Optimized free energies from bidirectional single-molecule force spectroscopy

An optimized method for estimating path-ensemble averages using data from processes driven in opposite directions is presented. Based on this estimator, bidirectional expressions for reconstructing free energies and potentials of mean force from single-molecule force spectroscopy-valid for biasing potentials of arbitrary stiffness-are developed. Numerical simulations on a model potential indicate that these methods perform better than unidirectional strategies.     

Hit-to-Lead Short Peptides against Dengue Type 2 Envelope Protein: Computational and Experimental Investigations

Data from the World Health Organisation show that the global incidence of dengue infection has risen drastically, with an estimated 400 million cases of dengue infection occurring annually. Despite this worrying trend, there is still no therapeutic treatment available. Herein, we investigated short peptide fragments with a varying total number of amino acid residues (peptide fragments) from previously reported dengue virus type 2 (DENV2) peptide-based inhibitors, DN58wt (GDSYIIIGVEPGQLKENWFKKGSSIGQMF), DN58opt (TWWCFYFCRRHHPFWFFYRHN), DS36wt (LITVNPIVTEKDSPVNIEAE), and DS36opt (RHWEQFYFRRRERKFWLFFW), aided by in silico approaches: peptide–protein molecular docking and 100 ns of molecular dynamics (MD) simulation via molecular mechanics using Poisson–Boltzmann surface area (MMPBSA) and molecular mechanics generalised Born surface area (MMGBSA) methods. A library of 11,699 peptide fragments was generated, subjected to in silico calculation, and the candidates with the excellent binding affinity and shown to be stable in the DI-DIII binding pocket of DENV2 envelope (E) protein were determined. Selected peptides were synthesised using conventional Fmoc solid-phase peptide chemistry, purified by RP-HPLC, and characterised using LCMS. In vitro studies followed, to test for the peptides’ toxicity and efficacy in inhibiting the DENV2 growth cycle. Our studies identified the electrostatic interaction (from free energy calculation) to be the driving stabilising force for the E protein–peptide interactions. Five key E protein residues were also identified that had the most interactions with the peptides: (polar) LYS36, ASN37, and ARG350, and (nonpolar) LEU351 and VAL354; these residues might play crucial roles in the effective binding interactions. One of the peptide fragments, DN58opt_8-13 (PFWFFYRH), showed the best inhibitory activity, at about 63% DENV2 plague reduction, compared with no treatment. This correlates well with the in silico studies in which the peptide possessed the lowest binding energy (−9.0 kcal/mol) and was maintained steadily within the binding pocket of DENV2 E protein during the MD simulations. This study demonstrates the use of computational studies to expand research on lead optimisation of antiviral peptides, thus explaining the inhibitory potential of the designed peptides.     

A novel, one-pot, three-component synthesis of 4H-pyrido[1,2-a]pyrimidines

A novel, one-pot, three-component synthesis of 4H-pyrido[1,2-a]pyrimidines is described. The reactive 1:1 zwitterionic intermediate, formed by the addition of isocyanides to dialkyl acetylenedicarboxylates, was trapped by N-(2-pyridyl)amides to produce the title compounds under mild reaction conditions in good yields.     

A new, one-pot, three-component synthesis of 4H-pyrido[1,2-a]pyrimidines, 4H-pyrimido[1,2-a]pyrimidines, and 4H-pyrazino[1,2-a]pyrimidines

A new, one-pot and three-component synthesis of 4H-pyrido[1,2-a]pyrimidines, 4H-pyrimido[1,2-a]pyrimidines, and 4H-pyrazino[1,2-a]pyrimidines is described. The reactive 1:1 zwitterionic intermediate, formed by the addition of isocyanides to dialkyl acetylenedicarboxylates, was trapped by N-(2-heteroaryl)amides to yield a ketenimine intermediate, which was cyclized and then rearranged under the reaction conditions to afford the title compounds under mild reaction conditions in good yields. Single-crystal X-ray analysis conclusively confirms the structure of the obtained bridgehead bicyclic 6-6 heterocyclic compounds.     

