De novo design approaches targeting an envelope protein pocket to identify small molecules against dengue virus.

Dengue fever is a mosquito-borne viral disease that has become a major public health concern worldwide. This disease presents with a wide range of clinical manifestations, from a mild cold-like illness to the more serious hemorrhagic dengue fever and dengue shock syndrome. Currently, neither an approved drug nor an effective vaccine for the treatment are available to fight the disease. The envelope protein (E) is a major component of the virion surface. This protein plays a key role during the viral entry process, constituting an attractive target for the development of antiviral drugs. The crystal structure of the E protein reveals the existence of a hydrophobic pocket occupied by the detergent n-octyl-ß-d-glucoside (ß-OG). This pocket lies at the hinge region between domains I and II and is important for the low pH-triggered conformational rearrangement required for the fusion of the virion with the host's cell. Aiming at the design of novel molecules which bind to E and act as virus entry inhibitors, we undertook a de novo design approach by "growing" molecules inside the hydrophobic site (ß-OG). From more than 240000 small-molecules generated, the 2,4 pyrimidine scaffold was selected as the best candidate, from which one synthesized compound displayed micromolar activity. Molecular dynamics-based optimization was performed on this hit, and thirty derivatives were designed in silico, synthesized and evaluated on their capacity to inhibit dengue virus entry into the host cell. Four compounds were found to be potent antiviral compounds in the low-micromolar range. The assessment of drug-like physicochemical and in vitro pharmacokinetic properties revealed that compounds 3e and 3h presented acceptable solubility values and were stable in mouse plasma, simulated gastric fluid, simulated intestinal fluid, and phosphate buffered saline solution.

New ruthenium nitrosyl complexes with tris(1-pyrazolyl)methane (tpm) and 2,2'-bipyridine (bpy) coligands. Structure, spectroscopy, and electrophilic and nucleophilic reactivities of bound nitrosyl.

The new compound [Ru(bpy)(tpm)NO](ClO4)3 [tpm = tris(1-pyrazolyl)methane; bpy = 2,2'-bipyridine] has been prepared in a stepwise procedure that involves the conversion of [Ru(bpy)(tpm)Cl]+ into the aqua and nitro intermediates, followed by acidification. The diamagnetic complex crystallizes to exhibit distorted octahedral geometry around the metal, with the Ru-N(O) bond length 1.774(12) A and the RuNO angle 179.1(12) degrees , typical for a {RuNO}6 description. The [Ru(bpy)(tpm)NO]3+ ion (I) has been characterized by 1H NMR and IR spectroscopies (nu(NO) = 1959 cm(-1)) and through density functional theory calculations. Intense electronic transitions in the 300-350-nm region are assigned through time-dependent (TD)DFT as intraligand pi --> pi for bpy and tpm. The dpi --> pi(bpy) metal-to-ligand charge-transfer transitions appear at higher energies. Aqueous cyclic voltammetric studies show a reversible wave at 0.31 V (vs Ag/AgCl, 3 M Cl-), which shifts to 0.60 V in MeCN, along with the onset of a wave of an irreversible process at -0.2 V. The waves are assigned to the one- and two-electron reductions centered at the NO ligand, leading to species with {RuNO}(7) and {RuNO}(8) configurations, respectively. Controlled potential reduction of I in MeCN led to the [Ru(bpy)(tpm)NO]2+ ion (II), revealing a significant downward shift of nu(NO) to 1660 cm(-1) as well as changes in the electronic absorption bands. II was also characterized by electron paramagnetic resonance, showing an anisotropic signal at 110 K that arises from an S = 1/2 electronic ground state; the g-matrix components and hyperfine coupling tensor resemble the behavior of related {RuNO}7 complexes. Both I and II were characterized through their main reactivity modes, electrophilic and nucleophilic, respectively. The addition of OH- into I generated the nitro complex, with k(OH) = 3.05 x 10(6) M(-1) s(-1) (25 degrees C). This value is among the highest obtained for related nitrosyl complexes and correlates with ENO+/NO, the one-electron redox potential. Complex II is a robust species toward NO release, although a conversion to I was observed in the presence of O2. This reaction afforded a second-order rate law with k = 3.5 M(-1) s(-1) (25 degrees C). The stabilization of the NO radical complex is attributed to the high positive charge of the precursor and to the geometrical and electronic structure as determined by the neutral tpm ligand.