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Article

Thienyl-Based Amides of M2 and Neuraminidase Inhibitors: Synthesis, Structural Characterization, and In Vitro Antiviral Activity Against Influenza a Viruses

1
Faculty of Mathematics and Natural Sciences, South-West University ‘‘Neofit Rilski’’, Ivan Mihailov Str. 66, 2700 Blagoevgrad, Bulgaria
2
Institute of Mineralogy and Crystallography “Acad. Ivan Kostov”, Bulgarian Academy of Sciences, Acad. G. Bonchev Bl. 107, 1113 Sofia, Bulgaria
3
Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Tiantan Xili, Beijing 100050, China
4
Institute of Neurobiology, Bulgarian Academy of Sciences, Acad. G. Bonchev Bl. 23, 1113 Sofia, Bulgaria
5
Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna Pot 113, 1000 Ljubljana, Slovenia
6
Section of Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12843 Prague, Czech Republic
*
Author to whom correspondence should be addressed.
Crystals 2025, 15(9), 772; https://doi.org/10.3390/cryst15090772
Submission received: 31 July 2025 / Revised: 23 August 2025 / Accepted: 24 August 2025 / Published: 29 August 2025
(This article belongs to the Special Issue Celebrating the 10th Anniversary of International Crystallography)

Abstract

Influenza A viruses that cause pandemics, as well as other harmful pathogens (e.g., SARS-CoV-2 variants), are known as the ‘silent bioterrorists’ of the 21st century. Due to high mutability, anti-influenza chemotherapeutic treatment is a vital defense strategy to combat both seasonal and pandemic influenza strains, especially when vaccines fail. Consequently, the development of novel therapies to combat this serious threat is of great concern. Hence, in this study, 3-(2-thienyl) acrylic acid (TA) was converted into amides of anti-influenza drugs (aminoadamantanes and oseltamivir) through TBTU-mediated coupling. The crystal structures of the thienyl-based amide hybrids (TA-Am (1), TA-Rim (2), TA-Os-OEt (3), and TA-OsC (4)) were also investigated using single-crystal X-ray diffraction, powder X-ray diffraction (PXRD), and differential scanning calorimetry (DSC). Moreover, the antiviral activities of the hybrids against influenza virus A/Fort Monmouth/1/1947 (H1N1), clinically isolated influenza strain A/Wuhan/359/1995 (H3N2), and oseltamivir-resistant A/Jinnan/15/2009 (H1N1) were evaluated in vitro. Amongst the tested thienyl-based amides, bisamide 8 (Boc-Os-Hda-TA) exhibited the most potent activity against influenza virus A (A/Wuhan/359/1995) with an IC50 value of 18.52 μg/mL and a selectivity index (SI) = 13.0.

1. Introduction

Human influenza, being a severe viral respiratory ailment, is caused by three types of influenza viruses, categorized as A, B, and C, representing the genus Orthomyxovirus [1]. It still remains a global challenge, characterized by yearly epidemics and sporadic pandemics [2,3], posing significant difficulties that need to be controlled. Currently, influenza A and B viruses contribute to seasonal epidemics, but only influenza A viruses are known to induce pandemics [4,5]. Both influenza epidemics and pandemics arise from antigenic variabilities and mutations of the influenza A virus genome, particularly through antigenic drift and antigenic shift [6,7]. These evolutionary mechanisms facilitate the virus’s avoidance of host immunity, contributing to widespread transmission and substantial medical and economic burdens worldwide [8]. On a global scale, seasonal influenza (the flu) annually contributes to approximately 650,000 respiratory deaths [9,10], while almost 60 million deaths have occurred due to influenza pandemics [11]. Over the past century, there have been five major influenza pandemics: the ‘Spanish flu’ (H1N1) in 1918, the ‘Asian flu’ (H2N2) in 1957, the 1968 ‘Hong Kong flu’ (H3N2), the 1977 ‘Russian flu’, and the most recent one in 2009—the swine-origin H1N1 pandemic (H1N1pdm09) [12,13,14,15,16,17]. Moreover, it has been estimated that the deadliest 1918 flu pandemic killed about seven times more individuals than the number of confirmed deaths from the COVID-19 pandemic [18].
Despite the essential progress that has been made in medical diagnostics and chemotherapies since the 1918 pandemic, the persistent fear of occasionally severe influenza pandemics has driven experts to intensify research efforts aimed at developing effective antivirals and other therapeutic strategies against influenza A virus infections. Two antiviral strategies are currently used against influenza viruses—vaccination and chemotherapy [19,20]. The limitations of the current vaccines are related to reduced efficacy in high-risk groups—infants and the elderly, as well as immunocompromised patients. Additionally, the development of an effective influenza vaccine resembling circulating strains usually requires at least six months to be accomplished [21], but sometimes, a mismatch between circulating strains and vaccine strains may occur. For instance, the World Health Organization (WHO) reported that the average efficacy of the influenza vaccine in 2017 was only 20% [22]. Thus, existing viral chemotherapy offers a better approach for the management of influenza, especially for alleviating clinical symptoms after infection and for reducing severe complications and mortality. Currently, three main classes of antiviral medications have been endorsed and applied in clinical management of influenza: M2 ion channel blockers (e.g., aminoadamantanes: amantadine hydrochloride (Am.HCl) and rimantadine hydrochloride (Rim.HCl)), neuraminidase inhibitors (e.g., oseltamivir phosphate (OsP; Tamiflu®), zanamivir (Relenza®), and peramivir (Rapivab)), and RNA-dependent RNA polymerase (RdRp) inhibitors (e.g., favipiravir) [23]. While M2 inhibitors are solely active against influenza A viruses, neuraminidase inhibitors (NAIs) have an influence against both influenza A and B viruses [24]. Additionally, M2 ion channel blockers disrupt the acidification of the inner medium of the virion, which is a crucial step in the viral uncoating process, and thus suppress the influenza infection process [25,26,27]. Unlike the mechanism of neuraminidase (NA) enzyme activity inhibition that involves competitive binding of NA inhibitors with sialic acid to the active site of the enzyme, the release and subsequent transmission of progeny virions to uninfected host cells are limited due to the suppression of sialic acid hydrolysis [28,29,30]. For over 15 years, NAIs have been among the most recommended by the WHO as antiviral drugs for the treatment of influenza A and B viruses [31].
Given the restricted availability of current antiviral agents, there is a crucial need for the design of novel, more potent compounds able to overcome influenza drug resistance.
Various studies have demonstrated that promising alternatives to anti-influenza strategies may be nature-derived therapies, including plants [32,33,34] or mushrooms [35,36], since nature is the oldest invaluable source of bioactive compounds and drugs [37]. Another possible approach to “resurrect” the antiviral activity of resistance classes is to tailor them with active skeletons, e.g., amino acid moieties and heterocycles [38,39,40], which would make it possible to disrupt the proton transport by the virus membrane. On the other hand, the S-heterocyclic core (thiophene) represents a small pharmacophore that ranks fourth in drug approval rankings by the United States Food and Drug Administration, along with around seven drug licenses for the last ten years [41,42]. Moreover, thiophene-containing compounds pose a great concern in the medical field due to their considerable diversity in biological properties, including antimicrobial [43], anticancer [44], antioxidant [45], and others. Recent research highlights the findings of a series of thiophene derivatives with potential anti-influenza activities [46]. In addition, Zhong et al. [47] designed several potent NA inhibitors by using the lead thiophene template, among which one compound demonstrated excellent antiviral activity against A/chicken/Hubei/327/2004 (H5N1-DW), surpassing the reference drug oseltamivir carboxylate.
Following influenza as a global health priority and in line with our ongoing project, thiophene heterocycle was chosen herein for the modification of influenza virus inhibitors, namely M2 ion blockers as well as neuraminidase inhibitors, in order to obtain lead structures that will be able to hit influenza targets (NA or M2).

