentage of B started at an initial of 5%, was increased up to 100% during 16 min, kept at 100% for 2 min, and flushed back to 5% in 2 min. All masses were reported as the protonated parent ion (M + H)+ or (M + Na)+ or (M)+. 1H NMR and 13C NMR spectra were performed either at the main Chemical Warfare Laboratories, Chemical Warfare Department, Ministry of Defense at 400 MHz using a Varian Mercury 400 Plus spectrometer or at HIPS, Saarland at 500 MHz using a Bruker DRX-500 spectrometer. All reactions were carried out under nitrogen when inert atmosphere was needed. All starting materials were obtained from commercial suppliers and were used without further purification.

General Synthetic Methods and Experimental Details for Some Key Compounds

General Procedure for Carbamates Synthesis

In a 250 mL round-bottom flask, 1 M NaOH (75 mL) was added and left to cool to 0 °C in an ice bath. After that, the respective amino acid (24 mmol) was added, and the solution was left to be stirred until it became homogeneous. Then, the respective chloroformate (33 mmol) and 1,4-dioxane (30 mL) were added dropwise. The reaction mixture was then allowed to stir at room temperature overnight. The solution was extracted with Et2O (3 × 50 mL). The aqueous layer was cooled to 0 °C in an ice bath, and concentrated HCl was added dropwise until pH = 2. The aqueous solution was extracted again with Et2O (3 × 100 mL). The organic layers were combined, dried over anhydrous Na2SO4, and concentrated in vacuo to give a viscous oily product. The compound was used for the next step without further purification.

(Methoxycarbonyl)-l-valine (Cap1)

The compound was synthesized according to the procedure for carbamate synthesis using l-valine amino acid and methyl chloroformate to give a white crystalline product: yield 55%; mp 109–113 °C; CAS no. 74761-42-5; C7H13NO4.

(Ethoxycarbonyl)-l-valine (Cap2)

The compound was synthesized according to the procedure for carbamate synthesis using l-valine amino acid and ethyl chloroformate to give a clear oily product: yield 59%; CAS no. 5701-14-4; C8H15NO4.

(Butoxycarbonyl)-l-valine (Cap3)

The compound was synthesized according to the procedure for carbamate synthesis using l-valine amino acid and butyl chloroformate to give a clear oily product: yield 58%; CAS no. 122315-77-9; C10H19NO4.

(Isobutoxycarbonyl)-l-valine (Cap4)

The compound was synthesized according to the procedure for carbamate synthesis using l-valine amino acid and isobutyl chloroformate to give a clear oily product: yield 54%; CAS no. 74761-42-5; C10H19NO4.

((Benzyloxy)carbonyl))-l-valine (Cap5)

The compound was synthesized according to the procedure for carbamate synthesis using l-valine amino acid and benzyl chloroformate to give a clear oily product: yield 61%; CAS no. 1149-26-4; C13H17NO4.

(Ethoxycarbonyl)-l-leucine (Cap6)

The compound was synthesized according to the procedure for carbamate synthesis using l-leucine amino acid and ethyl chloroformate to give a clear oily product: 57%; CAS no. 19887-30-0; C9H17NO4.

(S)-2-((Butoxycarbonyl)amino)-5-methylhexanoic Acid (Cap7)

The compound was synthesized according to the procedure for carbamate synthesis using l-leucine amino acid and butyl chloroformate to give a clear oily product: yield 59%; 1H NMR (500 MHz, DMSO-d6): δ 12.47 (s, 1H), 7.34 (d, J = 8.2 Hz, 1H), 3.96–3.84 (m, 3H), 1.63 (dt, J = 18.1, 6.5 Hz, 1H), 1.54–1.48 (m, 3H), 1.37–1.27 (m, 3H), 0.87 (ddd, J = 23.8, 11.2, 3.9 Hz, 11H); C12H23NO4.

(Ethoxycarbonyl)-l-alloisoleucine (Cap8)

The compound was synthesized according to the procedure for carbamate synthesis using l-isoleucine amino acid and ethyl chloroformate to give a clear oily product: yield 53%; CAS no. 19887-31-1; C9H17NO4.

(2S,4S)-2-((Butoxycarbonyl)amino)-4-methylhexanoic Acid (Cap9)

The compound was synthesized according to the procedure for carbamate synthesis using l-isoleucine amino acid and butyl chloroformate to give a clear oily product: yield 54%; 1H NMR (500 MHz, DMSO-d6): δ 12.50 (s, 1H), 7.27 (d, J = 8.4 Hz, 1H), 3.94 (t, J = 6.7 Hz, 2H), 3.90–3.81 (m, 1H), 3.33 (s, 1H), 1.80–1.67 (m, 1H), 1.60–1.43 (m, 2H), 1.43–1.25 (m, 3H), 1.26–1.11 (m, 1H), 1.00–0.75 (m, 10H); C12H23NO4.

(Ethoxycarbonyl)-d-valine (Cap10)

The compound was synthesized according to the procedure for carbamate synthesis using d-valine amino acid and ethyl chloroformate to give a clear oily product: yield 55%; CAS no. 160742-91-6; C8H15NO4.

(Ethoxycarbonyl)-d-leucine (Cap11)

The compound was synthesized according to the procedure for carbamate synthesis using d-leucine amino acid and ethyl chloroformate to give a clear oily product: 53%; CAS no. 136159-70-1; C9H17NO4.

((Benzyloxy)carbonyl))-l-leucine (Cap12)

The compound was synthesized according to the procedure for carbamate synthesis using l-leucine amino acid and benzyl chloroformate to give a clear oily product: yield 60%; CAS no. 2018-66-8; C14H19NO4.

(Methoxycarbonyl)-l-leucine (Cap13)

The compound was synthesized according to the procedure for carbamate synthesis using l-leucine amino acid and methyl chloroformate to give a clear oily product: yield 51%; CAS no. 74761-37-8; C8H15NO4.

((Benzyloxy)carbonyl))-l-alloisoleucine (Cap14)

The compound was synthesized according to the procedure for carbamate synthesis using l-isoleucine amino acid and benzyl chloroformate to give a clear oily product: yield 58%; CAS no. 3160-59-6; C14H19NO4.

(Methoxycarbonyl)-d-leucine (Cap15)

The compound was synthesized according to the procedure for carbamate synthesis using d-leucine amino acid and methyl chloroformate to give a clear oily product: yield 48%; CAS no. 791635-26-2; C8H15NO4.

General Procedure for Dianiline Core Synthesis

In a 250 mL round-bottom flask, ethynyl aniline derivative (0.23 g, 2 mmol) was added to Cu(OAc)2 (1 g, 5.5 mmol) in the pyridine/MeOH mixture with a ratio of 1:1 (v/v; 20 mL). The flask was left to reflux for 2 h. Volatile components were evaporated under vacuum to give a green semi-solid. The green semi-solid was dissolved in water and extracted using ethyl acetate (3 × 50 mL). The organic layers were collected, dried over anhydrous Na2SO4, and concentrated in vacuo. The compound was then purified using column chromatography.

4,4′-(Buta-1,3-diyne-1,4-diyl)dianiline (A1)

The compound was synthesized according to the procedure for the dianiline core synthesis using 4-ethynyl aniline and Cu(OAc)2. The product was purified by CC (CH2Cl2) to give a yellow solid: yield 0.194 g (84%); 1H NMR (500 MHz, DMSO-d6): δ 7.20–7.18 (m, 4H), 6.54–6.51 (m, 4H), 5.72 (s, 4H); 13C NMR (126 MHz, DMSO-d6): δ 150.15, 133.51, 113.54, 106.35, 82.88, 71.99; MS (ESI) m/z: 232.03 (M)+.

3,3′-(Buta-1,3-diyne-1,4-diyl)dianiline (A2)

The compound was synthesized according to the procedure for the dianiline core synthesis using 3-ethynyl aniline and Cu(OAc)2. The product was purified by CC (CH2Cl2/MeOH 99:1) to give a brown oily product: yield 100%; 1H NMR (500 MHz, DMSO-d6): δ 7.05 (t, J = 7.8 Hz, 2H), 6.70 (t, J = 5.1 Hz, 4H), 6.65 (dd, J = 8.7, 1.7 Hz, 2H), 5.32 (s, 4H); 13C NMR (126 MHz, DMSO-d6): δ 142.07, 129.37, 123.19, 122.32, 119.70, 116.57, 78.73, 74.50; MS (ESI) m/z: 233.04 (M + H)+.

