Structure-based optimization and synthesis of antiviral drug Arbidol analogues with significantly improved affinity to influenza hemagglutinin

Bioorganic and Medicinal Chemistry Letters

Volumn 27, Issue 16, 2017, Pages 3744-3748

  Wright, Zoë V F ^a   Wu, Nicholas C ^a   Kadam, Rameshwar U ^a   Wilson, Ian A ^a   Wolan, Dennis W ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Arbidol; Bio layer interferometry; Hemagglutinin; Influenza; Structure based drug design

Indexed keywords

ARBIDOL; ARBIDOL DERIVATIVE; ETHYL 5 ACETOXY 6 BROMO 2 [[(3 HYDROXYPHENYL)THIO]METHYL] 1 METHYL 1H NDOLE 3 CARBOXYLATE; ETHYL 6 BROMO 4 [(DIMETHYLAMINO)METHYL] 5 HYDROXY 2 [[(3 HYDROXYPHENYL)THIO]METHYL] 1 METHYL 1H INDOLE 3 CARBOXYLATE; ETHYL 6 BROMO 5 HYDROXY 2 [[(3 HYDROXYPHENYL)THIO]METHYL] 1 METHYL 1H INDOLE 3 CARBOXYLATE; HYDROXYL GROUP; INDOLE DERIVATIVE; INFLUENZA VIRUS HEMAGGLUTININ; THIOPHENOL; UNCLASSIFIED DRUG; VIRUS FUSION INHIBITOR; ANTIVIRUS AGENT; HEMAGGLUTININ;

ANTIVIRAL ACTIVITY; ARTICLE; BINDING AFFINITY; BROMINATION; COMPARATIVE STUDY; CONJUGATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DRUG BINDING SITE; DRUG DESIGN; DRUG POTENCY; DRUG PROTEIN BINDING; DRUG SYNTHESIS; HEMAGGLUTINATION INHIBITION; HYDROGEN BOND; INFLUENZA A VIRUS (A/PUERTO RICO/8/1934(H1N1)); INFLUENZA B VIRUS; INFLUENZA VIRUS; INTERFEROMETRY; ISOTHERM; NONHUMAN; PROTEIN CONFORMATION; STRUCTURE ACTIVITY RELATION; VIRUS ENTRY; CHEMICAL STRUCTURE; CHEMISTRY; DOSE RESPONSE; DRUG EFFECTS; HUMAN; INFLUENZA, HUMAN; METABOLISM; MOLECULAR MODEL; ORTHOMYXOVIRIDAE; SYNTHESIS; X RAY CRYSTALLOGRAPHY;

ANTIVIRAL AGENTS; CRYSTALLOGRAPHY, X-RAY; DOSE-RESPONSE RELATIONSHIP, DRUG; HEMAGGLUTININS; HUMANS; INDOLES; INFLUENZA, HUMAN; MODELS, MOLECULAR; MOLECULAR STRUCTURE; ORTHOMYXOVIRIDAE; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 85021842716     PISSN: 0960894X     EISSN: 14643405     Source Type: Journal    
DOI: 10.1016/j.bmcl.2017.06.074     Document Type: Article

References (25)

