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The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the pathogenic cause of coronavirus disease 2019 (COVID-19). The RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 is a potential target for the treatment of COVID-19. An RdRp complex:dsRNA structure suitable for docking simulations was prepared using a cryo-electron microscopy (cryo-EM) structure (PDB ID: 7AAP; resolution, 2.60 Å) that was reported recently. Structural refinement was performed using energy calculations. Structure-based virtual screening was performed using the ChEMBL database. Through 1,838,257 screenings, 249 drugs (37 approved, 93 clinical, and 119 preclinical drugs) were predicted to exhibit a high binding affinity for the RdRp complex:dsRNA. Nine nucleoside triphosphate analogs with anti-viral activity were included among these hit drugs, and among them, remdesivir-ribonucleoside triphosphate and favipiravir-ribonucleoside triphosphate adopted a similar docking mode as that observed in the cryo-EM structure. Additional docking simulations for the predicted compounds with high binding affinity for the RdRp complex:dsRNA suggested that 184 bioactive compounds could be anti-SARS-CoV-2 drug candidates. The hit bioactive compounds mainly consisted of a typical noncovalent major groove binder for dsRNA. Three-layer ONIOM (MP2/6-31G:AM1:AMBER) geometry optimization calculations and frequency analyses (MP2/6-31G:AMBER) were performed to estimate the binding free energy of a representative bioactive compound obtained from the docking simulation, and the fragment molecular orbital calculation at the MP2/6-31G level of theory was subsequently performed for analyzing the detailed interactions. The procedure used in this study represents a possible strategy for discovering anti-SARS-CoV-2 drugs from drug libraries that could significantly shorten the clinical development period for drug repositioning.

Anisakiasis is common in countries where raw or incompletely cooked marine fish are consumed. Currently, effective therapeutic methods to treat anisakiasis are unavailable. A recent study found that wood creosote inactivates the movement of Anisakis species. Essential oil of Origanum compactum containing carvacrol and thymol, which are similar to the constituents of wood creosote, was reported to inactivate Anisakis by inhibiting its acetylcholinesterase. We examined whether wood creosote can also inhibit acetylcholinesterase. We examined the effect of components of wood creosote using the same experimental method. A computer simulation experiment (molecular docking) was also performed. Here, we demonstrate that wood creosote inactivated acetylcholinesterase in a dose-dependent manner with an IC50 of 0.25 mg/mL. Components of wood creosote were also tested individually: 5-methylguaiacol, p-cresol, guaiacol, o-cresol, 2,4-dimethylphenol, m-cresol, phenol and 4-methylguaiacol inactivated the enzyme with an IC50 of 14.0, 5.6, 17.0, 6.3, 3.9, 10.0, 15.2 and 27.2 mM, respectively. The mechanism of acetylcholinesterase inactivation was analyzed using a computer-based molecular docking simulation, which employed a three-dimensional structure of acetylcholinesterase and above phenolic compounds as docking ligands. The simulation indicated that the phenolic compounds bind to the active site of the enzyme, thereby competitively blocking entry of the substrate acetylcholine. These findings suggest that the mechanism for the inactivation of Anisakis movement by wood creosote is due to inhibition of acetylcholinesterase needed for motor neuron activity.