General Procedure for the Coupled Derivative Synthesis

In a 250 mL round-bottom flask, the derivative of compound A (0.23 g, 1 mmol) was added to N-boc-d/l-proline (0.65 g, 3 mmol) and HBTU (1.14 g, 3 mmol). Then, TEA (0.77 g, 6 mmol) was added with CH2Cl2 (40 mL) and the mixture was left to stir at room temperature for 2 h. The volatile components were evaporated under vacuum. The compound was then purified using column chromatography.

Di-tert-butyl2,2′-(((buta-1,3-diyne-1,4-diylbis(4,1-phenylene))bis(azanediyl))bis(carbonyl))(2S,2′S)-bis(pyrrolidine-1-carboxylate) (B1)

The compound was synthesized according to the procedure for the coupled derivative synthesis using compound A1 and N-boc-l-proline. The product was purified by CC (ethyl acetate/hexane 40:60) to give a dark red oily product: yield 65%; 1H NMR (500 MHz, DMSO-d6): δ 10.27 (d, J = 3.8 Hz, 2H), 7.66 (d, J = 3.5 Hz, 4H), 7.54 (d, J = 4.7 Hz, 4H), 4.02 (t, J = 7.1 Hz, 2H), 3.34 (d, J = 11.2 Hz, 4H), 1.99 (d, J = 5.5 Hz, 4H), 1.90–1.87 (m, 4H), 1.30 (d, J = 7.7 Hz, 18H); 13C NMR (126 MHz, DMSO-d6): δ 171.90, 171.5, 170.34, 140.40, 133.18, 119.07, 118.95, 78.39, 73.039, 72.75, 60.10, 59.80, 46.17, 27.61; MS (ESI) m/z: 627.20 (M + H)+.

Di-tert-butyl2,2′-(((buta-1,3-diyne-1,4-diylbis(3,1-phenylene))bis(azanediyl))bis(carbonyl))(2S,2′S)-bis(pyrrolidine-1-carboxylate) (B2)

The compound was synthesized according to the procedure for the coupled derivative synthesis using compound A2 and N-boc-l-proline. The product was purified by CC (CH2Cl2/MeOH 99:1) to give a yellow oily product: yield 73%; 1H NMR (500 MHz, DMSO-d6): δ 10.17–10.15 (m, 2H), 7.90–7.88 (m, 2H), 7.65–7.63 (m, 2H), 7.40–7.38 (m, 2H), 7.31–7.29 (m, 2H), 4.15–4.13 (m, 2H), 3.74 (s, 2H), 3.51 (s, 2H), 2.17–2.16 (m, 2H), 2.03–2.01 (m, 2H), 2.00 (s, 2H), 1.98–1.97 (m, 2H), 1.40 (s, 18H); 13C NMR (126 MHz, DMSO-d6): δ 171.23, 155.92, 136.83, 128.32, 128.29, 126.16, 123.08, 121.48, 80.05, 77.24, 74.10, 68.81, 49.82, 29.32, 28.80, 23.94; MS (ESI) m/z: 627.02 (M + H)+.

Di-tert-butyl2,2′-(((buta-1,3-diyne-1,4-diylbis(3,1-phenylene))bis(azanediyl))bis(carbonyl))(2R,2′R)-bis(pyrrolidine-1-carboxylate) (B4)

The compound was synthesized according to the procedure for the coupled derivative synthesis using compound A2 and N-boc-d-proline. The product was purified by CC (CH2Cl2/MeOH 99:1) to give a yellow oily product: yield 68%; 1H NMR (500 MHz, DMSO-d6): δ 10.16 (s, 2H), 7.89 (s, 2H), 7.72–7.61 (m, 4H), 7.38 (d, J = 8.0 Hz, 2H), 4.18 (d, J = 12.9 Hz, 2H), 3.42 (s, 4H), 2.00 (d, J = 7.4 Hz, 2H), 1.89 (s, 6H), 1.26 (d, J = 7.3 Hz, 18H); 13C NMR (126 MHz, DMSO-d6): δ 171.80, 153.86, 139.48, 129.05, 127.17, 124.62, 123.17, 121.91, 79.15, 78.52, 74.24, 69.86, 48.59, 28.12, 27.92, 23.04; MS (ESI) m/z: 627.05 (M + H)+

General Procedure for the Deprotected Derivative Synthesis

In a 250 mL round-bottom flask, the derivative of compound B (0.46 g, 0.73 mmol) was dissolved in CH2Cl2 (40 mL). Then, CF3CO2H (6 mL) was added under N2 and the mixture was left to be stirred overnight at room temperature. The volatile components were evaporated under vacuum. Then, 2 M NaOH was added to the residue until the pH value reached 12 and extraction was done using EtOAc (3 × 50 mL). The organic layers were combined, dried over anhydrous Na2SO4, and concentrated in vacuo.

(2S,2′S)-N,N′-(Buta-1,3-diyne-1,4-diylbis(4,1-phenylene))bis(pyrrolidine-2-carboxamide) (C1)

The compound was synthesized according to the procedure for the deprotected derivative synthesis using compound B1 and CF3CO2H to give a pale yellow crystalline solid: yield 58%; 1H NMR (500 MHz, DMSO-d6): δ 10.27 (s, 2H), 7.83 (d, J = 1.3 Hz, 4H), 7.62 (d, J = 1.8 Hz, 4H), 3.79 (dd, J = 8.8, 5.7 Hz, 2H), 3.01–2.95 (m, 4H), 2.13 (ddd, J = 15.8, 12.5, 7.5 Hz, 2H), 1.87 (td, J = 12.7, 7.1 Hz, 4H), 1.76–1.69 (m, 4H); 13C NMR (126 MHz, DMSO-d6): δ 174.42, 140.35, 133.59, 119.60, 115.20, 82.35, 73.58, 61.34, 47.21, 30.90, 26.33; MS (ESI) m/z: 426.97 (M + H)+.

(2S,2′S)-N,N′-(Buta-1,3-diyne-1,4-diylbis(3,1-phenylene))bis(pyrrolidine-2-carboxamide) (C2)

The compound was synthesized according to the procedure for the deprotected derivative synthesis using compound B2 and CF3CO2H to give an orange oily product: yield 0.2 g (67%); 1H NMR (500 MHz, DMSO-d6): δ 10.14 (s, 2H), 8.01–7.89 (m, 2H), 7.77–7.65 (m, 2H), 7.39 (t, J = 7.9 Hz, 2H), 7.31 (dt, J = 7.7, 1.3 Hz, 2H), 3.76 (dd, J = 8.7, 5.7 Hz, 2H), 2.93 (t, J = 6.6 Hz, 4H), 2.51–2.49 (m, 2H), 2.16–2.00 (m, 2H), 1.86–1.75 (m, 2H), 1.74–1.63 (m, 4H); 13C NMR (126 MHz, DMSO-d6): δ 173.90, 139.38, 128.96, 126.82, 126.22, 121.10, 121.04, 82.22, 73.69, 64.33, 47.15, 29.56, 26.15; MS (ESI) m/z: 427.04 (M + H)+.

(2R,2′R)-N,N′-(Buta-1,3-diyne-1,4-diylbis(3,1-phenylene))bis(pyrrolidine-2-carboxamide) (C4)

The compound was synthesized according to the procedure for the deprotected derivative synthesis using compound B4 and CF3CO2H to give an orange oily product: yield 49%; 1H NMR (500 MHz, DMSO-d6): δ 10.19 (d, J = 14.0 Hz, 2H), 7.98–7.93 (m, 2H), 7.72 (ddd, J = 8.2, 2.1, 1.1 Hz, 2H), 7.38 (dd, J = 13.4, 5.4 Hz, 2H), 7.34–7.28 (m, 2H), 3.77 (dd, J = 8.6, 5.8 Hz, 2H), 2.93 (t, J = 6.6 Hz, 4H), 2.08 (ddd, J = 15.7, 12.6, 7.5 Hz, 2H), 1.80 (dd, J = 12.7, 5.7 Hz, 2H), 1.71–1.64 (m, 4H), 1.23 (s, 2H); 13C NMR (126 MHz, DMSO-d6): δ 173.20, 138.87, 129.42, 127.36, 122.44, 120.97, 120.57, 76.81, 73.17, 60.69, 46.62, 30.33, 25.59; MS (ESI) m/z: 426.88 (M)+.

General Procedure for Compound 1a–2q Synthesis

The respective carbamate (2.47 mmol) was added to the derivative of compound C (0.35 g, 0.822 mmol). After that, HBTU (0.94 g, 2.4 mmol), TEA (0.43 g, 3.29 mmol), and CH2Cl2 (50 mL) were added and the reaction was allowed to stir at room temperature for 4 h. The volatile components were evaporated under vacuum. The resulting product was then purified using column chromatography.