2. Materials and Methods

2.1. General Remarks

Thin-layer chromatography (TLC) was performed on precoated Kieselgel 60F254 plates (Merck, Darmstadt, Germany), with detection by UV absorption (λ = 254 nm). A spray Ce-PMo reagent, consisting of 10 g Ce (SO4)2, 25 g H3[P(Mo3O10)4] × H2O, 940 mL H2O, and 60 mL conc. H2SO4, was used for TLC visualization. Flash chromatography of the target amide was performed on a Pure C-805 system (BÜCHI GmbH) using FlashPure EcoFlex Flash Chromatography Cartridges.
All solvents, N-Boc-1,6-hexanediamine hydrochloride (Boc-Hda.HCl), were products from Thermo Fisher Scientific, Sofia, Bulgaria, while the TBTU reagent (N-[(1H-benzotriazol-1-yl)(dimethylamino)methylene]-N-methylmethanaminium tetrafluoroborate N-oxide) and 3-(2-thienyl)acrylic acid (TA) were products from BLDpharm. Oseltamivir phosphate (OP, NICPBP, lot number 101096-200901), OsC (Medchem, Princeton, NJ, USA), and Am.HCl (Sigma, lot number 665-66-7) were used as standards in antiviral assays.
Boc-oseltamivir carboxylate (Boc-OsC) was prepared with slight modification via an adapted protocol [48].

2.2. Boc Protection of Amino Group of Oseltamivir Carboxylate

To a solution of oseltamivir carboxylate (5.4 g; 19 mmol) in a mixture of water (10 mL), 1 N NaOH (19 mL), and 0.95 g NaHCO3, stirred and cooled at 0 °C, di-tert-butyl dicarbonate (5.4 g, 24.7 mmol) in isopropanol (38 mL) was added. The stirring was continued at RT for 8 h. After completion of the reaction and TLC control in CHCl3:CH3OH = 2.5:0.5, the i-PrOH solution was evaporated in vacuo. The resulting solution was diluted with 30 mL 5% NaHCO3 and then extracted with Et2O. Afterwards, the cooled NaHCO3 solution was acidified to pH 3 with solid NaHS04 in an ice water bath. Furthermore, the obtained acidic phase was extracted with ethyl acetate (3 × 30 mL). The combined organic extract was washed with brine (2 × 30 mL), dried over anhydrous Na2SO4, and evaporated in vacuo. The crude product was recrystallized with 96% EtOH/H2O with a yield of 75%.
Boc-OsC:
IR (ATR)umax: 3315, 2965, 2931, 2878, 1688, 1655, 1537, 1434, 1390, 1367, 1169, 1050 cm−1; 1H-NMR: δ 0.77 (t, J = 8.2 Hz, 3H, -CH2CH3), 0.83 (t, J = 7.2 Hz, 3H, -CH2CH3), 1.37 (s, 9H, -C(CH3)3), 1.43 (m, 4H, 2 × -CH2CH3), 1.79 (s, 3H, -C(O)CH3), 2.21 (dd, J = 17.7, 10 Hz, 1H, =CCH2a-), 2.46 (dd, J = 17.7, 5.1 Hz, 1H, =CCH2b-), 3.37 (m, 1H, >CHCH2CH3), 3.56 (m, 1H, -NHCH<), 3.69 (m, 1H, -HNCH<), 4.05 (d, J = 7.9 Hz, 1H, -OCH<), 6.57 (d, J = 9.3 Hz, 1H, -OC(O)NH-), 6.59 (s, 1H, =CH-), 7.79(d, J = 8.9 Hz, 1H, H3CC(O)NH-); 13C-NMR: δ 9.0 (-CHCH2CH3), 9.5 (-CHCH2CH3), 14.2 (-O-CH2CH3), 22.9 (-(O)CCH3), 25.2 (>CHCH2CH3), 26.4 (>CHCH2CH3), 25.8 (>CHCHCH2-), 28.2 (3 × -CH3), 30.3 (-CH2-), 49.0 (-HN-CH<), 54.3 (-C(O)HN-CH<), 75.1 (-OCH<), 77.7 ((CH3)3CO-), 81.0 (-O-CH(CH2CH3)2), 129.3 (=Cq), 137.7 (=CHCO-), 155.4 (-O(O)CNH-), 167.3 (-HNC(O)-), 167.8 (-C(O)OH), 169.7 (-HNC(O)CH3); ESI-MS: 385.2 [M+H]+, 407.1 [M+Na]+, 791.4 [2M+Na]+.

2.3. Synthesis of Monoamides and Bisamides

General TBTU Coupling Procedure [49,50]