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19. General experimental: Unless otherwise indicated, all reagents were obtained from chemical suppliers with no further purification. Sodium bicarbonate refers to a saturated solution of sodium hydrogen carbonate in water. All water used was either distilled using a Millipore MilliQ® water purifier with Q-Gard® 2 column and 0.22 µM filter from Millipore or used directly from a bottle of HPLC-grade water. All reactions were carried out in closed systems under Argon. NMR spectra were recorded using a Bruker AVIII HD-600, DRX-500, AVIII-400 and DPX-400 spectrometer (600 MHz, 500 MHz, 400 MHz and 400 MHz, respectively) and all samples were dissolved in deuterated chloroform unless otherwise stated. Offline data processing was carried out using the MestreNova software. Chemical shifts (δ) are given in ppm units relative to tetramethylsilane and coupling constants (J) are measured in Hertz. Proton (1H) NMR multiplicities are shown as s (singlet), d (doublet), t (triplet), q (quartet), m (multiplet), dd (double doublet), dt (double triplet), dq (doublet of quartets), dt (doublet of triplets), tt (triplet of triplets), br s (broad singlet), br d (broad doublet). HRMS refers to high resolution mass spectrometry. Electrospray ionization (ESI) accurate mass was determined using a ThermoFinnigan LTQ Ion Trap. Flash column chromatography was carried out using silica gel with particle size ∗60 μm and reverse phase column chromatography was carried out using silica gel 60 silanized (53–200 μm). Thin layer chromatography (TLC) was performed on aluminium backed Sigma-Aldrich TLC plates with F254 fluorescent indicator. Developed plates were air dried and analysed under a UV light or by staining with the appropriate indicator.
20. Synthesis of Arbidol analogues: Ethyl 5-acetoxy-6-bromo-2-(((3-hydroxyphenyl)thio)methyl)-1-methyl-1H-indole-3-carboxylate 8a: 3-hydroxythiophenol (117 µL, 1.15 mmol, 1.0 eq.) was added to a solution of sodium carbonate (367 mg, 3.46 mmol, 3.0 eq.) and bromo indole 2 (500 mg, 1.15 mmol, 1.0 eq.) in dry ethyl acetate (10 mL). The reaction was heated to 100 °C and stirred for 5 h before cooling, filtering and removing the solvent in vacuo. The compound was purified by column chromatography (40% EtOAc in Hexanes) to produce the title product as a pale yellow solid (240 mg, 44%). NMR: δH (500 MHz, CDCl3) 7.85 (s, 1H, H7), 7.56 (s, 1H, H4), 7.12 (t, J = 7.9 Hz, 1H, H13), 6.95 – 6.90 (m, 1H, H14), 6.78 (s, 1H, H10), 6.75-6.71 (m, 1H, H12), 4.69 (s, 2H, SCH2), 4.30 (q, J = 7.4 Hz, 3H, CO2CH2CH3), 3.66 (s, 3H, NCH3), 2.40 (s, 3H, COCH3), 1.38 (t, J = 7.4 Hz, 3H, CO2CH2CH3). δC (150 MHz, CDCl3) 169.8, 165.0, 156.1, 144.6, 143.3, 135.6, 135.1, 130.1, 126.1, 124.8, 119.3, 116.2, 115.3, 113.9, 111.1, 105.8, 60.1, 30.4, 29.9, 21.0, 14.6. Rf: 0.45 (30% EtOAc in Hexane). HRMS (ESI-TOF): C21H20BrNO5S ([M+H]+) requires 478.0318, found 478.0317.
21. Synthesis of Arbidol analogues: Ethyl 6-bromo-5-hydroxy-2-(((3-hydroxyphenyl)thio)methyl)-1-methyl-1H-indole-3-carboxylate 8: Sodium carbonate (106 mg, 1.00 mmol, 2.0 eq.) was added to a stirred solution of meta-hydroxy indole 8a (240 mg, 0.502 mmol, 1.0 eq.) in methanol (40 mL) and left to stir for 2 h. The solution was then filtered and the solvent removed in vacuo. The product was re-dissolved in ethyl acetate (10 mL) and washed once with water (10 mL) before drying (Na2SO4) and concentrating in vacuo to give the title product as a white solid, which could be used without further purification (160 mg, 67%). NMR: δH (600 MHz, MeOD) 7.60 (s, 1H, H7), 7.58 (s, 1H, H4), 7.07 (dd, J = 8.2, 7.7 Hz, 1H, H13), 6.83 - 6.81 (m, 1H, H14), 6.79 (ddd, J = 7.7, 1.8, 0.9, 1H, H10), 6.70 (dd, J = 8.2, 1.8, 0.9 Hz, 1H, H12), 4.70 (s, 2H, SCH2), 4.26 (q, J = 7.1 Hz, 2H, CO2CH2CH3), 3.64 (s, 3H, NCH3), 1.39 (t, J = 7.1 Hz, 3H, CO2CH2CH3). δC (150 MHz, MeOD) 166.9, 158.9, 150.6, 145.5, 136.4, 133.6, 131.0, 130.7, 128.0, 124.9, 120.5, 116.0, 114.8, 107.9, 104.8, 60.8, 30.5, 30.4, 14.8. Rf: 0.45 (1% MeOH in CH2Cl2). HRMS (ESI-TOF): C19H18BrNO4S ([M+H]+) requires 436.0213, found 436.0215.
22. Synthesis of Arbidol analogues: Ethyl 6-bromo-4-((dimethylamino)methyl)-5-hydroxy-2-(((3-hydroxyphenyl)thio)methyl)-1-methyl-1H-indole-3-carboxylate 11: Meta-hydroxy Indole 8 (30.0 mg, 0.069 mmol, 1.0 eq.) and N,N,N’,N’-tetramethyldiaminomethane (47.0 µL, 0.344 mmol, 5.0 eq.) were dissolved in CH2Cl2 (30 mL). The reaction was heated to reflux for 3.5 h before removing the solvent in vacuo to yield the title product as a pale yellow solid (34 mg, 99%). NMR: δH (500 MHz, CDCl3) 7.47 (s, 1H, H7), 7.12 (t, J = 7.9 Hz, 1H, H13), 6.90 (d, J = 7.9 Hz, 1H, H14), 6.90 (d, J = 7.9 Hz, 1H, H12), 6.66 (s, 1H, H10), 4.41 (s, 2H, CH2NMe2), 4.34 (s, 2H, CH2SPh), 4.15 (q, J = 7.1 Hz, 2H, CO2CH2CH3), 3.60 (s, 3H, NCH3), 2.55 (s, 6H, CH2N(CH3)2), 1.33 – 1.21 (m, 3H, CO2CH2CH3). δC (150 MHz, CDCl3) 165.9, 156.7, 150.9, 142.6, 135.1, 132.2, 131.0, 130.0, 128.9, 124.6, 124.3, 119.3, 115.5, 113.4, 108.6, 106.3, 60.8, 58.7, 44.0, 30.4, 29.9, 14.3. Rf: 0.15 (10% MeOH in CH2Cl2). HRMS (ESI-TOF): C22H25BrN2O4S ([M+H]+) requires 493.0791, found 493.0792.
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25. Bio-layer interferometry data and analysis: The Kd for ligand binding to influenza HA was determined by BLI using an Octet Red instrument (ForteBio). Biotinylated HAs, purified as described previously,23 were used for these measurements. HAs at ∼10–50 μg ml−1 in 1× kinetics buffer (PBS, pH 7.4, 2% DMSO and 0.002% Tween 20) were loaded onto streptavidin-coated biosensors and incubated with varying concentrations of small molecule in solution. All binding data were collected at 30 °C. The experiments comprised five steps: (1) baseline acquisition (60 s); (2) HA loading onto sensor (1800 s); (3) second baseline acquisition (120 s); (4) association of small molecule for the measurement of kon (180 s); and (5) dissociation of small molecule for the measurement of koff (180 s). Baseline and dissociation steps were carried out in buffer only. The ratio of kon to koff determines the Kd reported here and is subtracted from a reference well to remove the effects of non-specific binding, as previously described.24 The R2 for the model fitting and the standard error of mean (SEM) for the Kd values reported in Table 1 were computed by Octet Data Analysis software version 9.0 (ForteBio).