Dimethyl((2S,2′S)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(4,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(3-methyl-1-oxobutane-1,2-diyl))dicarbamate (1a)

The title compound was prepared by reaction of compound C1 with Cap1 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98:2) to give a yellow oily product; yield 28%; 1H NMR (400 MHz, DMSO-d6): δ 10.28 (d, J = 9.0 Hz, 2H), 7.64 (t, J = 6.6 Hz, 4H), 7.56–7.45 (m, 4H), 7.26 (d, J = 16.9 Hz, 2H), 4.47–4.43 (m, 2H), 4.04 (t, J = 8.3 Hz, 2H), 3.81–3.63 (m, 4H), 3.53 (s, 6H), 3.09 (s, 2H), 2.20–2.01 (m, 4H), 1.96–1.89 (m, 4H), 0.90 (dt, J = 15.6, 7.8 Hz, 12H); 13C NMR (100 MHz, DMSO-d6): δ 171.32, 170.87, 165.01, 142.97, 142.75, 121.37, 118.10, 74.78, 73.69, 60.78, 58.50, 51.98, 947.74, 30.31, 29.87, 25.09, 19.11; MS (ESI) m/z: 740.35 (M)+.

Dimethyl((2S,2′S)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(3,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(3-methyl-1-oxobutane-1,2-diyl))dicarbamate (2a)

The title compound was prepared by reaction of compound C2 and Cap1 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98:2) to give a yellow oily product; yield 44%; 1H NMR (500 MHz, DMSO-d6): δ 10.24 (s, 2H), 7.90 (s, 2H), 7.59 (d, J = 9.3 Hz, 2H), 7.40–7.31 (m, 4H), 7.31–7.26 (m, 2H), 4.44–4.39 (m, 4H), 3.81 (s, 6H), 3.52 (s, 4H), 3.36 (q, J = 7.2 Hz, 4H), 2.17 (d, J = 5.2 Hz, 2H), 1.90 (dd, J = 14.7, 5.5 Hz, 4H), 0.92 (dd, J = 29.1, 6.6 Hz, 12H); 13C NMR (126 MHz, DMSO-d6): δ 171.10, 170.35, 157.35, 139.48, 129.98, 127.35, 124.88, 121.59, 120.59, 77.38, 72.87, 65.34, 60.76, 55.17, 51.96, 45.57, 29.35, 22.92, 18.58, 8.61; MS (ESI) m/z: 741.31 (M + H)+.

Diethyl((2S,2′S)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(4,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(3-methyl-1-oxobutane-1,2-diyl))dicarbamate (1b)

The title compound was prepared by reaction of compound C1 and Cap2 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98:2) to give a yellow oily product; yield 24%; 1H NMR (500 MHz, DMSO-d6): δ 10.33 (s, 2H), 7.64 (d, J = 8.8 Hz, 4H), 7.53 (d, J = 8.7 Hz, 4H), 7.27 (d, J = 8.3 Hz, 2H), 4.44 (dd, J = 8.0, 5.1 Hz, 2H), 3.98–3.97 (m, 2H), 3.82 (dd, J = 16.1, 7.0 Hz, 2H), 3.62 (dd, J = 16.2, 6.9 Hz, 2H), 3.10 (q, J = 7.3 Hz, 4H), 2.20–2.12 (m, 2H), 2.00 (dd, J = 11.6, 6.6 Hz, 2H), 1.93–1.85 (m, 4H), 1.17–1.13 (m, 8H), 0.95–0.86 (m, 12H); 13C NMR (126 MHz, DMSO-d6): δ 170.80, 170.36, 164.56, 140.43, 133.21, 118.88, 114.51, 73.08, 60.24, 59.79, 57.79, 47.20, 45.70, 29.76, 29.37, 24.67, 18.83, 14.63; MS (ESI) m/z: 769.40 (M)+.

Diethyl((2S,2′S)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(3,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(3-methyl-1-oxobutane-1,2-diyl))dicarbamate (2b)

The title compound was prepared by reaction of compound C2 and Cap2 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98:2) to give a yellow oily product; yield 62%; 1H NMR (500 MHz, DMSO-d6): δ 10.05 (s, 2H), 8.68 (s, 2H), 7.72 (d, J = 9.7 Hz, 2H), 7.40 (ddd, J = 8.2, 2.1, 1.0 Hz, 2H), 7.19 (t, J = 8.0 Hz, 2H), 7.11–7.04 (m, 2H), 4.24 (dd, J = 8.2, 5.1 Hz, 2H), 3.87–3.74 (m, 6H), 3.67–3.59 (m, 2H), 3.44 (dd, J = 15.8, 7.0 Hz, 2H), 2.31 (dt, J = 3.7, 1.8 Hz, 2H), 1.98 (dd, J = 15.6, 10.8 Hz, 2H), 1.83–1.68 (m, 6H), 0.98 (s, 6H), 0.72 (dt, J = 19.1, 9.6 Hz, 12H); 13C NMR (126 MHz, DMSO-d6): δ 170.80, 170.41, 156.33, 139.47, 129.52, 127.05, 126.49, 122.04, 120.61, 81.70, 73.15, 60.20, 59.79, 57.81, 38.21, 29.38, 24.65, 18.86, 14.61, 8.56; MS (ESI) m/z: 769.30 (M + H)+.

Dibutyl((2S,2′S)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(4,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(3-methyl-1-oxobutane-1,2-diyl))dicarbamate (1c)

The title compound was prepared by reaction of compound C1 and Cap3 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (ethyl acetate/Hexane 40:60) to give a yellow oily product; yield 24%; 1H NMR (500 MHz, DMSO-d6): δ 8.84 (s, 2H), 7.64 (d, J = 8.8 Hz, 4H), 7.53 (d, J = 8.7 Hz, 4H), 7.27 (d, J = 8.8 Hz, 2H), 4.46–4.40 (m, 2H), 4.05–4.00 (m, J = 8.5 Hz, 2H), 3.96–3.91 (m, 4H), 3.83–3.81 (m, 2H), 3.62 (dd, J = 15.5, 6.0 Hz, 2H), 3.11–3.08 (m, 2H), 2.18–2.12 (m, 2H), 2.04–1.96 (m, 4H), 1.94–1.83 (m, 6H), 1.54–1.47 (m, 4H), 1.17 (t, J = 7.3 Hz, 6H), 0.89–0.87 (m, 12H); 13C NMR (126 MHz, DMSO-d6): δ 186.33, 173.29, 164.36, 140.44, 133.21, 118.94, 114.40, 91.18, 73.15, 67.20, 63.66, 59.24, 45.70, 30.62, 29.32, 24.52, 19.13, 18.37, 13.56, 8.55; MS (ESI) m/z: 825.37 (M)+.

Dibutyl((2S,2′S)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(3,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(3-methyl-1-oxobutane-1,2-diyl))dicarbamate (2c)

The title compound was prepared by reaction of compound C2 and Cap3 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98.75:1.25) to give a yellow oily product: yield 63%; 1H NMR (500 MHz, DMSO-d6): δ 10.03 (s, 2H), 7.71 (s, 2H), 7.42–7.37 (m, 2H), 7.19 (t, J = 8.0 Hz, 2H), 7.12–7.08 (m, 2H), 7.05 (d, J = 8.3 Hz, 2H), 4.24 (dd, J = 8.2, 5.0 Hz, 2H), 3.83 (d, J = 8.4 Hz, 2H), 3.77–3.73 (m, 4H), 3.64–3.61 (m, 2H), 3.47–3.41 (m, 2H), 1.98 (d, J = 6.6 Hz, 2H), 1.83–1.70 (m, 8H), 1.33 (d, J = 7.4 Hz, 4H), 1.14–1.10 (m, 4H), 0.97 (s, 12H), 0.76 (d, J = 6.7 Hz, 6H); 13C NMR (126 MHz, DMSO-d6): δ 173.35, 170.80, 156.62, 139.49, 129.52, 127.11, 125.15, 122.07, 120.58, 77.52, 73.15, 66.69, 65.12, 59.44, 51.96, 30.71, 29.78, 29.47, 24.65, 19.13, 18.53, 13.59; MS (ESI) m/z: 825.28 (M + H)+.

