From design to biological mechanism evaluation of phenylalanine-bearing HIV-1 capsid inhibitors targeting a vital assembly interface

HIV-1 capsid protein (CA) has emerged as a promising target for antiviral treatment considering its structural and regulatory roles in HIV-1 replication. Here, we disclose the design, synthesis, biological assessment, and mechanism investigation of a novel series of phenylalanine derivatives gained by further structural modification of PF74. The newly synthesized compounds demonstrated potent anti-HIV activity, represented by 7n displayed anti-HIV-1 activity 6.25-fold better than PF74, and 7h showed anti-HIV-2 activity with nearly 139 times improved efficacy over PF74. Surface plasmon resonance (SPR) studies of representative compounds proved that HIV-1 CA was the binding target. Competitive SPR studies using CPSF6 and NUP153 peptides identified that 7n binds to a vital CA assembly interface between the N-terminal and C-terminal domain (NTD-CTD interface). Action stage determination assay revealed that the newly synthesized compounds were antiviral with a dual-stage inhibitory profile. Molecular dynamics (MD) simulations offered the crucial foundation for the hopeful antiviral potency of 7n. Besides, 7m and 7n modestly increased metabolic stabilities in human liver microsome (HLM) and human plasma compared to PF74. Overall, these studies offer valuable insights and can regard as the beginning for succedent medicinal chemistry endeavors to discover promising HIV capsid inhibitors with improved efficacy and better drug-like characteristics.     

Crystal structures and photoisomerization behaviors of five novel pyrazolone derivatives containing furoyl group

Five novel pyrazolone derivatives containing a furoyl group, 1-phenyl-3-furoyl-4-(4-chlorobenzal)-5-pyrazolone thiosemicarbazone (PF4ClBP-TSC) (1)/methylthiosemicarbazone (PF4ClBP-MTSC) (2)/ethylthiosemicarbazone (PF4ClBP-ETSC) (3), 1-phenyl-3-furoyl-4-(2-chlorobenzal)/(3-chlorobenzal)-5-pyrazolone methylthiosemicarbazone (PF2ClBP-MTSC) (4)/(PF3ClBP-MTSC) (5), have been synthesized and characterized by elemental analysis, IR, ¹H NMR spectra, and the molecular structures of 2 and 5 were determined by X-ray single crystal diffraction. Photoisomerization properties have been studied by UV–vis and fluorescence spectra. Based on theoretical calculation and crystal structural analysis, the compounds undergo photoisomerization from the enol form to the keto form through an intermolecular proton transfer upon UV light irradiation. Moreover, the photoisomerization rate decreases with the increase of volume of substituent groups on 4-position of thiosemicarbazide and the steric hindrance of Cl atom on benzal of 4-positon on the pyrazolone ring.     

Biodegradation of organophosphorus insecticide chlorpyrifos into a major fuel additive 2,4-bis(1,1 dimethylethyl) phenol using white-rot fungal strain Trametes hirsuta MTCC-1171

Biodegradation of chlorpyrifos, a widely used organophosphorus insecticide, was accomplished by using a white-rot fungal strain (Trametes hirsuta MTCC-1171). The experimental results showed that the fungal strain can effectively and rapidly degrade chlorpyrifos while using it as a sole source of carbon and energy when provided with mineral salt medium (MSM). The optimum experimental conditions for degradation of chlorpyrifos in liquid media can be summed as follows: initial pH 6.0; mycelial inoculum 0.18 ​± ​0.01 ​g ​L⁻¹ (dry weight); chlorpyrifos concentration 150 ​mg ​L⁻¹; pH 6.0; temperature 30 ​°C; and shaking speed 150 ​rpm. Under these optimal experimental parameters, T. hirsuta MTCC-1171 achieved ≥95% degradation of chlorpyrifos in 16 ​h of incubation. The degradation rate was quantified by employing HPLC followed by identification of degradation metabolites using gas chromatography–mass spectrometry (GC-MS). 2,4-Bis (1,1 dimethylethyl) phenol, a fuel additive, was found to be a major metabolite product of chlorpyrifos degradation. However, no metabolite bioaccumulation was observed in the process. Additionally, soil studies were carried out to investigate the degradation ability of the strain against chlorpyrifos, in a natural environment. During the assessment 37 ​± ​2.3% degradation was observed after 15 days of incubation. These results illustrate that T. hirsuta MTCC-1171 has a potential of using chlorpyrifos as a sole source of carbon. Besides, fundamental understanding gained through this work lays a foundation to investigate efficient and rapid bioremediation processes in agricultural and forest environments.     

