Runtao Li

CovalentDock: Automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints

Covalent linkage formation is a very important mechanism for many covalent drugs to work. However, partly due to the limitations of proper computational tools for covalent docking, most covalent drugs are not discovered systematically. In this article, we present a new covalent docking package, the CovalentDock, built on the top of the source code of Autodock. We developed an empirical model of free energy change estimation for covalent linkage formation, which is compatible with existing scoring functions used in docking, while handling the molecular geometry constrains of the covalent linkage with special atom types and directional grid maps. Integrated preparation scripts are also written for the automation of the whole covalent docking workflow. The result tested on existing crystal structures with covalent linkage shows that CovalentDock can reproduce the native covalent complexes with significant improved accuracy when compared with the default covalent docking method in Autodock. Experiments also suggest that CovalentDock is capable of covalent virtual screening with satisfactory enrichment performance. In addition, the investigation on the results also shows that the chirality and target selectivity along with the molecular geometry constrains are well preserved by CovalentDock, showing great capability of this method in the application for covalent drug discovery.

Iodine–triphenylphosphine mediated sulfenylation of imidazoheterocycles with sodium sulfinates

An efficient approach to sulfenyl imidazoheterocycles has been developed via iodine–triphenylphosphine mediated direct sulfenylation of imidazoheterocycles with sodium sulfinates. The reactions proceed smoothly under transition-metal-free conditions with a broad range of substrate scope, giving the desired products in moderate to excellent yields.

Novel EGFR inhibitors prepared by combination of dithiocarbamic acid esters and 4-anilinoquinazolines.

On the basis of combination strategy, a novel series of EGFR inhibitors were designed and synthesized by combination of dithiocarbamic acid esters and 4-anilinoquinazolines. The effect of the synthesized compounds on cell proliferation was evaluated by MTT assay in three human cancer cell lines: MDA-MB-468, SK-BR-3 and HCT-116. Two compounds (11d and 11f) were found more potent against all three cell lines and five compounds (11a, 11d-11g) were found more potent against both MDA-MB-468 and SK-BR-3 than Lapatinib. SAR studies revealed that the substituents on C6 and C7 positions of quinazoline, the amine component of dithiocarbamate moiety and the linker greatly affected the activity. This work provides a promising new strategy for the preparation of potent tyrosine kinase inhibitors.

Design, synthesis and biological evaluation of tripeptide boronic acid proteasome inhibitors

A series of tripeptide boronate proteasome inhibitors were designed and synthesized on the basis of our previously built tripeptide aldehyde 3D-QSAR models. All the synthesized compounds were evaluated for their proteasome-inhibitory activities in an isolated 20S rabbit proteasome, and selected compounds were evaluated for their antitumor activities in vitro against four human cancer cell lines. Biological results showed bulky and negative substituents at P(2) position improved the proteasome-inhibitory potency obviously, which completely conformed to the theoretical models, while those at P(3) position thoroughly deviated from the 3D-QSAR model. Most of the screened compounds showed less than 1 nM inhibitory potency and high selectivity against 20S proteasome, of which 7f is the most potent (IC(50)=0.079 nM) and twofold more active than bortezomib (IC(50)=0.161 nM). Cell viability indicated hydrophilic 4-hydroxyphenyl substituent at P(2) or P(3) position was not favorable to the cellular activities. Especially for the two hematologic cancer cell lines, HL-60 and U266, 7f inhibited them at the level of less than 10 nM and was more potent than the control bortezomib. It is being considered a promising new lead to be developed for the treatment of various cancers.

Synthesis, in Vitro and in Vivo Biological Evaluation, Docking Studies, and Structure—Activity Relationship (SAR) Discussion of Dipeptidyl Boronic Acid Proteasome Inhibitors Composed of β-Amino Acids

A series of novel dipeptidyl boronic acid proteasome inhibitors composed of beta-amino acids were synthesized, in vitro and in vivo biologically evaluated, and theoretically modeled for the first time. From the screened racemic compounds in enzyme, 4i was the most active. The IC(50) value of its pure enantiomer 4q was 9.6 nM, 36-fold more active than its isomer 4p and as active as the marketed bortezomib in inhibiting human 20S proteasome. This candidate also showed good activities with IC(50) values nearly less than 5 microM against several human solid and hematologic tumor cell lines. Safety evaluation in vivo with zebrafish and Sprague-Dawley (SD) rats showed that the candidate 4q was less toxic than bortezomib. Pharmacokinetic profiles suggested candidate 4q showed a more plasma exposure and longer half-life than bortezomib. Docking results indicated that 4q nearly interacted with 20S proteasome in a similar way as bortezomib.

Primary 1,2-diamine catalysis III: an unexpected domino reaction for the synthesis of multisubstituted cyclohexa-1,3-dienamines

The first organocatalyzed multicomponent domino reactions of aryl ketones, aldehydes and malononitrile were carried out successfully to afford multisubstituted cyclohexa-1,3-dienamines in satisfactory yields.

Y(OTf)3-catalyzed novel Mannich reaction of N-alkoxycarbonylpyrroles, formaldehyde and primary amine hydrochlorides

Abstract A novel Mannich reaction between N- alkoxycarbonylpyrroles, formaldehyde and primary amine hydrochlorides is catalyzed by Y(OTf) 3 to afford a monoaminoalkylation product in good yield in aqueous media.

Discovery and optimization of novel dual dithiocarbamates as potent anticancer agents.

A series of dual dithiocarbamates were synthesized and evaluated for their in-vitro anticancer activities on human non-small cell lung cancer cell line H460. Nine compounds exhibited significant antiproliferative activities with IC50 less than 1 μM. Among them, compound 14m showed the highest inhibitory activity against H460 cell and inhibited the growth of nine types of tumor cells with IC50 values less than 1 μM. It also achieved IC50 of 54 nM and 23 nM against HepG2 and MCF-7 cell lines, respectively. Preliminary structure-activity relationship study indicated that: a) when the methyl group (region A) is substituted with benzene rings, ortho substitution on the benzene ring is favored for activity; b) substitution with heterocyclic structures at region A exhibited greater impact on the anti-tumor activity of compounds, in which pyridine ring, thiazole ring, coumarin and benzo[b]thiophene are favored and quinoline ring is the most favored; c) substitution with different amines (region B) also showed marked effect on the activity of compounds and dimethylamine and morpholine are preferred to other tested amines.

An Efficient One-Pot Synthesis of 2-Hydroxyalkyl Dithiocarbamates

Abstract In the presence of anhydrous potassium phosphate, epoxides reacted with carbon disulfide and primary or secondary amines in acetone to give the corresponding 2-hydroxyalkyl dithiocarbamates regioselectively in moderate to good yield.

Copper-mediated synthesis of N-fused heterocycles via Csp–S coupling reaction and 5-endo-dig cyclization sequence

A novel method was developed for the preparation of N-fused heterocycles via a Csp–S coupling reaction and a sequence of 5-endo-dig cyclization. This method involves the reaction of –NHC(S)NH-containing compounds and alkynes in the presence of CuCl and N,N′-dicyclohexylimidazolium chloride.