The corresponding carboxylic component TA/Boc-OsC/AdA (24 mmol) was suspended in 30–40 mL of CH2Cl2, and then, after adding Et3N (3.4 mL, 24 mmol), the resulting liquid was treated by TBTU (7.7 g, 24 mmol). After being stirred for ~8–10 min, the amino components Am, Rim, or TA-Hda.TFA (26.5 mmol) were added to the mixture along with Et3N (3.7 mL, 26.5 mmol) and dissolved in 30 mL CH2Cl2 and DMF (10 mL). Then, the reaction mixture was stirred at RT for 4 h and diluted with an additional 40 mL of CH2Cl2. The organic layer was washed subsequently with 5% aqueous NaHCO3 (5 × 50 mL) and saturated NaCl (3 × 50 mL), dried over Na2SO4, and concentrated in vacuo. Furthermore, after flash chromatography on EcoFlex Flash Silica Cartridges, the monoamides/bisamides were obtained.
Spectral data of the obtained amides:
Compound 1 (TA-Am, yield 62%):
IR (ATR)umax: 3304, 3067, 2906, 2848, 1664, 1651, 1610, 1542, cm−1; 1H-NMR: δ 1.62 (6H, 3 × -CH2-), 1.96 (6H, 3 × -CH2-), 2.01 (3H, 3 × >CH-), 6.42 (d, J = 15 Hz, 1H, =CH-), 7.07 (dd, J = 4.8, 3.5 Hz,1H, =CH-), 7.30 (d, J = 3.5 Hz, 1H, =CH-), 7.45 (d, J = 15 Hz, 1H, =CH-), 7.55 (d, J = 4.8 Hz, 1H, =CH-), 7.58 (s, 1H, >NH); 13C-NMR: δ 28.8 (3 × >CH-), 36.0 (3 × -CH2-), 41.0 (3 × -CH2-), 50.8 (-HNCq), 122.6 (=CH-), 127.5 (=CH-), 128.2(=CH-), 130.1(=CH-), 130.6 (=CH-), 140.1 (-S-Cq), 163.7 (-C(O)NH-); ESI-MS: 288.3 [M+H]+, 597.2 [2M+Na]+.
Compound 2 (TA-Rim, yield 54%):
IR (ATR)umax: 3280, 3069, 2976, 2898, 1664, 1647, 1615, 1549, 1311 cm−1; 1H-NMR: δ 0.95 (d, J = 6.8 Hz, 3H, -CH3), 1.45 (6H, 3 × -CH2-), 1.61 (6H, 3 × -CH2-), 1.92 (3H, 3 × >CH-), 3.61 ( m, 1H, -HNCHCH3), 6.49 (d, J = 16.2 Hz, 1H, =CH-), 7.08 (dd, J = 5.1, 3.7 Hz,1H, =CH-), 7.33 (d, J = 3.7 Hz, 1H, =CH-), 7.52 (d, J = 16.2 Hz, 1H, =CH-), 7.57 (d, J = 5.1 Hz, 1H, =CH-), 7.71 (d, J = 9.3 Hz, 1H, >NH); 13C-NMR: δ 14.2 (-CH3), 27.8 (3 × >CH-), 35.6 (Cq), 36.6 (3 × -CH2-), 37.9 (3 × -CH2-), 52.2 (-HNCH<), 121.6 (=CH-), 127.6 (=CH), 128.2 (=CH-), 130.3 (=CH-), 131.4 (=CH-), 140.1 (S-Cq), 164.0 (-HNC(O)-); ESI-MS: 316.3 [M+H]+, 338.3 [M+Na]+, 653.3 [2M+Na]+
Compound 3 (TA-Os-OEt, yield 38%):
IR (ATR)umax: 3302, 3275, 3087, 2968, 2937, 2874, 1725, 1715, 1644, 1614, 1544, 1455, 1256, 1153, 1055 cm−1; 1H-NMR: δ 0.75 (t, J = 7.5 Hz, 3H, -CH2CH3), 0.83 (t, J = 7.5 Hz, 3H, -CH2CH3), 1.21 (t, 3H, -CH3), 1.43 (m, 4H, 2 × -CH2CH3), 1.71 (s, 3H, -C(O)CH3), 2.22 (dd, J = 17.8, 10.5 Hz, 1H, =CCH2a-), 2.55 (dd, J = 17.8, 5.3 Hz, 1H, =CCH2b-), 3.40 (m, 1H, >CHCH2CH3), 3.79 (m, 1H, -NHCH<), 4.03 (m, 1H, -HNCH<), 4.11 (m, 1H,-OCH<), 4.14 (q, J = 7.1 Hz, 2H, -OCH2CH3), 6.32 (d, J = 15.5 Hz, 1H, =CH-), 6.65 (s, 1H, =CH-), 7.09 (dd, J = 5.1, 3.6 Hz, 1H, =CH-), 7.36 (d, J = 3.6 Hz, 1H, =CH-), 7.54 (d, J = 15.5 Hz, 1H, =CH-), 7.59 (d, J = 5.1 Hz, 1H, =CH-), 7.82 (d, J = 9.2 Hz, 1H, >NH), 8.01 (d, J = 9.2 Hz, 1H, >NH); 13C-NMR: δ 9.5 (>CHCH2CH3), 9.9 (>CHCH2CH3), 14.5 (-O-CH2CH3), 23.2 (-(O)CCH3), 25.7 (>CHCH2CH3), 26.2 (>CHCH2CH3), 30.7 (-CH2-), 47.9 (-HN-CH<), 54.3 (-C(O)HN-CH<), 60.9 (-OCH2CH3), 75.5 (-OCH<), 81.6 (-O-CH(CH2CH3)2), 121.5 (=CH-), 128.3 (=CH-), 128.8 (=CH-), 128.9 (=CH-), 131.0 (=CH-), 138.9 (=CH-), 140.3 (-S-Cq), 164.0 (-HNC(O)-), 165.9 (-C(O)OCH2CH3), 169.8 (-HNC(O)CH3); ESI-MS: 449.3 [M+H]+, 471.3 [M+Na]+.
Compound 5 (TA-Hda-Boc, yield 44%):
IR (ATR)umax: 3346, 3317, 2931, 2870, 1682, 1647, 1613, 1521, 1389, 1362, 731 cm−1; 1H-NMR: δ 1.25 (m, 4H, 2 × -CH2-), 1.34 (s, 9H, 3 × -CH3), 1.42 (m, 4H, 2 × -CH2-), 3.06 (dd, J = 13.2, 6.8 Hz, 2H, >NCH2-), 3.19 (ddd, J = 12.9, 6.8, 6.7 Hz, 2H, >NCH2-), 6.42 (d, J = 15.8 Hz, 1H, =CH-C(O)NH-), 7.03 (dd, J = 4.7, 3.5 Hz, 1H, -SCHCHCH<), 7.20 (t, J = 5.4 Hz, 1H, >NH), 7.31 (d, J = 3.5 Hz, 1H, -SCHCHCH=), 7.49 (d, J = 15.8 Hz, 1H, =CH-), 7.63 (d, J = 4.9 Hz, 1H, -SCH=), 7.95 (t, J = 5.6 Hz, 1H, >NH).
Compound 7 (Boc-Os-Hda-TA, yield 61%):
IR (ATR)umax: 3327, 3292, 3095, 2971, 2932, 2872, 1674, 1648, 1615, 1528, 1464, 1390, 1367, 1139, 1047, 712 cm−1; 1H-NMR: δ 0.76 (t, J = 7.8 Hz, 3H, -CH3), 0.82 (t, J = 7.8 Hz, 3H, -CH3), 1.25 (m, 4H, 2 × -CH2-), 1.36 (s, 9H, 3 × -CH3), 1.41 (m, 8H, 4 × -CH2-, 2 × -CH2CH3 + 2 × -CH2-), 1.77 (s, 3H, -HNC(O)CH3), 2.21 (dd, J = 17.0, 7.8 Hz, 1H, -CH2a-), 2.45 (dd, J = 17.0, 4.7 Hz, 1H, -CH2b-), 3.10 (m, 4H, 2 × >NCH2-), 3.35 (m, 1H, -CH(CH2CH3)2), 3.55 (m, 1H, >NCHCH2), 3.67 (q, J = 9.3 Hz, 1H, >NCHCHO), 4.02 (d, J = 9.3 Hz, 1H, -O-CH<), 6.27 (s, 1H, =CH-), 6.37 (d, J = 15.5 Hz, 1H, =CH-C(O)NH-), 6.51 (d, J = 8.8 Hz, 1H, >NH), 7.08 (dd, J = 4.9, 3.3 Hz, 1H, -SCHCHCH<), 7.33 (d, J = 3.3 Hz, 1H, -SCHCHCHC), 7.54 (d, J = 15.5 Hz, 1H, =CH-), 7.57 (d, J = 4.9 Hz, 1H, -SCH=), 7.76 (d, J = 8.8 Hz, >NH), 7.90 (t, J = 5.5 Hz, 1H, >NH), 8.08 (t, J = 5.5 Hz, 1H, >NH); 13C-NMR: δ 9.1 (2 × -CH3), 9.4 (-CH2CH3), 22.9 (-(O)CCH3), 25.2 (-CH2-), 25.8 (-CH2-), 26.1 (-CH2-), 28.2 (3 × -CH3), 29.0 (-CH2-), 30.4 (=CCH2-), 38.6 (-NHCH2-), 49.1 (>NCHCH2-), 54.3 (>NCHC(H)O), 75.2 (-OCH<), 77.5 (-OC(CH3)3), 80.8 (-O-CH(CH2CH3)2, 121.1 (=CH-), 127.7 (-SCH<), 128.3 (SCqCH), 130.4 (-SCHCHCH<), 131.3 (2CH, -HC=CH- + =CH-), 132.3 (=Cq), 140.0 (-SCq), 155.4 (-HNC(O)O-), 164.5 (-HC=CHC(O)NH-), 165.9 (-(CH2)6C(O)NH-), 166.3 (-C(O)NH-), 168.9 (-HNC(O)CH3); ESI-MS: 641.4 [M+Na]+.
Compound 8 (TA-Hda-AdA, yield 42%):
IR (ATR)umax: 3445, 3326, 3081, 2931, 2902, 2854, 1649, 1636, 1613, 1542, 1457, 727 cm−1; 1H-NMR: δ 1.23 (m, 4H, 2 × -CH2-), 1.39 (m, 4H, 2 × -CH2-), 1.63 (m, 6H, 3 × -CH2-), 1.73 (d, J = 2.5 Hz, 6H, 3 × -CH2-), 1.93 (br. s, 3H, >CH-), 3.01 (dd, J = 13.1, 6.9 Hz, 2H, >NCH2-), 3.13 (ddd, J = 12.8, 6.9, 6.6 Hz, 2H, >NCH2-), 6.36 (d, J = 15.9 Hz, =CH-C(O)NH-), 7.08 (dd, J = 4.7, 3.5 Hz, 1H, -SCHCHCH<), 7.28 (t, J = 5.5 Hz, 1H, >NH), 7.34 (d, J = 3.5 Hz, 1H, -SCHCHCHC), 7.54 (d, J = 15.9 Hz, 1H, =CH-), 7.57 (d, J = 4.7 Hz, 1H, -SCH=), 8.03 (t, J = 5.7 Hz, 1H, >NH); 13C-NMR: δ 26.0 (-CH2-), 27.7 (>CH-), 29.0 (-CH2-), 36.1 (-CH2-), 38.3 (-CH2-), 38.5 (-CH2-), 38.7 (-CH2-), 38.9 (Cq), 121.1 (=CH-), 127.4 (-SCH<), 128.1 (>CH-, >CHCHCHC), 130.3 (>CH-, >CHCHCHC), 131.3 (=CH-), 140.3 (Cq, -SCq), 164.5 (-HC=CH-C(O)NH-), 176.6 (-C(O)NH-); ESI-MS: 415.3 [M+H]+, 437.3 [M+Na]+, 453.3 [M+K]+.