Nonaqueous microemulsion-containing ionic liquid [bmim][PF6] as polar microenvironment

The phase behavior of toluene/Triton X-100 (TX-100)/1-butyl-3-methylimidazolium hexafluorophosphate([bmim][PF6]) was studied. It was demonstrated that the single-phase microemulsion area covered about 75% of the phase diagram at 25 °C. Electrical conductivities of the system with different w ([bmim][PF6]-to-TX-100 molar ratio) values were determined, and the results were used to locate the sub-regions of the single-phase microemulsion. The results showed that a transform from [bmim][PF6]-in-oil ([bmim][PF6]/O) microstructure via a bicontinuous region to an oil-in-[bmim][PF6] (O/[bmim][PF6]) microstructure occurred with the increase of Φ (weight fraction of TX-100 and [bmim][PF6] in the system). The aggregate size of the reverse microemulsions of [bmim][PF6]/O was determined using small-angle X-ray scattering. The results showed that the size of the reverse microemulsions depended markedly on the w values.     

Gasphasenreaktionen von H3PF2: Darstellung der Monohalogenphosphane H2PF und H2PCl

Gas Phase Reactions of H₃PF₂: Synthesis of the Monohalogenophosphanes H₂PF and H₂PCl Gas phase reactions of H₃PF₂ at ≤ 10 mbar with hydrides (B₂H₆, HSi(CH₃)₃, HSn(CH₃)₃), amines (H₃N, N(CH₃)₃) and electrophilic halides of B, Si and Ti in the beam of an IR interferometer have been investigated with a time delay of 15 sec. between successive measurements. Gas/solid phase reactions of H₃PF₂ with KF and AlCl₃ and reactions of H₃PF₃ and HPF₄ have been studied similarly. With H₃N, N(CH₃)₃ and electrophilic halides, H₃PF₂ was converted into its dehydrofluorination product H₂PF. This eliminates further HF in the presence of H₃N or N(CH₃)₃, while BCl₃ or TiCl₄ yield the hitherto unknown H₂PCl. The IR spectra of the short-lived species H₂PF and H₂PCl as well as their deuterated isotopomers, which reveal at room temperature and ≤ 10 mbar a halflife time of ≤ 12 min. and ≤ 50 sec. respectively, were recorded and analysed in order to characterize the novel species.     

Prepatellamide A, a new cyclic peptide from the ascidianLissoclinum patella

A new cyclic peptide, prepatellamide A (1), along with three known cyclic peptides (2)— (4), was isolated from the ascidianLissoclinum patella. The structure of prepatellamide A was determined from one- and two-dimensional¹H and¹³C NMR spectra. The known cyclic peptides were identified as patellamides A (2), B (3) and C (4).     

Struktur und Eigenschaften des Hydridomethyltetrafluorphosphatanions, [CH3PF4H]—

Structure and Properties of the Hydridomethyltetrafluorophosphate Anion, [CH₃PF₄H]^— Methyltrifluorphosphorane reacts with strong fluoride donors like CsF, (CH₃)₄NF and (CH₃)₄PF with formation of the corresponding hydridomethyltetrafluorophosphates. The salts are characterized by NMR, IR and Raman spectroscopy. The experimental results show that only the trans isomer is formed. For both isomers theoretical calculations (B3LYP/6‐31+G* and RHF/6‐31+G*) were carried out. The difference for the Gibbs free energy between the isomers was calculated to be 35.4 kJ/mol (B3LYP/6‐31+G*). The RHF/6‐31+G* calculation yields, for the almost octahedral trans isomer, bond distances of r(PF) = 167 pm, r(PC) = 184.5 pm and r(PH) = 138.1 pm.     