Diisobutyl((2S,2′S)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(4,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(3-methyl-1-oxobutane-1,2-diyl))dicarbamate (1d)

The title compound was prepared by reaction of compound C1 and Cap4 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98:2) to give a yellow oily product; yield 22%; 1H NMR (500 MHz, DMSO-d6): δ 8.54 (s, 2H), 7.67 (d, J = 8.7 Hz, 4H), 7.54 (d, J = 8.7 Hz, 4H), 4.48–4.44 (m, 2H), 4.03 (d, J = 8.5 Hz, 2H), 3.76–3.70 (m, 4H), 2.74 (s, 4H), 2.19–2.13 (m, 2H), 1.90 (s, 2H), 1.87–1.77 (m, 8H), 1.24 (s, 2H), 0.88 (d, J = 6.7 Hz, 24H); 13C NMR (126 MHz, DMSO-d6): δ 178.86, 173.79, 160.28, 139.13, 132.98, 120.42, 118.86, 89.62, 82.52, 73.34, 63.29, 61.63, 49.04, 31.84, 28.19, 26.91, 21.37, 19.37, 19.27; MS (ESI) m/z: 825.56 (M + H)+.

Diisobutyl((2S,2′S)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(3,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(3-methyl-1-oxobutane-1,2-diyl))dicarbamate (2d)

The title compound was prepared by reaction of compound C2 and Cap4 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98:2) to give a pale yellow oily product: yield 70%; 1H NMR (400 MHz, DMSO-d6): δ 9.70 (s, 2H), 8.84 (s, 2H), 7.87 (d, J = 18.1 Hz, 2H), 7.73 (d, J = 7.9 Hz, 2H), 7.37 (d, J = 8.0 Hz, 2H), 7.29 (d, J = 7.7 Hz, 2H), 4.43 (dd, J = 8.1, 2.4 Hz, 2H), 4.07 (t, J = 8.1 Hz, 2H), 3.82 (dt, J = 12.2, 6.1 Hz, 4H), 3.32 (s, 2H), 2.70 (s, 2H), 2.34–2.03 (m, 4H), 1.95 (t, J = 10.0 Hz, 8H), 0.92 (dd, J = 8.6, 4.2 Hz, 12H), 0.90–0.86 (m, 12H); 13C NMR (101 MHz, DMSO-d6): δ 171.14, 171.07, 157.29, 139.62, 129.90, 127.72, 122.90, 121.26, 121.02, 82.02, 73.64, 70.57, 60.86, 58.53, 46.22, 29.99, 28.09, 24.68, 19.42, 19.30, 18.91; MS (ESI) m/z: 825.44 (M + H)+

Dibenzyl((2S,2′S)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(4,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(3-methyl-1-oxobutane-1,2-diyl))dicarbamate (1e)

The title compound was prepared by reaction of compound C1 and Cap5 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98:2) to give a yellow oily product; yield 24%; 1H NMR (500 MHz, DMSO-d6): δ 10.33 (s, 2H), 7.65 (d, J = 8.7 Hz, 4H), 7.53 (d, J = 8.7 Hz, 4H), 7.39–7.28 (m, 12 H), 5.02 (q, J = 12.6 Hz, 4H), 4.44 (dd, J = 8.0, 5.1 Hz, 2H), 4.06 (t, J = 8.4 Hz, 2H), 3.86–3.79 (m, 2H), 3.64 (dd, J = 15.9, 6.7 Hz, 2H), 2.22–2.12 (m, 2H), 2.02–1.87 (m, 8H), 0.92 (dd, J = 27.0, 6.6 Hz, 12H); 13C NMR (126 MHz, DMSO-d6): δ 170.78, 170.28, 164.55, 140.48, 137.04, 133.21, 128.32, 127.76, 127.64, 118.88, 114.48, 81.88, 73.08, 65.36, 60.24, 57.93, 47.19, 29.79, 29.37, 24.67, 18.83; MS (ESI) m/z: 893.35 (M)+.

Dibenzyl((2S,2′S)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(3,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(3-methyl-1-oxobutane-1,2-diyl))dicarbamate (2e)

The title compound was prepared by reaction of compound C2 and Cap5 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98.5:1.5) to give a yellow oily product: yield 62%; 1H NMR (500 MHz, DMSO-d6): δ 10.05 (s, 2H), 7.71 (s, 2H), 7.41 (d, J = 8.3 Hz, 2H), 7.31 (d, J = 8.3 Hz, 2H), 7.22–7.15 (m, 10H), 7.14–7.12 (m, 2H), 7.10 (dd, J = 6.9, 5.6 Hz, 2H), 4.94–4.77 (m, 4H), 4.25 (dd, J = 8.3, 5.0 Hz, 2H), 3.88 (t, J = 8.4 Hz, 2H), 3.66–3.59 (m, 2H), 3.48–3.41 (m, 2H), 3.15 (s, 2H), 2.02–1.94 (m, 2H), 1.82–1.69 (m, 6H), 0.78–0.68 (m, 12H); 13C NMR (126 MHz, DMSO-d6): δ 173.56, 170.78, 156.20, 139.48, 137.05, 129.51, 128.31, 127.75, 127.62, 127.11, 122.50, 122.09, 120.59, 81.70, 73.15, 65.36, 60.21, 57.94, 47.19, 29.38, 24.65, 18.86, 18.55; MS (ESI) m/z: 893.31 (M + H)+.

Diethyl((2S,2′S)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(4,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(4-methyl-1-oxopentane-1,2-diyl))dicarbamate (1f)

The title compound was prepared by reaction of compound C1 and Cap6 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98:2) to give a yellow oily product; yield 23%; 1H NMR (500 MHz, DMSO-d6): δ 10.36 (s, 2H), 7.64 (d, J = 1.9 Hz, 4H), 7.53 (d, J = 8.8 Hz, 4H), 7.30 (d, J = 8.0 Hz, 2H), 4.44 (dd, J = 8.2, 4.9 Hz, 2H), 4.32–4.23 (m, 2H), 3.96 (q, J = 7.1 Hz, 4H), 3.76–3.68 (m, 2H), 3.59–3.50 (m, 2H), 2.21–2.12 (m, 2H), 2.01 (tt, J = 12.5, 6.4 Hz, 2H), 1.96–1.83 (m, 4H), 1.71–1.62 (m, 2H), 1.49–1.33 (m, 4H), 1.14 (t, J = 7.1 Hz, 6H), 0.90 (d, J = 6.6 Hz, 12H); 13C NMR (126 MHz, DMSO-d6): δ 170.80, 170.53, 156.27, 140.54, 133.19, 118.89, 114.48, 81.92, 73.08, 62.78, 60.23, 59.79, 47.20, 35.75, 29.40, 24.62, 14.71, 14.60, 10.53; MS (ESI) m/z: 797.46 (M + H)+.

Diethyl((2S,2′S)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(3,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(4-methyl-1-oxopentane-1,2-diyl))dicarbamate (2f)

The title compound was prepared by reaction of compound C2 and Cap6 according to the general procedure for compounds 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98.25:1.75) to give a yellow oily product: yield 88%; 1H NMR (500 MHz, DMSO-d6):δ 9.54 (d, J = 8.6 Hz, 2H), 7.69 (d, J = 12.2 Hz, 2H), 7.54 (d, J = 8.3 Hz, 2H), 7.20 (dd, J = 15.8, 7.9 Hz, 6H), 4.21–4.18 (m, 2H), 4.13 (s, 2H), 3.86–3.78 (m, 6H), 3.25 (d, J = 6.8 Hz, 2H), 2.12 (d, J = 12.7 Hz, 2H), 1.94 (d, J = 8.9 Hz, 2H), 1.87 (s, 2H), 1.77 (s, 6H), 1.46 (s, 2H), 1.04 (s, 6H), 0.97 (s, 12H); 13C NMR (126 MHz, DMSO-d6): δ 171.54, 171.03, 156.34, 136.13, 129.95, 129.45, 124.19, 122.41, 120.51, 76.43, 74.30, 62.49, 54.51, 51.96, 42.72, 41.98, 23.27, 23.17, 21.30, 17.63, 14.56; MS (ESI) m/z: 797.32 (M + Na)+.