2.4. Characterization Methods

Infrared spectra (ATR-IR) of the samples were measured on a Thermo Scientific Nicolet iS10 FT-IR spectrometer, equipped with an ID5 ATR accessory. The desired measurements were accomplished in the 4000–650 cm−1 range with a 4cm−1 resolution over 32 scans at 293 K.
1H- and 13C-NMR spectra were obtained on a Bruker Ascend neo NMR 600 instrument (Bruker, Billerica, MA, USA) at 600 MHz for 1H and at 151 MHz for 13C nuclei. The chemical shifts were expressed as parts per million (ppm) in DMSO-d6, and TMS ((CH3)4Si)) was used as an internal standard.
Electrospray ionization mass spectrometry (ESI-MS) analyses were performed on a Bruker QqTOF compact apparatus operated using Compass otofControl 4.0 (Bruker Daltonics, Bremen, Germany) software. Compass DataAnalysis 4.4 (Build 200.55.2969) (Bruker Daltonics, Bremen, Germany) software was applied for data processing. The data were acquired in positive ion mode at a scan range from m/z 50 to m/z 1000. The temperature of the drying gas was set to 220 °C, with a flow rate of 3.0 L min−1. The cone voltage was 2800 V. The samples were injected at a flow rate of 3 L min−1 into the nebulizer by a syringe pump (Cole Parmer, Vernon Hills, IL, USA).

2.4.1. Single-Crystal X-Ray Diffraction (SCXRD)

Dry powders of thienyl-based amides (TA-Os-OEt (3), TA-OsC (4), TA-Rim (2), and TA-Am (1)) were dissolved in ethanol, methanol, or acetone at room temperature. Approximately 50 mg of each compound was dissolved in ~5 mL of solvent, with the solutions monitored to ensure complete dissolution. Additional solvent drops were added when necessary to avoid supersaturation, and heating was avoided to minimize the risk of rapid supersaturation upon cooling. Single crystals were obtained by slow solvent evaporation over 2–3 days. A single crystal of each compound was fixed on the top of a glass capillary, mounted and centered on the Kappa goniometer of an Oxford Diffraction Supernova diffractometer equipped with a micro-focus Mo-Kα radiation source (λ = 0.71013 Å), and diffraction images were collected at room temperature (290 K). The data reduction, e.g., unit cell parameter determination, data integration, scaling, and absorption corrections, was conducted using CrysalisPro [51]. The structures were solved via direct methods with ShelxS-2018. Structural refinement was carried out through multiple cycles of full-matrix least-squares refinement on F2 using the ShelxL-2018 package [52,53].
Nitrogen-bound hydrogen atoms were located from difference Fourier maps, while all other hydrogen atoms were placed in idealized positions. Non-hydrogen atoms were refined anisotropically, and hydrogen atoms were refined using a riding model [52,53].
Crystallographic data (excluding structure factors) for the structural analysis (see Supplementary Data B) were deposited at the Cambridge Crystallographic Data Centre (CCDC) as follows: Deposition Number 2474375 for compound TA-Am (1); Deposition Number 2474380 for compound TA-Rim (2); Deposition Number 2474379 for compound TA-Os-OEt (3); Deposition Number 2474378 for compound TA-OsC (4). A copy of this information can be obtained free of charge from The Director, CCDC, 12 Union Road, Cambridge, CB2 1EZ, UK (fax: +44 1223 336 033; e-mail: deposit@ccdc.cam.ac.uk; www.ccdc.cam.ac.uk, accessed on 21 July 2025).
Molecular visualizations of the asymmetric units of 1–4 were generated using ORTEP [54], while Mercury was employed to depict the three-dimensional packing and hydrogen bonding interactions The crystallographic data (including atomic coordinates and structure factors) in the Crystallographic Information File (CIF) were validated using the IUCr checkCIF/PLATON tool [55].

2.4.2. Powder X-Ray Diffraction (PXRD)

Powder XRD patterns were determined for the physical powders of the compounds TA-Os-OEt (3), TA-OsC (4), TA-Rim (2), and TA-Am (1) to establish crystalline properties and bulk purity. Powder X-ray diffraction (PXRD) analysis was performed on an Empyrean diffractometer (Malvern Panalytical, Almelo, The Netherlands) equipped with a PIXcel3D detector, using Cu-Kα radiation (λ = 1.5406 Å) over a 2θ range of 2–50°. The experimental PXRD patterns were compared with those simulated from single-crystal X-ray diffraction (SCXRD) data to confirm phase purity and detect any potential impurities.