Synthesis and Dynamic NMR Spectroscopic Study of Dialkyl 4-Ethoxy-1-(1-naphthyl)-5-oxo-4,5-dihydro-1<Emphasis Type="Italic">H</Emphasis>-pyrrole-2,3-dicarboxylates

Summary. Protonation of the reactive 1:1 intermediate produced in the reaction between triphenylphosphine and dialkyl acetylenedicarboxylates with ethyl 2-(1-naphthylamino)-2-oxoacetate, leads to a vinylphosphonium salt, which undergoes intramolecular Wittig reaction to produce dialkyl 4-ethoxy-1-(1-naphthyl)-5-oxo-4,5-dihydro-1H-pyrrole-2,3-dicarboxylates in excellent yields. A dynamic NMR effect is observed in the ¹H NMR spectra of the title compounds as a result of restricted rotation around the single bond linking the naphthalene moiety and the heterocyclic system, which is attributed to the peri interaction between the pyrrole residue and the peri CH group. The free energy of activation (G ) for this process is 58±2kJmol^–1.Received December 6, 2002; accepted December 11, 2002 Published online June 12, 2003     

An efficient one-pot,multi-component diastereoselective synthesis of functionalized cyclopenta[c]chromenes

A novel one-pot, multi-component diastereoselective synthesis of functionalized cyclopenta[c]chromenes is described. This transformation proceeds via a Michael addition-cyclization reaction sequence between trialkyl phosphites, dialkyl acetylenedicarboxylates and in situ generated 2-(1-(2-oxo-2H-chromen-3-yl)alkylidene)malononitriles from the condensation of 3-acyl-2H-chromen-2-ones and malononitrile.     

An efficient synthesis of fully substituted pyrazolo[3,4-b]pyridin-5-amines from α-azidochalcones

A facile, mild and efficient procedure for the synthesis of fully substituted pyrazolo[3,4-b]pyridin-5-amines is reported. A mixture of an α-azidochalcone, a 5-aminopyrazole and t-BuOK was stirred in DMF at ambient temperature for 5?min to afford the corresponding pyrazolo[3,4-b]pyridin-5-amines in good to excellent yields.     

CuI catalyzed-novel one-pot synthesis of aryl alkenyl thioethers through Ullmann-type coupling reactions using carbon disulfide as a sulfur surrogate in the presence of nitroalkanes and aryl iodides

A mild, general and efficient copper-catalyzed system for C-S bond formation is developed. With CuI as catalyst and l-Proline as ligand, the S-arylation of nitroalkane-CS₂ adducts with aryl iodides were performed under mild conditions to give the corresponding products in good to excellent yields.     

<Emphasis Type="Italic">Ab initio</Emphasis> Study of Structural and Conformational Properties of Five- to Nine-Membered Cyclic 1,2,3-Trienes

Summary.  The structures and relative energies of fundamental conformations of cyclopenta-1,2,3-triene, cyclohexa-1,2,3-triene, cylohepta-1,2,3-triene, cycloocta-1,2,3-triene, and cyclonona-1,2,3-triene were calculated by the HF/6-31G^* and MP2/6-31G^*//HF/6-31G^* methods. Only a C _2v symmetric planar conformation is available to cyclopenta-1,2,3-triene and cyclohexa-1,2,3-triene. The calculated energy barrier for ring inversion of the C _S symmetric puckerd conformation of cyclohepta-1,2,3-triene via the planar geometry is 62.2 kJ·mol⁻¹. The C ₂ symmetric twist conformation of cycloocta-1,2,3-triene was calculated to be the most stable one. Conformational racemization of the twist form takes place via the C _S symmetric half-chair geometry, which is by 60.8 kJ·mol⁻¹ less stable than the twist conformer. The C _S symmetric chair and unsymmetrical twist-boat conformations of cyclonona-1,2,3-triene were calculated to have similar energies; their interconversion takes place via an unsymmetrical low-energy (18.4 kJ·mol⁻¹) transition state. The twist (C ₂) and boat (C _S) geometries of cyclonona-1,2,3-triene are higher in energy by 13.2 and 33.9 kJ·mol⁻¹, respectively. Ring inversion in chair and twist-boat conformations takes place via a twist form as intermediate and requires 33.6 kJ·mol⁻¹. Corresponding author. E-mail: isayavar@yahoo.com Received March 25, 2002; accepted April 4, 2002     

One‐Pot Four‐Component Synthesis of N2‐Alkyl‐N3‐[2‐(1,3,4‐oxadiazol‐2‐yl)aryl]benzofuran‐2,3‐diamines

A simple synthesis of N²‐alkyl‐N³‐[2‐(1,3,4‐oxadiazol‐2‐yl)aryl]benzofuran‐2,3‐diamines 5 via a one‐pot four‐component reaction is described (Scheme 1). A mixture of N‐(isocyanoimino)triphenylphosphorane ( 1 ), a 2‐aminobenzoic acid 2 , a 2‐hydroxybenzaldehyde 3 , and an isocyanide 4 in absolute EtOH at room temperature undergoes a smooth reaction to afford 5 in excellent yields (Table).