Dibutyl((2S,2′S)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(4,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(4-methyl-1-oxopentane-1,2-diyl))dicarbamate (1g)

The title compound was prepared by reaction of compound C1 and Cap7 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98:2) to give a yellow oily product; yield 23%; 1H NMR (500 MHz, DMSO-d6): δ 8.81 (s, 2H), 7.62 (d, J = 8.8 Hz, 4H), 7.51 (d, J = 8.7 Hz, 4H), 7.24 (s, 2H), 4.43 (d, J = 5.1 Hz, 2H), 4.05 (t, J = 8.8 Hz, 2H), 3.91–3.80 (m, 4H), 3.07 (t, J = 7.3 Hz, 4H), 2.89–2.70 (m, 4H), 2.04 (dd, J = 48.2, 17.7 Hz, 4H), 1.89–1.84 (m, 2H), 1.48 (dd, J = 14.6, 6.7 Hz, 4H), 1.32–1.28 (m, 4H), 1.27 (d, J = 7.2 Hz, 4H), 0.85 (d, J = 5.7 Hz, 12H), 0.79 (t, J = 7.3 Hz, 6H); 13C NMR (126 MHz, DMSO-d6): δ 171.25, 171.00, 165.02, 156.56, 140.94, 133.66, 119.36, 82.33, 73.55, 64.07, 63.21, 60.71, 56.82, 31.17, 29.83, 25.09, 18.97, 15.20, 14.05, 12.22, 10.99; MS (ESI) m/z: 853.63 (M + H)+.

Dibutyl((2S,2′S)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(3,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(4-methyl-1-oxopentane-1,2-diyl))dicarbamate (2g)

The title compound was prepared by reaction of compound C2 and Cap7 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98.5:1.5) to give a pale yellow oily product: yield 25%; 1H NMR (500 MHz, DMSO-d6): δ 10.19 (s, 2H), 7.89 (s, 2H), 7.58 (d, J = 8.3 Hz, 2H), 7.38 (t, J = 8.0 Hz, 2H), 7.30–7.27 (m, 4H), 4.43 (dd, J = 8.4, 4.8 Hz, 2H), 4.31–4.24 (m, 2H), 3.92 (t, J = 6.4 Hz, 4H), 3.57–3.52 (m, 4H), 2.15 (dd, J = 13.4, 5.8 Hz, 2H), 2.05–1.99 (m, 2H), 1.96–1.85 (m, 6H), 1.52–1.49 (m, 4H), 1.42–1.34 (m, 4H), 1.22 (dd, J = 13.7, 6.6 Hz, 4H), 1.05 (t, J = 3.6 Hz, 6H), 1.04–0.99 (m, 12H); 13C NMR (126 MHz, DMSO-d6): δ 172.02, 170.87, 156.33, 139.43, 129.50, 127.13, 125.64, 122.16, 120.58, 78.85, 73.14, 65.23, 60.16, 50.67, 46.68, 45.74, 30.69, 24.67, 23.15, 21.28, 20.25, 18.53, 13.57; MS (ESI) m/z: 853.30 (M + H)+.

Diethyl((2S,2′S)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(4,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(3-methyl-1-oxopentane-1,2-diyl))dicarbamate (1h)

The title compound was prepared by reaction of compound C1 and Cap8 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98:2) to give a yellow oily product; yield 24%; 1H NMR (500 MHz, DMSO-d6): δ 10.42 (s, 2H), 7.66 (d, J = 8.8 Hz, 4H), 7.53 (d, J = 8.8 Hz, 4H), 7.32 (d, J = 8.4 Hz, 2H), 4.45 (dd, J = 8.1, 5.0 Hz, 2H), 4.07 (t, J = 8.9 Hz, 2H), 4.02–3.92 (m, 4H), 3.87–3.79 (m, 2H), 3.62 (dt, J = 13.3, 6.8 Hz, 2H), 2.20–2.11 (m, 2H), 2.05–1.97 (m, 2H), 1.92–1.83 (m, 4H), 1.71 (dt, J = 13.3, 6.5 Hz, 2H), 1.55–1.45 (m, 2H), 1.14 (t, J = 7.1 Hz, 6H), 1.12–1.06 (m, 2H), 0.90 (d, J = 6.8 Hz, 6H), 0.81 (t, J = 7.4 Hz, 6H); 13C NMR (126 MHz, DMSO-d6): δ 170.84, 170.80, 170.53, 140.54, 133.19, 118.89, 114.48, 81.92, 73.08, 60.23, 59.79, 56.32, 47.20, 38.21, 35.75, 29.40, 24.62, 14.71, 14.60, 10.53; MS (ESI) m/z: 797.43 (M)+.

Ethyl((2S,3S)-1-((S)-2-((3-((3-((S)-1-((ethoxycarbonyl)-l-alloisoleucyl)pyrrolidine-2-carboxamido)phenyl)buta-1,3-diyn-1-yl)phenyl)carbamoyl)pyrrolidin-1-yl)-3-methyl-1-oxopentan-2-yl)carbamate (2h)

The title compound was prepared by reaction of compound C2 and Cap8 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98:2) to give a yellow oily product: yield 60%; 1H NMR (500 MHz, DMSO-d6): δ 10.04 (s, 2H), 7.72 (s, 2H), 7.40 (ddd, J = 8.3, 2.1, 1.1 Hz, 2H), 7.19 (t, J = 7.9 Hz, 2H), 7.11–7.08 (m, 4H), 4.24 (dd, J = 8.0, 5.0 Hz, 2H), 3.88 (dd, J = 19.3, 10.5 Hz, 2H), 3.67 (dd, J = 13.5, 7.4 Hz, 4H), 3.43 (t, J = 6.8 Hz, 2H), 3.04 (t, J = 7.4 Hz, 2H), 2.57–2.55 (m, 2H), 2.36–2.34 (m, 2H), 1.98 (dd, J = 12.8, 8.7 Hz, 2H), 1.85–1.79 (m, 2H), 1.72–1.69 (m, 2H), 1.56 (dd, J = 8.5, 4.4 Hz, 4H), 1.00 (s, 12H), 0.97 (s, 6H); 13C NMR (126 MHz, DMSO-d6): δ 173.36, 170.78, 156.38, 139.49, 129.51, 128.89, 127.10, 122.09, 120.59, 75.40, 73.15, 68.84, 59.79, 58.39, 56.33, 45.74, 38.20, 29.37, 24.62, 15.56, 14.58, 8.60; MS (ESI) m/z: 797.36 (M + H)+.

Dibutyl((2S,2′S)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(4,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(3-methyl-1-oxopentane-1,2-diyl))dicarbamate (1i)

The title compound was prepared by reaction of compound C1 and Cap9 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98:2) to give a yellow oily product; yield 24%; 1H NMR (400 MHz, DMSO-d6): δ 8.84 (s, 2H), 7.65 (d, J = 8.8 Hz, 4H), 7.53 (d, J = 8.7 Hz, 4H), 7.27 (s, 2H), 4.45 (d, J = 5.1 Hz, 2H), 4.08 (t, J = 8.8 Hz, 2H), 3.90 (s, J = 10.8, 6.7 Hz, 4H), 3.67–3.59 (m, 2H), 3.09 (t, J = 7.3 Hz, 6H), 2.16 (s, 2H), 1.99 (t, J = 9.5 Hz, 2H), 1.92–1.86 (m, 2H), 1.50 (dd, J = 14.6, 6.7 Hz, 4H), 1.34–1.30 (m, 4H), 1.30 (d, J = 7.2 Hz, 4H), 0.88 (d, J = 5.7 Hz, 6H), 0.82 (t, J = 7.3 Hz, 12H); 13C NMR (101 MHz, DMSO-d6): δ 171.25, 171.00, 165.02, 140.94, 133.66, 119.36, 114.99, 82.33, 73.55, 64.07, 63.21, 60.71, 56.82, 31.17, 29.83, 25.09, 18.97, 15.20, 14.05, 12.22, 10.99, 9.02; MS (ESI) m/z: 853.59 (M + H)+.

Butyl((2S,3S)-1-((S)-2-((3-((3-((S)-1-((butoxycarbonyl)-l-alloisoleucyl)pyrrolidine-2-carboxamido)phenyl)buta-1,3-diyn-1-yl)phenyl)carbamoyl)pyrrolidin-1-yl)-3-methyl-1-oxopentan-2-yl)carbamate (2i)

The title compound was prepared by reaction of compound C2 and Cap9 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98.75:1.25) to give a yellow oily product: yield 66%; 1H NMR (500 MHz, DMSO-d6): δ 10.03–10.03 (m, 2H), 7.72 (s, 4H) 7.41–7.41 (m, 2H), 7.39 (s, 2H), 7.26 (d, J = 2.9 Hz, 2H), 4.24–4.23 (m, 4H), 3.66–3.64 (m, 6H), 3.42–3.41 (m, 2H), 2.36 (s, 2H), 2.17 (d, J = 1.9 Hz, 2H), 1.98–1.97 (m, 4H), 1.77 (s, 2H), 1.32 (s, 12H), 1.04 (dd, J = 5.7, 4.0 Hz, 6H), 0.85 (s, 12H); 13C NMR (126 MHz, DMSO-d6): δ 172.73, 170.28, 156.72, 139.31, 128.50, 127.71, 124.05, 123.21, 120.59, 84.03, 77.71, 63.36, 58.61, 56.49, 45.74, 33.06, 30.70, 24.67, 24.33, 19.75, 18.52, 13.55, 8.59; MS (ESI) m/z: 853.31 (M + H)+.