2.4.3. Thermal Analysis (DSC)

The thermotropic properties and thermal behavior of the compounds TA-Am (1), TA-Rim (2), TA-Os-OEt (3), TA-OsC (4), TA-Hda-Boc (5), TA-Hda-TFA (6), and BOC-OsC- Hda-TA (7) were investigated using differential scanning calorimetry. Measurements were conducted using a Discovery DSC250 instrument (TA Instruments, New Castle, DE, USA). Samples (1–5 mg) were sealed in aluminum pans and subjected to heating cycles from 20 to 350 °C at a constant rate of 10 °C·min−1 under argon atmosphere (flow rate: 10 mL·min−1). The DSC thermograms were analyzed for endothermic and exothermic events associated with phase transitions, including melting and solvent evaporation processes.

2.5. Antiviral Studies In Vitro

2.5.1. Cells and Viruses

Madin–Darby canine kidney (MDCK) cells were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA) and cultured in minimum essential medium (MEM) supplemented with 10% fetal bovine serum (FBS), 1% penicillin–streptomycin, and 1% non-essential amino acids solution (NEAA). All cell culture-related reagents were purchased from Gibco (Thermo Fisher Scientific, Waltham, MA, USA).
The influenza virus strains used in this study included A/Fort Monmouth/1/1947 (H1N1) from the ATCC and A/Wuhan/359/1995 (H3N2) and oseltamivir-resistant A/Jinnan/15/2009 (H1N1), both generously provided by the Institute for Viral Disease Control and Prevention, China Centers for Disease Control and Prevention. Viral stocks were propagated in 10-day-old embryonated chicken eggs for 2–3 days prior to use.

2.5.2. Cytotoxicity Assay

The cytotoxicity of the compounds was assessed based on cytopathic effect (CPE) evaluation in MDCK cells. Cells were seeded in 96-well plates and subsequently exposed to threefold serial dilutions of the test compounds for 48 h. The cytopathic effects were visualized under an inverted microscope, and the median cytotoxic concentration (TC50) values were calculated according to the Reed–Muench method [56].

2.5.3. Cytopathic Effect (CPE) Reduction Assay

Confluent MDCK monolayers in 96-well plates were washed with PBS and infected with viral inoculum (100 TCID50/well). Following 2 h adsorption at 37 °C, the inoculum was replaced with a maintenance medium supplemented with 2 μg/mL TPCK-trypsin (Worthington, Houston, TX, USA) and 0.08% BSA (Yuanheng Golden Horse Biotechnology, Beijing, China), with or without the test compounds. Antiviral activity was assessed when virus control wells exhibited complete CPE (grade 4), with IC50 values determined by the Reed–Muench method. Selectivity indices (SIs) were calculated as the ratio of TC50 to IC50 [56].

2.6. QSAR/ADMET In Silico Analysis

Some of the available ADMET web tools and services and their related databases and algorithms, like Admetlab 3.0 and admetSAR 1.0, were used to evaluate and prognosticate various attributes, characteristics, and impacts of the newly synthesized compounds in regard to their possible biological activity and pharmacokinetics, like general and specific organ toxicity, absorption, metabolism, and excretion [57,58,59].

3. Results

3.1. Chemistry

Considering thiophene as a potent multitargeted pharmacological scaffold [60] in order to improve the effectiveness of anti-influenza inhibitors of our choice, we incorporated its nucleus herein as an attractive isostere for further drug development.
In the present work, the target thienyl-based amides of anti-influenza inhibitors were performed through two pathways A and B (Scheme 1), utilizing TBTU (N-[(1H-benzotriazol-1-yl)(dimethylamino)methylene]-N-methylmethanaminium tetrafluoroborate N-oxide) as a classical peptide method (a) [49,61].
In path A (Scheme 1), 3-(2-thienyl) propenoic acid (or 3-(2-thienyl)acrylic acid; TA) was directly linked to anti-influenza drugs, namely aminoadamantanes (amantadine hydrochloride (Am.HCl) and rimantadine hydrochloride (Rim.HCl)) and a neuraminidase inhibitor Tamiflu (oseltamivir phosphate (OP)).
Briefly, by treatment with the tertiary amine triethylamine (Et3N), TA was firstly deprotonated, and then, TBTU-mediated carboxylate activation was performed. Furthermore, the corresponding amino components (anti-influenza inhibitors) were reacted with the in situ generated carboxylic active ester, giving the thienyl-propenoic acid monoamides (1–3). Afterwards, following a saponification process (b), combining 2 N NaOH in methanol, the ester group of amide 3 was hydrolyzed to its carboxylate form (compound 4).
On the other hand, the synthesis of bisamides 7 and 8 (path B) was performed by applying the same TBTU-directed amidation reaction (a). However, in order to develop those bisamides, the intermediate 6 (TA-Hda.TFA) was preliminarily synthesized by using commercially available unsymmetrical N-tert-butyloxycarbonyl (N-Boc-protected 1,6-diaminohexane hydrochloride (Boc-Hda.HCl)), followed by acidolytic deblocking of the Boc group [62] from N-Boc-protected amide 5 with 50% TFA in CH2Cl2 at 0 °C (c), affording the trifluoroacetic salt of compound 6.
As revealed in Scheme 1 (path B), the further transformations of monoamide 6 to bisamides required prior protection of the amino group in oseltamivir carboxylate (OsC) to prevent undesired polymerization during the activation process (a) of the carboxylic acid.
To introduce the acid-labile Boc group, di-tert-butyl dicarbonate (Boc2O) was the reagent of our choice. According to the known procedure [62], the desired urethane derivative, -N-tert-butyloxycarbonyl-oseltamivir carboxylate (Boc-OsC), was synthesized in an organic–alkaline medium (i-PrOH and 1 M NaOH/NaHCO3). Then, parallel couplings of Boc-OsC/or 1-adamantane carboxylic acid (AdA), mediated by TBTU, afforded the corresponding bisamides 7 and 8 in good yields (see Scheme 1, path B).
The thienyl-based amides were isolated in pure form after flash chromatography, and their structures were elucidated by means of spectral methods.
Additionally, X-ray diffraction data collection and processing and structure refinement of the thienylacrylic acid amides (1–4) were also conducted.