Chikungunya fever, a mosquito-borne disease manifested by fever, rash, myalgia, and arthralgia, is caused by chikungunya virus (CHIKV), which belongs to the genus Alphavirus of the family Togaviridae. Anti-CHIKV IgG from convalescent patients is known to directly neutralize CHIKV, and the state of immunity lasts throughout life. Here, we examined the epitope of a neutralizing mouse monoclonal antibody against CHIKV, CHE19, which inhibits viral fusion and release. In silico docking analysis showed that the epitope of CHE19 was localized in the viral E2 envelope and consisted of two separate segments, an N-linker and a β-ribbon connector, and that its bound Fab fragment on E2 overlapped the position that the E3 glycoprotein originally occupied. We showed that CHIKV-E2 is lost during the viral internalization and that CHE19 inhibits the elimination of CHIKV-E2. These findings suggested that CHE19 stabilizes the E2-E1 heterodimer instead of E3 and inhibits the protrusion of the E1 fusion loop and subsequent membrane fusion. In addition, the antigen-bound Fab fragment configuration showed that CHE19 connects to the CHIKV spikes existing on the two individual virions, leading us to conclude that the CHE19-CHIKV complex was responsible for the large virus aggregations. In our subsequent filtration experiments, large viral aggregations by CHE19 were trapped by a 0.45-μm filter. This virion-connecting characteristic of CHE19 could explain the inhibition of viral release from infected cells by the tethering effect of the virion itself. These findings provide clues toward the development of effective prophylactic and therapeutic monoclonal antibodies against the Alphavirus infection. IMPORTANCE Recent outbreaks of chikungunya fever have increased its clinical importance. Neither a specific antiviral drug nor a commercial vaccine for CHIKV infection are available. Here, we show a detailed model of the docking between the envelope glycoprotein of CHIKV and our unique anti-CHIKV-neutralizing monoclonal antibody (CHE19), which inhibits CHIKV membrane fusion and virion release from CHIKV-infected cells. Homology modeling of the neutralizing antibody CHE19 and protein-protein docking analysis of the CHIKV envelope glycoprotein and CHE19 suggested that CHE19 inhibits the viral membrane fusion by stabilizing the E2-E1 heterodimer and inhibits virion release by facilitating the formation of virus aggregation due to the connecting virions, and these predictions were confirmed by experiments. Sequence information of CHE19 and the CHIKV envelope glycoprotein and their docking model will contribute to future development of an effective prophylactic and therapeutic agent.

Understanding and identifying the receptor subtype selectivity of a ligand is an important issue in the field of drug discovery. Using a combination of classical molecular mechanics and quantum mechanical calculations, this report assesses the receptor subtype selectivity for the human retinoid X receptor (hRXR) and retinoic acid receptor (hRAR) ligand‐binding domains (LBDs) complexed with retinoid ligands. The calculated energies show good correlation with the experimentally reported binding affinities. The technique proposed here is a promising method as it reveals the origin of the receptor subtype selectivity of selective ligands.

Recently, we confirmed that in human aortic valve interstitial cells (HAVICs) isolated from patients with aortic valve stenosis (AVS), calcification is induced in high inorganic phosphate (high-Pi) medium by warfarin (WFN). Because WFN is known as a vitamin K antagonist, reducing the formation of blood clots by vitamin K cycle, we hypothesized that vitamin K regulates WFN-induced HAVIC calcification. Here, we sought to determine whether WFN-induced HAVIC calcification in high-Pi medium is inhibited by menaquinone-4 (MK-4), the most common form of vitamin K2 in animals. HAVICs obtained from patients with AVS were cultured in α-modified Eagle's medium containing 10% FBS, and when the cells reached 80%-90% confluency, they were further cultured in the presence or absence of MK-4 and WFN for 7 days in high-Pi medium (3.2 mM Pi). Intriguingly, in high-Pi medium, MK-4 dose-dependently accelerated WFN-induced HAVIC calcification and also accelerated the calcification when used alone (at 10 nM). Furthermore, MK-4 enhanced alkaline phosphatase (ALP) activity in HAVICs, and 7 days of MK-4 treatment markedly upregulated the gene expression of the calcification marker bone morphogenetic protein 2 (BMP2). Notably, MK-4-induced calcification was potently suppressed by two pregnane X receptor (PXR) inhibitors, ketoconazole and coumestrol; conversely, PXR activity was weakly increased, but in a statistically significant and dose-dependent manner, by MK-4. Lastly, in physiologic-Pi medium, MK-4 increased BMP2 gene expression and accelerated excess BMP2 (30 ng/ml)-induced HAVIC calcification. These results suggest that MK-4, namely vitamin K2, accelerates calcification of HAVICs from patients with AVS like WFN via PXR-BMP2-ALP pathway. SIGNIFICANCE STATEMENT: For aortic valve stenosis (AVS) induced by irreversible valve calcification, the most effective treatment is surgical aortic or transcatheter aortic valve replacement, but ∼20% of patients are deemed unsuitable because of its invasiveness. For effective drug treatment strategies for AVS, the mechanisms underlying aortic valve calcification must be elucidated. Here, we show that menaquinone-4 accelerates warfarin-induced calcification of AVS-patient human aortic valve interstitial cells in high inorganic phosphate medium; this effect is mediated by pregnane X receptor-bone morphogenetic protein 2-alkaline phosphatase signaling, which could be targeted for novel drug development.