Diethyl((2S,2′S)-((2R,2′R)-(((buta-1,3-diyne-1,4-diylbis(4,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(3-methyl-1-oxobutane-1,2-diyl))dicarbamate (1j)

The title compound was prepared by reaction of compound C3 and Cap2 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98:2) to give a yellow oily product; yield 26%; 1H NMR (400 MHz, DMSO-d6): δ 10.01 (s, 2H), 7.67 (d, J = 8.7 Hz, 4H), 7.53 (d, J = 8.8 Hz, 4H), 7.14 (s, 2H), 3.98 (t, J = 7.1 Hz, 2H), 3.81 (d, J = 2.5 Hz, 2H), 3.40–3.32 (m, 4H), 3.25 (dd, J = 14.5, 7.3 Hz, 4H), 2.88 (d, J = 3.3 Hz, 2H), 2.67–2.59 (m, 4H), 2.07–2.01 (m, 4H), 1.32 (t, J = 7.3 Hz, 6H), 0.88 (d, J = 6.9 Hz, 12H); 13C NMR (101 MHz, DMSO-d6): δ 173.96, 170.73, 164.91, 133.33, 126.01, 110.73, 103.81, 89.24, 85.07, 72.24, 60.10, 56.57, 47.59, 30.46, 30.19, 27.11, 19.78, 14.90; MS (ESI) m/z: 769.35 (M)+.

Diethyl((2S,2′S)-((2R,2′R)-(((buta-1,3-diyne-1,4-diylbis(3,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(3-methyl-1-oxobutane-1,2-diyl))dicarbamate (2j)

The title compound was prepared by reaction of compound C4 and Cap2 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 97:3) to give a yellow oily product: yield 70%; 1H NMR (500 MHz, DMSO-d6): δ 9.57 (s, 2H), 7.76 (s, 2H), 7.68 (d, J = 16.1 Hz, 2H), 7.53 (d, J = 7.8 Hz, 2H), 7.18 (dd, J = 16.7, 8.4 Hz, 4H), 4.22 (d, J = 8.6 Hz, 2H), 3.79 (s, 6H), 3.64 (d, J = 2.4 Hz, 2H), 3.43 (d, J = 9.4 Hz, 2H), 2.70–2.70 (m, 2H), 2.54 (s, 2H), 1.83 (dt, J = 13.4, 6.8 Hz, 6H), 0.72 (d, J = 6.7 Hz, 6H), 0.70 (d, J = 4.3 Hz, 12H); 13C NMR (126 MHz, DMSO-d6): δ 173.30, 170.52, 156.47, 139.19, 129.47, 128.69, 125.41, 122.64, 120.71, 77.73, 73.13, 61.87, 59.79, 57.99, 47.75, 29.46, 24.26, 19.14, 17.99, 14.59; MS (ESI) m/z: 769.32 (M + H)+.

Diethyl((2R,2′R)-((2R,2′R)-(((buta-1,3-diyne-1,4-diylbis(4,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(3-methyl-1-oxobutane-1,2-diyl))dicarbamate (1k)

The title compound was prepared by reaction of compound C3 and Cap10 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98:2) to give a yellow oily product; 26%; 1H NMR (400 MHz, DMSO-d6): δ 7.64 (d, J = 8.8 Hz, 4H), 7.53 (d, J = 8.7 Hz, 4H), 4.68–4.63 (m, 2H), 4.39 (s, 2H), 3.99 (q, J = 7.1 Hz, 4H), 3.84–3.78 (m, 4H), 3.25–3.16 (m, 2H), 2.90–2.86 (m, 4H), 2.04–2.00 (m, 4H), 1.32 (t, J = 7.3 Hz, 6H), 0.88 (d, J = 3.7 Hz, 12H); 13C NMR (101 MHz, DMSO-d6): δ 173.96, 170.71, 164.91, 144.43, 133.34, 130.19, 119.47, 89.94, 86.09, 60.10, 58.69, 56.95, 47.19, 30.19, 24.67, 19.48, 18.06, 15.32; MS (ESI) m/z: 769.40 (M)+.

Diethyl((2R,2′R)-((2R,2′R)-(((buta-1,3-diyne-1,4-diylbis(3,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(3-methyl-1-oxobutane-1,2-diyl))dicarbamate (2k)

The title compound was prepared by reaction of compound C4 and Cap10 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 97.5:2.5) to give a yellow oily product: yield 44%; 1H NMR (500 MHz, DMSO-d6): δ 10.04 (s, 2H), 7.71 (s, 2H), 7.40 (dd, J = 5.2, 4.1 Hz, 2H), 7.19 (t, J = 7.9 Hz, 2H), 7.10 (dd, J = 5.3, 3.8 Hz, 2H), 7.05 (s, 2H), 4.26–4.22 (m, 2H), 3.79 (d, J = 2.6 Hz, 6H), 3.63 (d, J = 2.6 Hz, 2H), 3.45–3.43 (m, 2H), 2.71–2.69 (m, 2H), 2.54 (dd, J = 5.9, 0.6 Hz, 2H), 1.97 (s, 2H), 1.85–1.82 (m, 4H), 0.70 (s, 6H), 0.68 (d, J = 1.5 Hz, 12H); 13C NMR (126 MHz, DMSO-d6): δ 173.38, 170.39, 156.48, 139.81, 129.66, 128.44, 122.59, 122.07, 121.06, 80.52, 72.46, 59.78, 59.43, 45.71, 38.21, 29.49, 26.99, 19.15, 17.99, 14.59; MS (ESI) m/z: 769.38 (M + Na)+.

Diethyl((2S,2′S)-((2R,2′R)-(((buta-1,3-diyne-1,4-diylbis(4,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(4-methyl-1-oxopentane-1,2-diyl))dicarbamate (1l)

The title compound was prepared by reaction of compound C3 and Cap6 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98:2) to give a yellow oily product; yield 26%; 1H NMR (400 MHz, DMSO-d6): δ 8.74–8.67 (m, 2H), 7.64 (d, J = 8.8 Hz, 4H), 7.53 (d, J = 8.7 Hz, 4H), 7.22 (s, 2H), 4.49–4.21 (m, 2H), 4.01–3.94 (m, 6H), 3.44 (d, J = 70.2 Hz, 4H), 2.98–2.76 (m, 4H), 2.25–1.86 (m, 4H), 1.73 (d, J = 9.0 Hz, 2H), 1.49–1.39 (m, 4H), 1.34 (t, J = 7.3 Hz, 6H), 0.89–0.84 (m, J = 7.2 Hz, 12H); 13C NMR (101 MHz, DMSO-d6): δ 171.31, 174.99, 164.91, 133.64, 128.13, 119.09, 115.29, 77.75, 60.09, 54.20, 52.77, 47.91, 46.22, 36.95, 24.99, 23.25, 21.69, 21.52, 14.58; MS (ESI) m/z: 797.44 (M + H)+.

Diethyl((2S,2′S)-((2R,2′R)-(((buta-1,3-diyne-1,4-diylbis(3,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(4-methyl-1-oxopentane-1,2-diyl))dicarbamate (2l)

The title compound was prepared by reaction of compound C4 and Cap6 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 97.5:2.5) to give a yellow oily product: yield 68%; 1H NMR (500 MHz, DMSO-d6): δ 10.00 (s, 2H), 7.76 (s, 2H), 7.70 (t, J = 1.8 Hz, 2H), 7.41–7.38 (m, 2H), 7.10 (d, J = 8.8 Hz, 4H), 4.24 (dd, J = 8.4, 4.9 Hz, 2H), 4.10 (d, J = 8.2 Hz, 2H), 3.78 (q, J = 7.1 Hz, 4H), 3.53 (t, J = 8.1 Hz, 2H), 3.40–3.34 (m, 2H), 2.54 (s, 2H), 1.98 (dd, J = 12.1, 7.9 Hz, 2H), 1.83 (dd, J = 12.8, 6.1 Hz, 2H), 1.73 (ddd, J = 17.1, 12.2, 5.6 Hz, 4H), 1.48 (s, 2H), 1.30–1.25 (m, 2H), 1.04 (t, J = 7.3 Hz, 6H), 0.71 (t, J = 5.5 Hz, 12H); 13C NMR (126 MHz, DMSO-d6): δ 174.29, 169.44, 156.22, 140.12, 130.27, 127.12, 125.76, 124.16, 120.62, 79.80, 75.18, 62.47, 59.72, 51.94, 43.55, 42.30, 24.08, 23.16, 21.30, 18.74, 8.62; MS (ESI) m/z: 797.36 (M + Na)+.