Pd(0) and Pd(II) derivatives with heteroannularly bridged chiral ferrocenyl diphosphine ligands - A stereochemical analysis

The ligands (S_c, S_p)-1-diphenylphosphino-2,1′-(1-dicyclohexylphosphinopropanediyl)ferrocene, (S_c, S_p)-PP^CyPF, and (S_c, S_p)-1-diphenylphosphino-2,1′-(1-diphenylphosphinopropanediyl)ferrocene, (S_c, S_p)-PP^PhPF, have been used in the synthesis of the new Pd(0) and Pd(II) derivatives [Pd(PP^CyPF)(DMFU)] (1) (DMFU = dimethylfumarate), [Pd(PP^CyPF)(MA)] (2) (MA = maleic anhydride), [Pd(η³-2-Me-C₃H₄)(PP)]OTf (PP = PP^CyPF, 3; PP^PhPF, 4) (OTf = triflate), [PdRR′(PP)] (R = Me, R′ = Cl, PP = PP^CyPF, 5, PP^PhPF, 6; R = R′ = Me, PP = PP^CyPF, 7, PP^PhPF, 8; R = R′ = C₆F₅, PP = PP^CyPF, 9, PP^PhPF, 10). The molecular structure of 7 has been determined by X-ray diffraction. In the cases of complexes 1-4 two isomers are formed depending on the orientation of the ancillary ligand with respect to the ferrocenyl core. The stereochemistry of these complexes has been determined. In complex 6 the two possible isomers are obtained whereas in complex 5 the derivative with the Me group trans to PPh₂ is selectively formed. Restricted rotation of the pentafluorophenyl groups with respect to the Pd-C bond has been found in 9 and 10. In all derivatives the conformation of the ferrocenyl ligand is the same as that seen by X-ray diffraction and deduced from NMR data.     

Acetylation of DMSO:PF solutions of cellulose

Three different techniques for esterifying solutions of cellulose dissolved in mixtures of dimethyl sulfoxide (DMSO) and paraformaldehyde (PF) were evaluated and are herein described. The evaluation and development of suitable synthetic procedures and the characteristics of the resulting acetylated cellulose are reported. Glacial acetic acid (glacial HOAc), acetyl chloride (AcCl), and acetic anhydride (Ac₂O) were compared as acetylating agents for solutions of cellulose in DMSO:PF, and it was demonstrated that mixtures of pyridine (Py) and Ac₂O rapidly acetylated the cellulose to yield beige to amber acetone-soluble cellulose acetates which were partially oxidized. These thermoplastic resins exhibited softening points between 80 and 110°C and thermal stabilities (in nitrogen atmospheres) similar to those of native celluloses (350 to 375°C). Degree of acetyl substitution (DS) values ranged from 0 to 2.0 as a function of acetylation time.     

Study of the structure and stability of compounds PF n,n=1–5, and their anions by the density functional method

The electronic and geometrical structure of phosphorus fluorides PF_n, n = 1–5, and their singly-charged negative ions was calculated using the density functional method. Both the ground and low-lying excited states of the two series were considered. The structural parameters of neutral radicals PF₂, PF₄, and their anions were obtained for the first time. The adiabatic and vertical electron affinities (EA) of the neutral phosphorus fluorides, and the first ionization potentials of the anions were calculated. According to the calculation results, all the phosphorus fluorides have positive EA_ad, except for PF₃, which has an EA of about zero, and requires further investigation. The dissociation energies of both the neutral and negatively charged phosphorus fluorides were calculated through different channels. All the PF_n and PF _n ^– , n = 1–5, are stable in the gaseous phase. The PF^–, PF ₂ ^– , PF ₃ ^– , and PF ₅ ^– anions have excited states which are stable with respect to both the splitting off of an outer electron and to dissociation.Institute of Chemical Physics in Chernogolovka, Russian Academy of Sciences, 142432 Chernogolovka. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 10, pp. 2219–2232, October, 1992.     