We successfully simulated receptor-ligand complex holo-form formation using the human retinoid X receptor-α ligand-binding domain (LBD) and its natural ligand, 9-cis retinoic acid. The success of this simulation was strongly dependent on the findings for an initial structure between the apo-LBD and the ligand as well as the discovery of the driving forces underlying the ligand-trapping and subsequent ligand-induction processes. Here, we would like to propose the "helix H3 three-point initial-binding hypothesis," which was instrumental in simulating the nuclear receptor (NR) superfamily. Using this hypothesis, we also succeeded in simulating holo-form formation of the human retinoic acid receptor-γ LBD and its natural ligand, all-trans retinoic acid. It is hoped that this hypothesis will facilitate novel understanding of both the ligand-trapping mechanism and the simultaneous C-terminal folding process in NR LBDs, as well as provide a new approach to drug design using a structure-based perspective.

Sterically unbiased bicyclic and tricyclic olefins were reacted with electrophiles to assess the π-facial stereoselectivity. The stereochemical preference of the reactions of these olefins with electrophiles is attributed to the HOMO, which is derived from the interaction between a higher-lying π orbital and particular lower-lying σ orbitals. The selectivity of electrophilic reactions of these olefinic molecules is thought to be controlled by two types of HOMO, which are formed by a combination of different orbitals, depending on the geometrical conditions. A novel interpretation of orbital interactions enabled us to account for the facial selectivity in a unified manner.

Structural and sequence alignment analyses have revealed the existence of class-dependent and -independent local motifs involved in the overall fold of the ligand-binding domain (LBD) in the nuclear receptor (NR) superfamily. Of these local motifs, three local motifs, i.e., AF-2 fixed motifs, were involved in the agonist conformation of the activation function-2 (AF-2) region of the LBD. Receptor–agonist interactions increased the stability of these AF-2 fixed motifs in the agonist conformation. In contrast, perturbation of the AF-2 fixed motifs by a ligand or another protein molecule led the AF-2 architecture to adopt an antagonist conformation. Knowledge of this process should provide us with novel insights into the ‘agonism’ and ‘antagonism’ of NRs.

A number of N-acyl-L-proline derivatives were synthesized and their biological activities were investigated by using lettuce (Lactuca sativa L. cv. Sacramento) seedling test. A wide variety of these compounds promoted root growth at 25°C both under light and in darkness. Of the compounds tested, N-(2-ftuorobenzoyl)-L-proline methyl ester (4) showed the highest activity and caused a 270% increase in the root elongation compared to the control. N-(2-Naphthoyl)-L-proline methyl ester (14) promoted the root growth, while N-(1-naphthoyl)-L-proline methyl ester inhibited it. L-Proline, benzoic acid, and 2-naphthoic acid had no significant effect on lettuce seedlings. Compounds 4 and 14, and N-(2-chlorobenzoyl)-L-proline methyl ester (7) reduced the inhibitory effect of 1 ppm ABA on the root growth, while the D-isomer of 4 was less activite than compound 4. Compounds 4, 7, and 14 did not show any rescue-activity for the complete inhibition of germination that was caused by treating 10 ppm of ABA.

Retinoid X receptors (RXRs) are ligand-controlled transcription factors which heterodimerize with other nuclear receptors to regulate gene transcriptions associated with crucial biological events. 9-cis retinoic acid (9cRA), which transactivates RXRs, is believed to be an endogenous RXR ligand. All-trans retinoic acid (ATRA) is a natural ligand for retinoic acid receptors (RARs), which heterodimerize with RXRs. Although the concentration of 9cRA in tissues is very low, ATRA is relatively abundant and some reports show that ATRA activates RXRs. We computationally studied the possibility of ATRA binding to RXRs using two different docking methods with our developed programs to assess the binding affinities of naturally occurring retinoids. The simulations showed good correlations to the reported binding affinities of these molecules for RXRs and RARs.