Diethyl((2R,2′R)-((2R,2′R)-(((buta-1,3-diyne-1,4-diylbis(4,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(4-methyl-1-oxopentane-1,2-diyl))dicarbamate (1m)

The title compound was prepared by reaction of compound C3 and Cap11 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98:2) to give a yellow oily product; yield 26%; 1H NMR (400 MHz, DMSO-d6): δ 7.64 (d, J = 8.7 Hz, 4H), 7.52 (d, J = 8.7 Hz, 4H), 3.93–3.90 (m, J = 7.1 Hz, 8H), 2.90–2.85 (m, 4H), 2.53 (t, J = 7.5 Hz, 4H), 2.24–1.86 (m, 4H), 1.76–1.69 (m, 2H), 1.51 (dd, J = 10.1, 5.1 Hz, 4H), 1.33 (t, J = 7.2 Hz, 6H), 0.92–0.84 (m, 12H); 13C NMR (101 MHz, DMSO-d6): δ 174.98, 171.03, 164.91, 140.66, 133.64, 120.49, 119.48, 84.35, 73.25, 60.11, 53.77, 47.08, 46.18, 38.61, 24.66, 23.25, 21.51, 16.65, 14.91; MS (ESI) m/z: 797.36 (M + H)+.

Diethyl((2R,2′R)-((2R,2′R)-(((buta-1,3-diyne-1,4-diylbis(3,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(4-methyl-1-oxopentane-1,2-diyl))dicarbamate (2m)

The title compound was prepared by reaction of compound C4 and Cap11 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 97.5:2.5) to give a yellow oily product: yield 69%; 1H NMR (500 MHz, DMSO-d6): δ 10.00 (s, 2H), 7.70 (s, 2H), 7.51 (dt, J = 16.1, 4.6 Hz, 2H), 7.40 (d, J = 8.1 Hz, 2H), 7.19 (t, J = 7.9 Hz, 2H), 7.11 (s, 2H), 4.26–4.22 (m, 2H), 4.09 (s, 2H), 3.77 (t, J = 7.1 Hz, 4H), 3.52 (s, 2H), 3.36 (s, 2H), 2.54 (d, J = 0.6 Hz, 2H), 1.99 (s, 2H), 1.82 (s, 2H), 1.80–1.65 (m, 6H), 1.28 (s, 2H), 1.11 (t, J = 7.3 Hz, 6H), 1.05 (d, J = 7.2 Hz, 12H); 13C NMR (126 MHz, DMSO-d6): δ 171.72, 170.41, 156.01, 137.68, 127.70, 127.14, 126.91, 124.19, 120.58, 79.22, 75.34, 67.89, 61.11, 51.96, 49.01, 38.21, 29.20, 24.67, 23.16, 21.29, 14.60; MS (ESI) m/z: 797.33 (M + Na)+.

Diethyl((2R,2′R)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(4,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(3-methyl-1-oxobutane-1,2-diyl))dicarbamate (1n)

The title compound was prepared by reaction of compound C1 and Cap10 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98:2) to give a yellow oily product; yield 23%; 1H NMR (500 MHz, DMSO-d6): δ 10.02 (s, 2H), 7.66 (d, J = 8.7 Hz, 4H), 7.54 (d, J = 8.3 Hz, 4H), 7.29 (d, J = 8.8 Hz, 2H), 4.48–4.37 (m, 2H), 4.13–4.06 (m, 2H), 4.04–3.91 (m, 4H), 3.83–3.42 (m, 4H), 3.19–2.67 (m, 2H), 2.23–2.02 (m, 4H), 2.00–1.88 (m, 4H), 1.17–1.13 (m, 6H), 0.88 (t, J = 7.3 Hz, 12H); 13C NMR (126 MHz, DMSO-d6): δ 170.78, 170.29, 156.50, 140.28, 133.14, 118.99, 114.63, 81.86, 73.12, 60.29, 59.97, 57.87, 46.96, 29.64, 29.31, 24.31, 19.02, 14.54; MS (ESI) m/z: 769.54 (M)+.

Diethyl((2R,2′R)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(3,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(3-methyl-1-oxobutane-1,2-diyl))dicarbamate (2n)

The title compound was prepared by reaction of compound C2 and Cap10 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98.25:1.75) to give a yellow oily product: yield 48%; 1H NMR (500 MHz, DMSO-d6): δ 9.75 (s, 2H), 7.85 (s, 2H), 7.72 (d, J = 8.5 Hz, 2H), 7.37 (dd, J = 16.3, 8.3 Hz, 4H), 7.29 (d, J = 7.6 Hz, 2H), 4.44–4.37 (m, 2H), 4.07–3.98 (m, 6H), 3.82 (s, 2H), 3.62 (d, J = 9.5 Hz, 2H), 3.07 (s, 2H), 2.50–2.50 (m, 4H), 2.13 (d, J = 8.5 Hz, 2H), 1.94 (s, 2H), 1.16 (s, 6H), 0.89 (dd, J = 13.4, 6.7 Hz, 12H); 13C NMR (126 MHz, DMSO-d6): δ 174.39, 171.66, 156.20, 138.21, 129.48, 127.20, 125.57, 123.18, 120.29, 76.79, 72.12, 62.48, 60.06, 51.96, 45.73, 31.84, 26.30, 24.23, 21.61, 8.63; MS (ESI) m/z: 769.32 (M + Na)+.

Dibenzyl((2S,2′S)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(4,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(4-methyl-1-oxopentane-1,2-diyl))dicarbamate (1o)

The title compound was prepared by reaction of compound C1 and Cap12 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98:2) to give a yellow oily product; yield 23%; 1H NMR (400 MHz, DMSO-d6): δ 8.53 (s, 2H), 7.65 (d, J = 8.8 Hz, 4H), 7.52 (d, J = 8.7 Hz, 4H), 7.34 (d, J = 4.5 Hz, 12H), 5.01 (s, 4H), 4.45 (d, J = 7.6 Hz, 2H), 4.30 (s, 2H), 3.54 (s, 4H), 2.11 (d, J = 40.9 Hz, 4H), 1.88 (s, 2H), 1.70 (s, 4H), 1.50–1.38 (m, 4H), 0.90 (d, J = 6.5 Hz, 12H); 13C NMR (101 MHz, DMSO-d6): δ 170.79, 170.40, 162.52, 153.23, 137.14, 133.19, 128.32, 127.76, 127.63, 122.25, 118.90, 87.12, 73.08, 65.37, 62.79, 52.44, 51.65, 35.78, 29.42, 24.61, 21.65, 14.37; MS (ESI) m/z: 921.43 (M + H)+.

Dimethyl((2S,2′S)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(3,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(4-methyl-1-oxopentane-1,2-diyl))dicarbamate (2o)

The title compound was prepared by reaction of compound C2 and Cap13 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 99.75:0.25) to give a pale yellow oily product: yield 6.5%; 1H NMR (500 MHz, DMSO-d6): δ 7.74–7.73 (m, 4H), 7.73–7.72 (m, 4H), 7.37 (d, J = 1.2 Hz, 2H), 7.34 (d, J = 1.2 Hz, 2H), 7.29 (d, J = 1.2 Hz, 2H), 7.27 (d, J = 1.2 Hz, 2H), 3.60 (d, 6H), 3.37 (s, 4H), 3.31 (s, 2H), 3.29 (s, 2H), 2.64–2.62 (m, 4H), 2.37–2.35 (m, 4H), 1.23 (s, 12H), 1.16–1.12 (m, 2H); 13C NMR (126 MHz, DMSO-d6): δ 175.63, 170.47, 158.57, 139.38, 128.28, 127.23, 124.58, 121.96, 119.69, 87.98, 81.32, 59.16, 55.19, 45.61, 42.25, 41.33, 23.13, 21.79, 20.62, 19.84; MS (ESI) m/z: 769.2 (M + H)+.