3.2. Crystallography

Large single crystals (~0.3 × 0.1 × 0.1 mm3) suitable for SCXRD analysis were obtained for compounds 14, with methanol producing the highest-quality crystals. In contrast, attempts to grow single crystals of Boc-Os-Hda-TA (7) and TA-Hda-AdA (8) were unsuccessful under the tested conditions.
Single-crystal X-ray studies elucidated the crystallization patterns of the compounds TA-Os-OEt (3) and TA-OsC (4), which crystallized in non-centrosymmetric monoclinic space groups: P21 (No. 4) and C2 (No. 5), respectively. In contrast, the compounds TA-Rim (2) and TA-Am (1) exhibited a centrosymmetric arrangement, both conforming to the monoclinic space group P21/c (No. 14). All the structures did not incorporate any solvent or water molecules, which helped to enhance the clarity of the crystallographic data. The representative molecules of the four studied compounds are shown in Figure 1, and a summary of the most important crystal data and refinement indicators is provided in Table S1 (see Supplementary Data).
The bond lengths and angles in the four molecules are comparable, as detailed in Tables S2–S9 (see Supplementary Data A). The thienyl ring systems of all four compounds exhibit a nearly planar conformation, with a root mean square deviation (rmsd) ranging from 0.05 Å to 0.025 Å. Furthermore, the geometry of the thienyl-based amides remains consistently preserved across the compounds (Figure 2, Figure 3b, and Figure 4). Indeed, in TA-Os-OEt (3), the main difference between the two molecules present in the asymmetric unit is due to the different orientation of the ethyl fragment (Figure 2). In TA-Os-OEt (3) and TA-OsC (4), the geometry of both the thienyl and cyclohexenyl rings bearing the substituents is conserved. On the other hand, the “linkage” between the two mentioned moieties is subject to a significant variation, thus producing distinct molecular geometries.
In TA-Am (1) and TA-Rim (2), thienyl is also present, but the second moiety is now an aminoadamantane nucleus. Similarly to TA-Os-OEt (3) and TA-OsC (4), the molecular geometry of the moieties is conserved, while the linkage between those slightly varies (Figure 4).
Given the observed similarities in bond lengths and angles, it is reasonable to expect analogous hydrogen bonding interactions, with variations primarily arising from the differences in side chains. In all four structures, the intermolecular N-H…O hydrogen bonds are particularly prominent (Table S10, Supplementary Data) and play an essential role for the stabilization of the crystal structure. These interactions act as directional, moderately strong intermolecular forces that link adjacent molecules into a three-dimensional network, reducing structural flexibility and enhancing lattice cohesion. This hydrogen-bond network helps stabilize the crystal packing by maximizing intermolecular contact and minimizing free volume. As shown in Figure 5a, in the compound TA-Os-OEt (3), the N-H…O hydrogen bonds produce propagation along the b-axis. In Figure 5b, TA-OsC (4), in addition to forming chains typical for the -COOH moiety R22(8) motif, links the adjacent molecules, thus producing dimmers. Similarly, Figure 6 illustrates that TA-Am (1) and TA-Rim (2) adopt comparable hydrogen-bonding schemes, where the N–H…O interactions extend into chain-like motifs that support their centrosymmetric packing. These consistent hydrogen-bonding patterns highlight the role of the thienyl amide framework in directing supramolecular assembly, while subtle differences in side-chain substituents account for the observed variations in packing topology.
The three-dimensional packing of the molecules in all four compounds is governed by the bulkier moieties, e.g., adamantane, acetyl, and methoxy pentane. In all four compounds, a pseudo-layered structure is observed, with the hydrogen bonding interaction buried in the core of the layers while the bulkier moieties decorate the outside of the layers (Figure S1). The observed geometrical features are not only crystallographically consistent but may also influence the biological potential of these compounds. The nearly planar thienyl ring system facilitates π–π stacking and enhances conjugation, features often associated with improved binding interactions at aromatic or hydrophobic protein pockets. The conserved bond lengths and angles across the series suggest a rigid thienyl–amide core, which may help maintain a favorable binding geometry irrespective of the attached substituent. At the same time, variations in the linkage between the thienyl scaffold and the adamantane-derived moiety introduce conformational diversity that could modulate molecular recognition and adaptability toward viral targets. The structural analysis provides a rationale for how these geometrical differences may translate into differences in antiviral activity observed in vitro.

3.3. Evaluation of Phase Purity and Thermal Stability

The crystal phase purity and thermal stability of the studied compounds were evaluated using comparative powder X-ray diffraction analysis and differential scanning calorimetry. The registered powder diffraction patterns of TA-Am (1), TA-Rim (2), TA-Os-OEt (3), and TA-OsC (4) shown in Figure 7 are in good agreement with the single-crystal data as no evident impurity diffraction maxima are registered. The thermal stability and purity of the compounds were further confirmed by the registered DSC thermograms (Figure 8 and Figure S5). The data show only one endothermic effect that is related to the melting of the compounds. TA-Rim (2) exhibited the lowest melting point at 148.1 °C, followed by TA-Am (1) at 213.9 °C, while TA-Os-OEt (3) and TA-OsC (4) melted at higher temperatures of 230.9 °C and 237.2 °C, respectively. The absence of additional thermal events indicates that all compounds are thermally stable in the investigated range and do not undergo polymorphic transitions or solvent loss prior to melting. The DSC data collection was aborted slightly after the melting as the sulfur present in all compounds may poison the thermocouple of the equipment upon decomposition.

3.4. Antiviral Investigation of the Tested Compounds Against Influenza Viruses In Vitro

In pursuance of putative inhibitors of the M2 channel and neuraminidase, the synthesized thiophene-based compounds were studied herein in vitro for their antiviral activities against three influenza A strains (A/Fort Monmouth/1/1947, A/Jinnan/15/2009, and A/Wuhan/359/1995) by applying a CPE assay. For comparison, oseltamivir phosphate (OP), oseltamivir carboxylate (OC), and amantadine hydrochloride (Am.HCl) were used as positive control drugs in anti-influenza assays.
As summarized in Table 1, the TC50 values of the amide compounds and control drugs in MDCK cells, as well as their IC50 values against tested influenza viruses, were determined.
Concerning the obtained results, it can be seen that almost all compounds possessed antiviral potency. The synthetic compounds TA-Hda-AdA (8), TA-Am (1), and TA-Rim (2) demonstrated significant antiviral activity against the replication of the tested influenza A virus strains.
It is noteworthy that in our study, the 3-(2-thienyl) propenoic acid amides of aminoadamantanes (compounds 1 and 2) exhibited antiviral activity against an oseltamivir-resistant influenza strain (A/Jinnan/15/2009).
Although there was an inhibitory effect against the A/Jinnan/15/2009 (H1N1) strain by amide 8, interestingly, the same compound exhibited moderate antiviral activity against an antigenically related H1N1 strain, circulating in 1947, suggesting potential strain-specific efficacy. Moreover, compound 8 exerted a pronounced antiviral effect against influenza A (H3N2) virus, exhibiting a selective index (SI) of 13, comparable to that of the reference—amantadine hydrochloride.
Given the current global prevalence of resistance to M2 inhibitors such as amantadine and rimantadine, the identification of structurally related compounds with preserved antiviral potency represents a promising basis for further investigations.

3.5. QSAR/ADMET Investigation of the Tested Compounds

The results of the performed QSAR/ADMET analysis showed that the newly synthesized compounds are expected to have low to moderate toxicity when applied via the oral route in a rat model organism (see Table 2). The new compounds based on the adamantane scaffold are expected to have good to moderate absorption and permeability as determined by the Caco-2 permeability evaluator, which they seem to inherit partially from their parents—amantadine or rimantadine. However, the new compounds based on the oseltamivir scaffold are expected to have moderate to poor performance on this parameter, which is, nevertheless, better than the parent molecule oseltamivir. As for the expected efflux through the kidneys, all compounds showed negligible MDCK permeability, so they will likely have another route of excretion. The predicted toxicity of the liver shows moderate to high values for most of the new compounds, with the exception of compounds 1, 3, and 4, which are expected to have low to moderate hepatotoxicity. However, when the newly synthesized compounds are compared to the parent molecules, many of the new hybrids may outperform them, as is the case with compounds 1, 3, 4, and 7. However, considering that the arsenal of agents to combat some of the new influenza strains is rather limited, some of the new compounds may be a viable solution, even with their pharmacological and metabolite issues.