We obtained two crystal structures of electronically interesting dicarba-closo-dodecaborane(12)s (hereafter, "carboranes") substituted with a cyclopropyl group at a caged carbon atom, i.e., C-cyclopropyl-o-carborane (4) and C-cyclopropyl-o-carboranylphenylmethanol (9), at 123 K. In these C-cyclopropyl-o-carboranes, the cyclopropyl group adopted a slightly twisted perpendicular conformation with respect to the electron-deficient carbon-carbon (C-C) bond axis in the o-carborane cage. In contrast, it has previously been shown that a phenyl group substituted at the caged carbon atom, i.e., C-phenyl-o-carborane (3), is almost parallel to this axis at both 150 and 199 K. In other words, the pi system of the phenyl ring adopted an almost bisected conformation in 3. The preferred conformation of the cyclopropane ring in these C-cyclopropyl-o-carboranes was compared among the solid, the solution, and the gaseous states and was retained under the present conditions. Moreover, we found that the C-C bond length in the o-carborane cage not only varied along the rotation of the cyclopropyl group in 4 but also was longer than that in 3, which bears a phenyl group at the dominant conformation. These phenomena may be related to homoconjugations between the caged o-carborane system that serves as an electron acceptor and the homoconjugative substituent that serves as an electron donor. In these C-cyclopropyl-o-carboranes, two types of homoconjugations would result in a slightly twisted perpendicular conformation and 4 would be more strongly stabilized than would the phenyl derivative 3. On the basis of these studies, we propose the existence of a third type of strongly stabilizing interactive geometry for a cyclopropane ring in an o-carborane system.

Previous studies on the structural development of tumor necrosis factor alpha (TNF-alpha) production regulators derived from thalidomide (N-alpha-phthalimidoglutarimide) revealed that a hydrophobic substituent at the nitrogen atom of the phthalimide ring is critical for potent activity. We have designed and prepared phthalimide derivatives bearing a boron cluster, dicarba-closo-dodecaborane (carborane), which has a hydrophobic character and spherical geometry, as a novel candidate of biological response modifiers. These compounds were shown to regulate TNF-alpha production by HL-60 cells, as expected. The result provides a further example of the application of carborane as a hydrophobic pharmacophore of biologically active molecules.

Benzo[b]- and benzo[c]fluorenes bearing a ketone, an olefin, or a diene substitutent in spiro geometry were synthesized to characterize the π facial selectivity, in comparison with that of the sterically biased benzo[a]fluorene system. We found that fully spiro-conjugated dienes show facially selective behaviors as Diels-Alder dienes, the favored direction depending on the aromatic system. This is in sharp contrast to the olefin analogues, which show essentially no preference.

We describe a reverse perturbation effect of a cyclopropyl group on facial selectivities in two bicyclic systems, bicyclo[2.2.2]octane and norbornane (bicyclo[2.2.1]heptane). In terms of facial selective behavior, the cyclopropyl group embedded in the bicyclo[2.2.2]octene seems to be equivalent to a substitution of an electron-withdrawing group, although this is in sharp contrast to the conventional understanding of this group as strongly electron-donating. © 1997 Elsevier Science Ltd.

Benzobicyclo[2.2.2]octatrienes bearing electron-withdrawing groups such as ester and cyano groups on one of the olefin moieties showed anti-facial preference toward oxidative electrophiles in epoxidation and dihydroxylation. The magnitude of the selectivity changed significantly upon aromatic nitration.

Benzobicyclo[2.2.2]octatrienes bearing electron-withdrawing groups such as ester and cyano groups on one of the olefin moieties showed anti-facial preference toward oxidative electrophiles in epoxidation and dihydroxylation. The magnitude of the selectivity changed significantly upon aromatic nitration.

We have synthesized all three possible isomers of C-hydroxycarborane from the corresponding amines via diazotization. The O-protonated C-hydroxycarboranes were characterized using the NMR spectrum measurements. Attempts at generating of carboranyl carbocations were carried out by the solvolyses of C-tosylates and C-triflates, as well as by treatment with superacids. Anchimeric assistance of both homoconjugative and hyperconjugative substituents was also investigated, as demonstrated by a successful strategy devised for the solvolytic generation of a phenyl cation. However, we have not been able to chemically provide any evidence of carboranyl carbocations, although the carboranyl carbocation may be an intermediate in the decomposition of the C-carboranediazonium ion.