Metabolites from the marine-facultative Aspergillus sp. MEXU 27854 and Gymnoascus hyalinosporus MEXU 29901 from Caleta Bay,Mexico

During our ongoing research on fungal strains from unexplored sources, the reinvestigation of the CHCl₃?MeOH extract of the marine-facultative Aspergillus sp. MEXU 27854 yielded a new N-methyl cyclic pentapeptide (1) along with known butyrolactone II and PF1233 A. In addition, from the marine-facultative Gymnoascus hyalinosporus MEXU 29901, a new alternariol glucoside, 10-O-[β-d-(4-methoxyl-glucopyranosyl)]-4-O-methylalternariol (2) and known alternariol 4-O-methyl ether, alternariol and beauvericin, were isolated. The structures of 1 and 2 were established by detailed spectroscopic data, and their absolute configuration was ascertained by Marfey’s analysis and HRESIMS-MS/MS data for 1, and by chemical degradation and optical rotation analysis for 2.     

Some INDO calculations of 1J(PC) and 1J(PF) values

INDO parameterized calculations, employing phosphorus s, p and d valence orbitals, are reported for values of ¹J(PC) and ¹J(PF) relating to phosphorus in formal tri- and pentavalent states. The ¹J(PC), interactions are mainly controlled by the contact term. Thus, trivalent phosphorus compounds have negative values for ¹J(PC), whereas those for pentavalent phosphorus are positive due to the s lone-pair effect. The inclusion of phosphorus 3d orbitals is shown to be important for an understanding of the processes contributing to ¹J(PF) interactions. ¹J(PF) values are shown to be negative for both tri- and pentavalent phosphorus compounds. The contact and orbital interactions are significant for the trivalent phosphorus molecules, whereas in the pentavalent phosphorus case ¹J(PF) is dominated by the orbital term.     

Electron transfer across α-helical peptides: Potential influence of molecular dynamics

Three hydrophobic leucine-rich peptides Fc18L, Ac18L and 18LAc were prepared. These peptides are equipped with a cystein sulfhydryl group which enables the formation of thin films on gold surfaces. Using these peptides, two types of films of α-helical peptides have been prepared, in which the redox-active peptide Fc18L is diluted by Ac18L (SAM1) or by a mixture of Ac18L and 18LAc (SAM2). In SAM1, the dipole moments of the peptides are aligned in the same direction, whereas in SAM2, they are opposite. Reflection absorption infrared spectroscopy (RAIRS) revealed that the peptides are more vertically oriented in SAM2 compared to those in SAM1. The interaction among the macroscopic helix dipoles gives tighter packing of the peptides in SAM2. Importantly, the electron transfer properties in the two films are significantly different, which is rationalized by differences in the molecular dynamics of the two films.     

New aeruginazoles,a group of thiazole-containing cyclic peptides from Microcystis aeruginosa blooms

Three related cyclic peptides, aeruginazole DA1497 (1), aeruginazole DA1304 (2), and aeruginazole DA1274 (3), were isolated from the freshwater cyanobacteria, Microcystis aeruginosa, bloom material collected on October 2007 from the Dalton water-reservoir in Northern Israel. Aeruginazoles DA1304 (2), DA1338 (4), and DA1372 (5) were isolated as an inseparable mixture from a bloom material of M. aeruginosa collected from the same water-reservoir on August 2000. Their structures were elucidated using a combination of various spectroscopic techniques, mainly NMR and MS, while the absolute stereochemistry of the chiral centers were determined by Marfey’s method. Aeruginazoles 1–3 were tested in various bioassays (antibacterial, cytotoxicity, and protease inhibition). Aeruginazole DA1497 (1) showed a mild antimicrobial activity against Staphylococcus aureus, but was inactive like the rest of the compounds in all other bioassays.     

Zur disproportionierung der phenylfluorphosphane (C6H5)2PF und (C6H5)PF2

Ph₂P-PF₂Ph₂ has been identified by means ¹⁹F- and ³¹P- NMR spectroscopy as an intermediate product of the disproportionation of Ph₂PF. The disproportionation is catalyzed by acids. The reaction mechanism is discussed. PhPF₂ disproportionates faster in solution in acetonitrile than neat, forming (PhP)₆, instead of (PhP)₅.     