4. Conclusions

In summary, TBTU-directed amidation reactions were chosen for the functionalization of diverse anti-influenza inhibitors, including aminoadamantanes (M2 ion blockers—amantadine and rimantadine) and the neuraminidase inhibitor oseltamivir, with 3-thienyl-propenoic acid. The thienyl-based amides (1–8) were obtained in moderate yields, and their structures were confirmed by spectral analysis. Moreover, the crystal structures of the synthesized amides (1–4) were also assessed using single-crystal X-ray diffraction, powder X-ray diffraction (PXRD), and differential scanning calorimetry (DSC). The single-crystal X-ray analysis revealed that the hybrids TA-Am (1) and TA-Rim (2) crystallize in a centrosymmetric manner, both in the monoclinic space group (SG) P21/c (No. 14), while the compounds TA-Os-OEt (3) and TA-OsC (4) crystallize in non-centrosymmetric monoclinic space groups (SG) P21 (No. 4) and (SG) C2 (No. 5), respectively.
Furthermore, the compounds were screened for anti-influenza activity in vitro. Importantly, almost all the tested amides (1–4, 7, 8) displayed inhibitory activities against three different influenza strains. Moreover, the thienyl-based amides of amantadine and rimantadine, compounds 1 and 2, respectively, showed inhibiting abilities against oseltamivir-resistant A/Jinnan/15/2009 (H1N1). However, compound 8 displayed a pronounced antiviral effect against influenza A (H3N2) virus, exhibiting a selective index (SI) of 13, comparable to that of the reference drug—amantadine hydrochloride.
Our preliminary antiviral investigation indicates that such a compound could serve as a core structure for the design of novel influenza inhibitors based on a thiophene nucleus.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/cryst15090772/s1, Supporting Information A includes Figures S1–S5 and Tables S1–S10. Figure S1. Residual electron density around C2 (top) and modeled disorder over two positions (bottom); the minor component is shown as dashed lines. Figure S2. Residual electron density around OEt groups (top) and modeled disorder of the OEt groups (bottom); the minor component is shown as dashed lines. Figure S3. Visualization of the three-dimensional packing observed in (a) TA-Os-OEt (3), (b) TA-Rim (2) and (c) TA-Am (1). Figure S4. Powder diffraction data for TA-Hda-Boc (5), TA-Hda-TFA (6) and BOC-OsC- Hda-TA (7). Figure S5. DSC thermograms for TA-Hda-Boc (5), TA-Hda-TFA (6) and BOC-OsC- Hda-TA (7). Table S1. Crystallographic data-collection statistics for Compound TA-Am (1), Compound TA-Rim (2), Compound TA-Os-OEt (3), and Compound TA-Os-OH (4). Table S2. Selected geometric parameters for Compound TA-Os-OEt (3). Bond Lengths [Å]. Table S3. Selected geometric parameters for Compound TA-Os-OH (4). Bond Lengths [Å]. Table S4. Selected geometric parameters for Compound TA-Rim (2). Bond Lengths [Å]. Table S5. Selected geometric parameters for Compound TA-Am (1). Bond Lengths [Å]. Table S6. Selected geometric parameters for Compound TA-Os-OEt (3). Bond Angles/°. Table S7. Selected geometric parameters for Compound TA-Os-OH (4). Bond Angles/°. Table S8. Selected geometric parameters for Compound TA-Rim (2). Bond Angles/°. Table S9. Selected geometric parameters for Compound TA-Am (1). Bond Angles/°. Table S10. Hydrogen Bonds geometry (Å, °) for Compound TA-Os-OEt (3), Compound TA-Os-OH (4), Compound TA-Rim (2) and Compound TA-AM (1).

Author Contributions

Conceptualization, M.C.; investigation, M.C., B.S. (Boyka Stoykova), M.A., H.S.-D., R.R., Y.L., A.P., N.P., M.Š. and B.S. (Boris Shivachev); writing—original draft, M.C., H.S.-D., A.P. and B.S. (Boris Shivachev); visualization, M.C., M.A., H.S.-D., R.R. and B.S. (Boris Shivachev). All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Bulgarian National Science Fund (BNSF), grant number KP-06-H79/7 (15 December 2023).

Data Availability Statement

Crystallographic data (excluding structure factors) for the structural analysis were deposited at the Cambridge Crystallographic Data Centre (CCDC) as follows: Deposition Number 2474375 for compound TA-Am (1); Deposition Number 2474380 for compound TA-Rim (2); Deposition Number 2474379 for compound TA-OS-OEt (3); Deposition Number 2474378 for compound TA-OsC (4). A copy of this information can be obtained free of charge from The Director, CCDC, 12 Union Road, Cambridge, CB2 1EZ, UK (fax: +44-1223-336-033; e-mail: deposit@ccdc.cam.ac.uk; www.ccdc.cam.ac.uk, accessed on 21 July 2025).

Conflicts of Interest

The authors declare no conflicts of interest.

Abbreviations

DMFDimethylformamide
NAIsNeuraminidase inhibitors
TA3-(2-Thienyl) acrylic acid or 3-(2-thienyl) propenoic acid
WHOWorld Health Organization