Several dibenzodiazepine derivatives were identified as novel retinoid X receptor (RXR) antagonists on the basis of inhibitory activity on retinoid-induced cell differentiation of human promyelocytic leukemia cells HL-60 and transactivation assay using retinoic acid receptors (RARs) and RXRs in COS-1 cells. 4-(5H-2,3-(2,5-Dimethyl-2,5-hexano)-5-n- propyldibenzo[b,e][1,4]diazepin-11-yl)benzoic acid (HX603, 6c) is an N-n-propyl derivative of an RXR pan-agonist HX600 (6a), and exhibited RXR-selective antagonistic activity. Similar RXR-antagonistic activities were observed with 4-(5H-2,3-(2,5-dimethyl-2,5-hexano)-5-methyl- 8-nitrodibenzo[b,e][1,4]diazepin-11-yl)benzoic acid (HX531, 7a) and 4-(5H-10,11-dihydro-5,10-dimethyl-2,3-(2,5-dimethyl- 2,5-hexano)-dibenzo[b,e][1,4]diazepin-11-yl)benzoic acid (HX711, 8b), which also inhibited transactivation of RARs induced by an RAR agonist, Am80. These compounds inhibited HL-60 cell differentiation induced by the combination of a low concentration of the retinoid agonist Am80 with an RXR agonist (a retinoid synergist, HX600). These results indicated that HX603 (6c), and the related RXR antagonists inhibit the activation of RAR-RXR heterodimers as well as RXR homodimers, which is a distinct characteristic different from that of the known RXR antagonist, LG100754 (9).

Synthesis and biological evaluation of the first dicarba-closo-dodecaborane (carborane) derivatives of retinoids are described. Their retinoidal activity were examined in terms of the differentiation-inducing ability toward human promyelocytic leukemia HL-60 cells. High retinoidal activity (agonist or antagonist for retinoic acid receptor (RAR)) requires a carboxylic acid moiety and an appropriate hydrophobic group located at a suitable position on the molecule. The 4-carboranyl-substituted compounds (7, 11) showed antagonistic activity but no agonistic activity even in the presence of the potent synergist HX630. On the other hand, the 3-carboranyl-substituted compounds (8, 12) showed potential agonistic activity, but no antagonistic activity. The results indicates that carboranes are applicable as the hydrophobic moiety of biologically active molecules.

4-[N-(5,6,7,8-Tetrahydro-5,5,8,8-tetramethyl-2-naphthyl)amino]benzoic acid (5) exhibited weak retinoidal and retinoid synergistic activities in HL-60 cell differentiation assay. N-Alkylation of 5 caused decrease or loss of differentiation-inducing activity, but enhanced the synergistic activity with a synthetic retinoid Am80 (2), as reflected in the potent synergistic EC50 (SEC50) values of DA023 (11, 1.6 x 10(-10) M) and DA113 (14, 1.4 x 10(-10) M) in the presence of 1.0 x 10(-10) M Am80 (2).

The preparation and reactivity of poly-B-methyl-1, 12-dicarba-closo-dodecaborane (poly-B-methyl-p-carborane) derivatives are described. 2, 3, 4, 5, 6, 7, 8, 9, 10, 11-Decamethyl-1, 12-dicarba-closo-dodecaborane(12)-1-carboxylic acid was prepared from 2, 3, 4, 5, 6, 7, 8, 9, 10, 11-decamethyl-1, 12-decarba-closo-dodecaborane(12) by lithiation with methyllithium, followed by carboxylaiton. Conversion of the carboxylic acid into its ester and amide were achieved through its acyl chloride. The ester and the amide could not be hydrolyzed due to severe steric hindrance around the carbonyl group of the molecules owing to the adjacent B-methyl groups.

Several polyenylidene thiazolidine or 2-thioxo-4-thiazolidinone derivatives were synthesized and their retinoidal activities were examined in terms of the differentiation-inducing ability towards human promyelocytic leukemia HL-60 cells and inhibitory effect on interleukin (IL)-1 alpha-induced IL-6 production in MC3T3-E1 cells. Compounds containing a trimethylcyclohexenyl ring induced HL-60 cell differentiation with weaker activity than retinoic acid (1a) by one or two orders of magnitude. The thiazolidinedione derivatives (2, 5, 7) showed stronger activity than the corresponding 2-thioxo-4-thiazolidinone derivatives (3, 6, 8). The effects of a retinoid antagonist (LE540) and synergists (retinoid X receptor (RXR) agonists, HX600 or HX630) on the activities of thiazolidine derivatives indicate that these compounds elicit their activities through the nuclear retinoic acid receptors (RARs). All the thiazolidines examined also inhibited IL-1 alpha-induced IL-6 production with IC50 values of 10 nM order. The retinoidal activities of the thiazolidines are significant, considering that replacement of the carboxylic acid in retinoid structures with bioisosteric functional groups is generally ineffective, as seen in the structure-activity relationships of retinoidal benzoic acids.