New antimitotic bicyclic peptides, celogentins D-H, and J, from the seeds of Celosia argentea

Six new bicyclic peptides, celogentins D-H (1-5) and J (6) have been isolated from the seeds of Celosia argentea, and the structures including its absolute stereochemistry were determined by using extensive NMR methods and chemical means. Celogentins E-H (2-5) and J (6) showed potent inhibition of tubulin polymerization, while the inhibitory activity of celogentin D (1) was modest. Structure-activity relationship study indicates that ring size of the bicyclic ring system including unusual β^s-Leu, Trp, and His residues would be important for their biological activity.     

The trifluorophosphonium ion, PF3H+, preparation and structure

The PF3H+ ion is prepared as PF3H+.SbF6-.HF by protonation of PF3 with HF/SbF5 at low temperatures in anhydrous HF. Crystals are obtained directly from this solvent. A crystal structure determination shows the presence of a pseudo-tetrahedral PF3H+ ion with a mean P-F distance of 148.7(2) pm, a P-H distance of 122(4) pm, and a mean PF2 angle of 106.1(1) degrees. Raman spectra were recorded of PF3H+SbF6-.HF and PF3D+.SbF6-.DF and assigned with the help of ab initio calculations. AsF3 does not react with HF/SbF5, whereas SF4 forms SF3+SbF6-.HF, which is isostructural with PF3H+SbF6-.HF.     

Biosynthetic studies on the antibiotics PF1140: a novel pathway for a 2-pyridone framework

Incorporation of labeled acetate and l-serine into PF1140 in Eupenicillium sp. indicated that the skeleton of PF1140 is derived from five acetates and a l-serine. Upon administration of [1,3-¹³C₂]glycerol, a precursor of biotransformation into l-[1,3-¹³C₂]serine, the isotopic labels became contiguous in the resultant 2-pyridone of PF1140. Based on the feeding experiments, a novel and potentially general biosynthetic pathway for a 2-pyridone framework has been proposed, in which an acyl tetramic acid precursor could be converted via a ring expansion with loss of the hydroxyl group.     

Solid-phase synthesis of backbone-cyclized β-helical peptides

This paper describes the synthesis and purification of two 22-residue cyclic peptides, cyclo{[(l-Val-d-Val)₄-(l-Val-d-Pro-Gly)]₂-} 3 and cyclo{[(d-Leu-l-Leu)₄-(d-Leu-l-Pro-Gly)]₂-} 4, that were designed to fold into double-stranded antiparallel β-helical structures. Due to intramolecular hydrogen bonding and the conformational constraints imposed by the two reverse-turn segments (d-Pro-Gly and l-Pro-Gly, respectively), the linear precursors to 3 and 4 (lin-3 and lin-4) were expected to adopt preorganized conformations that would bring the N and C termini close together and thereby favor ring closure. Precursors lin-3 and lin-4 were constructed by stepwise Boc solid-phase peptide synthesis using the commercially available alkanesulfonamide ‘safety-catch’ linker and cyclized head-to-tail via the method of cleavage-by-cyclization. The crude cyclic peptides were highly hydrophobic and contained minor impurities that could not be removed solely by reversed-phase HPLC (RP-HPLC); however, two-step purification—first by RP-HPLC with i-PrOH/water gradients, followed by gel-permeation chromatography (GPC) on Sephadex LH-20 with CHCl₃/MeOH—afforded both peptides in pure form (≥95% by ¹H NMR) and in acceptable yield (23%). Subsequent ¹H NMR experiments supported the expected structures of 3 and 4. The successful formation of the 66-membered rings of 3 and 4 is consistent with the notion of conformational preorganization in the linear precursors; furthermore, the protocols for synthesis and purification described should prove useful for preparing additional cyclic β-helical peptides, including longer peptides and peptides having polar residues.     

Lyngbyacyclamides A and B, novel cytotoxic peptides from marine cyanobacteria Lyngbya sp.

Lyngbyacyclamides A (1) and B (2), novel cyclic peptides, were isolated from marine cyanobacteria Lyngbya sp. collected in Okinawa, Japan. Their structures were determined by spectroscopic analyses and degradation studies. They moderately inhibited the growth of B16 mouse melanoma cells.