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Scheme 1. Synthesis of various mono- and bisamides, containing thienyl scaffold. Reaction conditions: (a) TBTU-directed carboxylate activation, Et3N, CH2Cl2, RT, 3–4 h; (b) alkaline hydrolysis, 2 N NaOH, CH3OH; (c) acidolysis, 50% TFA in CH2Cl2 at 0 °C.
Scheme 1. Synthesis of various mono- and bisamides, containing thienyl scaffold. Reaction conditions: (a) TBTU-directed carboxylate activation, Et3N, CH2Cl2, RT, 3–4 h; (b) alkaline hydrolysis, 2 N NaOH, CH3OH; (c) acidolysis, 50% TFA in CH2Cl2 at 0 °C.
Crystals 15 00772 sch001
Figure 1. Depiction of the molecules of the compounds (a) TA-Os-OEt (3), (b) TA-Am (1), (c) TA-OsC (4), and (d) TA-Rim (2); thermal ellipsoids are displayed at 50% probability, and hydrogen atoms are represented as spheres with arbitrary radii. For clarity of the representation for compounds (3) and (1), only one of the two molecules present in the asymmetric unit is drawn (discussed below). Color scheme: C = blue, H = white, O = red, N = purple, S = yellow.
Figure 1. Depiction of the molecules of the compounds (a) TA-Os-OEt (3), (b) TA-Am (1), (c) TA-OsC (4), and (d) TA-Rim (2); thermal ellipsoids are displayed at 50% probability, and hydrogen atoms are represented as spheres with arbitrary radii. For clarity of the representation for compounds (3) and (1), only one of the two molecules present in the asymmetric unit is drawn (discussed below). Color scheme: C = blue, H = white, O = red, N = purple, S = yellow.
Crystals 15 00772 g001
Figure 2. Overlay of the molecules present in the asymmetric unit of TA-Os-OEt (3), disclosing the conserved geometry of the thienyl amide moiety along with the difference in the two molecules in the rotation of the ethyl moiety.
Figure 2. Overlay of the molecules present in the asymmetric unit of TA-Os-OEt (3), disclosing the conserved geometry of the thienyl amide moiety along with the difference in the two molecules in the rotation of the ethyl moiety.
Crystals 15 00772 g002
Figure 3. Visualization of the conserved molecular features of TA-Os-OEt (3) (in red) and TA-OsC (4) (in green), namely (a) ethyl 4-((1-hydroxyethyl)amino)-3-(pentan-3-yloxy)cyclohexene-1-carboxylate and (b) thienyl moieties.
Figure 3. Visualization of the conserved molecular features of TA-Os-OEt (3) (in red) and TA-OsC (4) (in green), namely (a) ethyl 4-((1-hydroxyethyl)amino)-3-(pentan-3-yloxy)cyclohexene-1-carboxylate and (b) thienyl moieties.
Crystals 15 00772 g003
Figure 4. Comparison of the molecular geometries of TA-Am (1) (in red) and TA-Rim (2) (in green).
Figure 4. Comparison of the molecular geometries of TA-Am (1) (in red) and TA-Rim (2) (in green).
Crystals 15 00772 g004
Figure 5. Hydrogen-bonding interactions in (a) TA-Os-OEt (3), where N–H···O bonds generate infinite chains propagating along the b-axis, and (b) TA-OsC (4), which, in addition to chain formation, exhibits the classical R22(8) motif of the –COOH group, linking molecules into dimers and reinforcing lattice cohesion.
Figure 5. Hydrogen-bonding interactions in (a) TA-Os-OEt (3), where N–H···O bonds generate infinite chains propagating along the b-axis, and (b) TA-OsC (4), which, in addition to chain formation, exhibits the classical R22(8) motif of the –COOH group, linking molecules into dimers and reinforcing lattice cohesion.
Crystals 15 00772 g005
Figure 6. Hydrogen-bonding patterns in (a) TA-Rim (2) and (b) TA-Am (1), showing N–H···O interactions that extend into chain-like motifs. These consistent supramolecular linkages contribute to the stabilization of their centrosymmetric crystal packing.
Figure 6. Hydrogen-bonding patterns in (a) TA-Rim (2) and (b) TA-Am (1), showing N–H···O interactions that extend into chain-like motifs. These consistent supramolecular linkages contribute to the stabilization of their centrosymmetric crystal packing.
Crystals 15 00772 g006
Figure 7. Comparison of collected powder diffraction data and diffraction patterns generated from single-crystal data for the compounds (a) TA-Os-OEt (3), (b) TA-OsC (4), (c) TA-Rim (2), and (d) TA-Am (1).
Figure 7. Comparison of collected powder diffraction data and diffraction patterns generated from single-crystal data for the compounds (a) TA-Os-OEt (3), (b) TA-OsC (4), (c) TA-Rim (2), and (d) TA-Am (1).
Crystals 15 00772 g007
Figure 8. DSC thermograms for (a) TA-OsC (4), (b) TA-Os-OEt (3), (c) TA-Am (1), and (d) TA-Rim (2).
Figure 8. DSC thermograms for (a) TA-OsC (4), (b) TA-Os-OEt (3), (c) TA-Am (1), and (d) TA-Rim (2).
Crystals 15 00772 g008
Table 1. Antiviral activities of compounds against 3 influenza strains.
Table 1. Antiviral activities of compounds against 3 influenza strains.
CompoundsTC50
μg/mL
A/Fort Monmouth/1/1947A/Jinnan/15/2009A/Wuhan/359/1995
IC50 (μg/mL)SIIC50 (μg/mL)SIIC50 (μg/mL)SI
TA-Am (1)12.843.563.64.792.74.792.7
TA-Rim (2)6.172.063.02.063.02.063.0
TA-Os-OEt (3)80.12>18.52->18.52->18.52-
TA-OsC (4)>210.26NT NT 40.47>5.2
Boc-Os-Hda-TA (7)>500115.56>4.3>166.67-115.56>4.3
TA-Hda-AdA (8)240.3732.087.5>18.52-18.5213.0
OsP577.352.47233.7115.475.03.12185.0
OsC14.22NT NT 0.034416.74
Am.HCl39.220.32122.62.8613.712.8613.71
Note: “-“ means no antiviral activity; NT: not tested; TC50: 50% toxicity concentration; IC50: 50% inhibitory concentration; SI: selectivity index; SI = TC50/IC50.
Table 2. QSAR/ADMET probability prediction of pharmacological parameters of the tested compounds.
Table 2. QSAR/ADMET probability prediction of pharmacological parameters of the tested compounds.
123478AmRimOs
Rat oral
Acute
Toxicity
0.4410.3660.0720.1150.3460.490.3230.4840.25
Caco-2 permeability (log values)−4.979−5.313−5.234−5.369−4.811−5.435−5.073−5.038−5.545
MDCK permeability000000000
Human hepatotoxicity0.520.80.3830.3340.7480.8850.7770.690.681
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Chochkova, M.; Stoykova, B.; Angelova, M.; Sbirkova-Dimitrova, H.; Rusew, R.; Li, Y.; Popatanasov, A.; Petek, N.; Štícha, M.; Shivachev, B. Thienyl-Based Amides of M2 and Neuraminidase Inhibitors: Synthesis, Structural Characterization, and In Vitro Antiviral Activity Against Influenza a Viruses. Crystals 2025, 15, 772. https://doi.org/10.3390/cryst15090772

AMA Style

Chochkova M, Stoykova B, Angelova M, Sbirkova-Dimitrova H, Rusew R, Li Y, Popatanasov A, Petek N, Štícha M, Shivachev B. Thienyl-Based Amides of M2 and Neuraminidase Inhibitors: Synthesis, Structural Characterization, and In Vitro Antiviral Activity Against Influenza a Viruses. Crystals. 2025; 15(9):772. https://doi.org/10.3390/cryst15090772

Chicago/Turabian Style

Chochkova, Maya, Boyka Stoykova, Magdalena Angelova, Hristina Sbirkova-Dimitrova, Rusi Rusew, Yuhuan Li, Andrey Popatanasov, Nejc Petek, Martin Štícha, and Boris Shivachev. 2025. "Thienyl-Based Amides of M2 and Neuraminidase Inhibitors: Synthesis, Structural Characterization, and In Vitro Antiviral Activity Against Influenza a Viruses" Crystals 15, no. 9: 772. https://doi.org/10.3390/cryst15090772

APA Style

Chochkova, M., Stoykova, B., Angelova, M., Sbirkova-Dimitrova, H., Rusew, R., Li, Y., Popatanasov, A., Petek, N., Štícha, M., & Shivachev, B. (2025). Thienyl-Based Amides of M2 and Neuraminidase Inhibitors: Synthesis, Structural Characterization, and In Vitro Antiviral Activity Against Influenza a Viruses. Crystals, 15(9), 772. https://doi.org/10.3390/cryst15090772

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