RNA dependent RNA polymerase (RdRP) from positive-stranded RNA viruses has always been a hot target for designing of new drugs. Major class of drugs that are targeted against RdRP are nucleotide analogues. Extensive docking and molecular dynamics study describing the binding of natural nucleotides (NTPs) and its analogues leading to significant structural variation in the RdRP has been presented here. RdRP simulations in its apo, NTP-bound, and analogue-bound form have been performed. Nucleotide analogues included in this study were, favipiravir, galidesivir, lamivudine, ribavirin, remdesivir and sofosbuvir. The conformational flexibility of the RdRP molecule has been explored using principal component (PCA) and Markov state modeling (MSM) analysis. PCA inferred the presence of correlated motions among the conserved motifs of RdRP. Inter-domain distances between the finger and thumb subdomain flanking the nascent RNA template entry site sampled open and closed conformations. The ligand and template binding motifs F and G showed negatively correlated motions. K551, R553, and R555, a part of motif F appear to form strong interactions with the ligand molecules. R836, a primer binding residue was observed to strongly bind to the analogues. MSM analysis helped to extract statistically distinct conformations explored by the RdRP. Ensemble docking of the ligands on the Markov states also suggested the involvement of the above residues in ligand interactions. Markov states obtained clearly demarcated the open/closed conformations of the template entry site. These observations on residues from the conserved motifs involved in binding to the ligands may provide an insight into designing new inhibitors.Communicated by Ramaswamy H. Sarma.

2022-10-01·Journal of Biological Chemistry

DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation

Article

作者: Dukatz, Michael ; de Mendoza, Alex ; Jeltsch, Albert ; Adam, Sabrina ; Dittrich, Marianna ; Bashtrykov, Pavel ; Stahl, Elias

Specific DNA methylation at CpG and non-CpG sites is essential for chromatin regulation. The DNA methyltransferase DNMT3A interacts with target sites surrounded by variable DNA sequences with its TRD and RD loops, but the functional necessity of these interactions is unclear. We investigated CpG and non-CpG methylation in a randomized sequence context using WT DNMT3A and several DNMT3A variants containing mutations at DNA-interacting residues. Our data revealed that the flanking sequence of target sites between the -2 and up to the +8 position modulates methylation rates >100-fold. Non-CpG methylation flanking preferences were even stronger and favor C(+1). R836 and N838 in concert mediate recognition of the CpG guanine. R836 changes its conformation in a flanking sequence-dependent manner and either contacts the CpG guanine or the +1/+2 flank, thereby coupling the interaction with both sequence elements. R836 suppresses activity at CNT sites but supports methylation of CAC substrates, the preferred target for non-CpG methylation of DNMT3A in cells. N838 helps to balance this effect and prevent the preference for C(+1) from becoming too strong. Surprisingly, we found L883 reduces DNMT3A activity despite being highly conserved in evolution. However, mutations at L883 disrupt the DNMT3A-specific DNA interactions of the RD loop, leading to altered flanking sequence preferences. Similar effects occur after the R882H mutation in cancer cells. Our data reveal that DNMT3A forms flexible and interdependent interaction networks with the CpG guanine and flanking residues that ensure recognition of the CpG and efficient methylation of the cytosine in contexts of variable flanking sequences.

1987-04-01·Archives internationales de pharmacodynamie et de therapie

Bronchodilator and other pharmacological activities of R-836 (2,5-diethyl-7-(4-thiomorpholino)-1,2,4-triazolo[1,5-c]pyrimidin e).

Article

作者: Hammerbeck, D M ; Swingle, K F ; Stelzer, V L ; Schmid, J R ; Reiter, M J ; Peterson, A M ; Wade, J J

The bronchodilator activity of R-386 (2,5-diethyl-7-(4-thiomorpholino)-1,2,4-triazolo[1,5-c]pyrimidine) was demonstrated in isolated guinea-pig tracheal preparations and in vivo in dogs, guinea-pigs and rats. Guinea-pig tracheal preparations contracted by histamine, acetylcholine, BaCl2, leukotriene C4 or antigen were relaxed 50% by concentrations (IC-50 values) of R-836 of approximately 0.3 microgram/ml (10(-6) M) in all cases. In the conscious guinea-pig, oral or i.p. administration of R-836 prevented asphyxial collapse, death or dyspneic changes produced by histamine, antigen of LTC4. In anesthetized guinea-pigs, R-836 reduced bronchoconstriction produced by antigen or PAF (Konzett-Rössler preparation). In the dog, i.v. or intraduodenal administration of R-836 reduced bronchoconstriction produced by methacholine or histamine. In the rat, i.p. administration of R-836 reduced bronchoconstriction produced by 5-HT or antigenic challenge. In these in vivo models, when direct comparisons were made, R-836 was estimated to possess 2 to 3 times the potency of theophylline. R-836, at doses 80 times those necessary to produce bronchodilation, had no effect on blood pressure or heart rate of guinea-pigs. R-836 was not a CNS stimulant in mice, was not diuretic in rats, only marginally inhibited adenosine-induced responses in mice and guinea-pigs and was a weak inhibitor of phosphodiesterase in vitro.

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