Dibenzyl((2S,2′S)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(4,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(3-methyl-1-oxopentane-1,2-diyl))dicarbamate (1p)

The title compound was prepared by reaction of compound C1 and Cap14 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98:2) to give a yellow oily product: yield 24%; 1H NMR (500 MHz, DMSO-d6): δ 10.47 (s, 2H), 7.66 (d, J = 8.7 Hz, 4H), 7.53 (d, J = 8.7 Hz, 4H), 7.39–7.23 (m, 12H), 5.01 (dt, J = 22.1, 8.3 Hz, 4H), 4.46 (dd, J = 8.1, 4.9 Hz, 2H), 4.10 (t, J = 8.9 Hz, 2H), 3.88–3.78 (m, 2H), 3.68–3.59 (m, 2H), 2.17 (d, J = 5.2 Hz, 2H), 1.94–1.83 (m, 4H), 1.73 (d, J = 9.1 Hz, 2H), 1.50 (d, J = 7.6 Hz, 2H), 1.15–1.07 (m, 4H), 0.92 (t, J = 8.0 Hz, 6H), 0.81 (t, J = 7.4 Hz, 6H); 13C NMR (126 MHz, DMSO-d6): δ 170.84, 170.40, 165.25, 143.79, 140.49, 133.15, 128.38, 127.73, 127.51, 122.20, 118.90, 86.98, 73.12, 65.26, 62.81, 52.39, 35.73, 33.23, 29.42, 24.65, 23.04, 21.66, 11.24; MS (ESI) m/z: 921.50 (M + H)+.

Dimethyl((2R,2′R)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(3,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(4-methyl-1-oxopentane-1,2-diyl))dicarbamate (2p)

The title compound was prepared by reaction of compound C2 and Cap15 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 97.5:2.5) to give a pale yellow oily product: yield 15%; 1H NMR (400 MHz, DMSO-d6): δ 8.85 (s, 4H), 7.88 (s, 2H), 7.65 (t, J = 8.4 Hz, 2H), 7.42–7.36 (m, 2H), 7.34–7.26 (m, 2H), 4.38–4.29 (m, 2H), 3.54–3.49 (m, 8H), 3.43 (t, J = 7.2 Hz, 2H), 1.95 (d, J = 4.0 Hz, 4H), 1.48 (dd, J = 14.1, 10.2 Hz, 2H), 1.24–1.20 (m, 6H), 1.03 (dd, J = 12.0, 5.0 Hz, 2H), 0.99–0.95 (m, 2H), 0.90–0.84 (m, 8H), 0.84–0.81 (m, 2H), 0.70 (d, J = 6.3 Hz, 2H); 13C NMR (101 MHz, DMSO-d6): δ 171.40, 171.16, 157.21, 139.72, 129.98, 129.90, 124.02, 122.92, 121.02, 82.07, 73.56, 60.97, 52.44, 47.15, 46.22, 38.68, 24.58, 23.62, 21.77, 20.94; MS (ESI) m/z: 769.38 (M + H)+.

Diethyl((2R,2′R)-((2S,2′S)-(((buta-1,3-diyne-1,4-diylbis(3,1-phenylene))bis(azanediyl))bis(carbonyl))bis(pyrrolidine-2,1-diyl))bis(4-methyl-1-oxopentane-1,2-diyl))dicarbamate (2q)

The title compound was prepared by reaction of compound C2 and Cap11 according to the general procedure for compound 1a–2q synthesis. The product was purified by CC (CH2Cl2/MeOH 98.25:1.75) to give a yellow oily product: yield 88%; 1H NMR (500 MHz, DMSO-d6): δ 9.73 (d, J = 8.0 Hz, 2H), 7.87 (s, 2H), 7.72 (s, 2H), 7.39 (dd, J = 17.1, 9.0 Hz, 6H), 4.38 (d, J = 7.6 Hz, 2H), 4.32 (s, 2H), 3.52 (s, 4H), 3.44 (s, 4H), 2.34–2.24 (m, 2H), 2.12 (s, 2H), 2.08–2.02 (m, 2H), 1.85–1.81 (m, 2H), 1.50 (s, 4H), 1.36 (s, 2H), 1.21 (s, 6H), 0.89 (dd, J = 6.6, 2.8 Hz, 12H); 13C NMR (126 MHz, DMSO-d6): δ 171.65, 170.30, 155.03, 139.70, 131.53, 130.57, 126.03, 123.69, 122.05, 78.18, 75.58, 62.48, 51.96, 50.22, 45.74, 41.47, 28.92, 23.92, 23.17, 21.30, 14.56; MS (ESI) m/z: 797.32 (M + Na)+.

Biological Assays

Cell Culture

The Huh5-2[26] stable cell line harbors the subgenomic HCV 1b reporter replicon I389luc-ubi-neo/NS3-3′/Con1/5.1 (strain Con1). Huh7.5-3a and Huh7.5-4a cells harbor the subgenomic replicons S52-SG (Feo) (AII) and ED43-SG (Feo) (VYG) (kindly provided by C.M. Rice, The Rockefeller University, NY)[27] of HCV 3a (strain S52) and 4a (strain ED43), respectively.[28]

Cells were cultured using Dulbecco’s modified minimum essential medium with high glucose (25 mM) (Invitrogen), supplemented with 2 mM l-glutamine, 0.1 mM nonessential amino acids, 100 U/mL penicillin, 100 μg/mL streptomycin, 10% (v/v) fetal calf serum [complete Dulbecco’s modified eagle medium (DMEM)], and either 500 μg/mL G418 for Huh5-2, 750 μg/mL G418 for Huh7.5-3a, or 350 μg/mL G418 for Huh7.5-4a.

Cell-Based Antiviral Assays

Viral replication was determined by measuring F-Luc activity in replicon cells seeded 104 per well in a 96-well plate, cultured with G418 in complete DMEM for 24 h at 37 °C (5% CO2), and further incubated in the presence of serial dilutions of the compounds, or their solvent DMSO, in a total volume of 100 μL in complete DMEM without G418. Three days post-treatment, cells were lysed and F-Luc activity was quantified and expressed as relative units of luminescence (RLU) per μg of total protein. The compound concentration that reduces luciferase expression by 50% (median effective concentration—EC50) was determined after conversion of drug concentrations to log X and nonlinear regression analysis (Prism 5.0 software, GraphPad Software Inc.).

Luciferase and Bradford Assays

F-Luc measurement in cell lysates was performed with a chemiluminescent assay kit (Promega) in accordance to manufacturer’s instructions, in a GloMax 20/20 single tube luminometer (Promega) for 10 s. F-Luc activity levels were normalized to total intracellular protein amounts as determined by Bradford assay (Pierce).

Cytotoxicity Assay

The effect of the compounds on cell viability was evaluated by quantifying intracellular ATP levels in cells seeded 104 per well in a 96-well plate, cultured in complete DMEM for 24 h, and further incubated with the compounds or their solvent DMSO. Three days post-treatment, cells were lysed and ATP was measured. The compound concentration causing 50% cell death (CC50) was calculated after conversion of drug concentration to log X and nonlinear regression analysis (Prism 5.0 software, GraphPad Software Inc.).

Measurement of Intracellular ATP Levels

ATP levels were determined using the ViaLight HS chemiluminescence-based assay kit (Lonza) in accordance to the manufacturer’s instructions, in a GloMax 20/20 single-tube luminometer (Promega) for 1 s, and normalized to total intracellular protein amounts (Bradford assay, Pierce).

Indirect Immunofluorescence

Indirect immunofluorescence for Con1 NS5A was carried out as previously described.[29] DNA staining was performed using PI (Sigma-Aldrich). Images were obtained using the Leica TCS-SP5II Two-photon Confocal Microscope with Spectra Physics Mai Tai infrared laser source.

Total RNA Extraction and HCV RNA Quantification

Total RNA from Huh5-2 cells was extracted using the TRIzol reagent (Ambion), according to the manufacturer’s instructions. HCV RNA levels were determined with RT and qPCR. RT reaction was performed using Moloney murine leukemia virus reverse transcriptase (Promega) and the reverse primer 5′-GGATTCGTGCTCATGGTGCA-3′ specific for Con1 IRES (IRES-R). qPCR reactions were carried out using KAPA SYBR FAST qPCR Master Mix (Kapa Biosystems) and the Con1 IRES specific primers IRES-F (5′-GGCCTTGTGGTACTGCCTGATA-3′) and IRES-R. The housekeeping gene YWHAZ was used for normalization (primers 5′-GCTGGTGATGACAAGAAAGG-3′ and 5′-GGATGTGTTGGTTGCATTTCCT-3′).

Statistical Analysis

Statistical analysis was performed using Student’s t-test in Excel Microsoft Office. Only results with p ≤ 0.05 were considered as statistically significant and shown.