Substrate Envelope-Designed Potent HIV-1 Protease Inhibitors to Avoid Drug Resistance

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THERMODYNAMIC AND PARTICLE-DYNAMIC STUDIES ON SYNTHESIS OF SILICA NANOPARTICLES USING MICROWAVE-INDUCED PLASMA CVD

1. Introduction1.1 Silica nanoparticles and synthesis methods Silica (SiO2) nanoparticles are widely used in industry asan active filler for polymer reinforcement, a rheologicaladditive in fluids, a free flow agent in powders, and anagent for chemical mechanical polishing during IC (inte-grated circuit) fabrication (Sniegowski & de Boer, 2000).Silica powder is also used for producing silicon carbide(Koc & Cattamanchi, 1998) or opaque silica aerosols (Leeet al., 1995). Many methods can …     

Nonlinear compression of optical solitons

In this paper, we consider nonlinear Schrödinger (NLS) equations, both in the anomalous and normal dispersive regimes, which govern the propagation of a single field in a fiber medium with phase modulation and fibre gain (or loss). The integrability conditions are arrived from linear eigen value problem. The variable transformations which connect the integrable form of modified NLS equations are presented. We succeed in Hirota bilinearzing the equations and on solving, exact bright and dark soliton solutions are obtained. From the results, we show that the soliton is alive, i.e. pulse area can be conserved by the inclusion of gain (or loss) and phase modulation effects.     

Symplectic supercuspidal representations and related problems

In this paper, we summarize the basic structures and properties of irreducible symplectic supercuspidal representations of GLn(F) over a p-adic local field F with characteristic zero, and explore possible topics for further investigation.     

HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants

The acquisition of drug-resistant mutations by infectious pathogens remains a pressing health concern, and the development of strategies to combat this threat is a priority. Here we have applied a general strategy, inverse design using the substrate envelope, to develop inhibitors of HIV-1 protease. Structure-based computation was used to design inhibitors predicted to stay within a consensus substrate volume in the binding site. Two rounds of design, synthesis, experimental testing, and structural analysis were carried out, resulting in a total of 51 compounds. Improvements in design methodology led to a roughly 1000-fold affinity enhancement to a wild-type protease for the best binders, from a Ki of 30-50 nM in round one to below 100 pM in round two. Crystal structures of a subset of complexes revealed a binding mode similar to each design that respected the substrate envelope in nearly all cases. All four best binders from round one exhibited broad specificity against a clinically relevant panel of drug-resistant HIV-1 protease variants, losing no more than 6-13-fold affinity relative to wild type. Testing a subset of second-round compounds against the panel of resistant variants revealed three classes of inhibitors: robust binders (maximum affinity loss of 14-16-fold), moderate binders (35-80-fold), and susceptible binders (greater than 100-fold). Although for especially high-affinity inhibitors additional factors may also be important, overall, these results suggest that designing inhibitors using the substrate envelope may be a useful strategy in the development of therapeutics with low susceptibility to resistance.     

Ultra-low-frequency dust-electromagnetic modes in self-gravitating magnetized dusty plasmas

Obliquely propagating altra-low-frequency dust-electromagnetic waves in a self-gravitating, warm, magnetized, two fluid dusty plasma system have been investigated. Two special cases, namely, dust-Alfvén mode propagating parallel to the external magnetic field and dustmagnetosonic mode propagating perpendicular to the external magnetic field have also been considered. It has been shown that effects of self-gravitational field, dust fluid temperature, and obliqueness significantly modify the dispersion properties of these ultra-low-frequency dust-electromagnetic modes. It is also found that in parallel propagating dust-Alfvén mode these effects play no role, but in obliquely propagating dust-Alfvén mode or perpendicular propagating dust-magnetosonic mode the effect of self-gravitational field plays destabilizing role whereas the effect of dust/ion fluid temperature plays stabilizing role.     

Anchor dependency for non-glycerol based cationic lipofectins: mixed bag of regular and anomalous transfection profiles

Although detailed structure-activity, physicochemical and biophysical investigations in probing the anchor influence in liposomal gene delivery have been reported for glycerol-based transfection lipids, the corresponding investigation for non-glycerol based simple monocationic transfection lipids have not yet been undertaken. Towards this end, herein, we delineate our structure-activity and physicochemical approach in deciphering the anchor dependency in liposomal gene delivery using fifteen new structural analogues (lipids 1-15) of recently reported non-glycerol based monocationic transfection lipids. The C(14) analogues in both series 1 (lipids 1-6) and series 2 (lipids 7-15) showed maximum efficiency in transfecting COS-1 and CHO cells. However, the C(12) analogue of the ether series (lipid 3) exhibited a seemingly anomalous behavior compared with its transfection efficient C(10) and C(14) analogues (lipids 2 and 4) in being completely inefficient to transfect both COS-1 and CHO cells. The present structure-activity investigation also convincingly demonstrates that enhancement of transfection efficiencies through incorporation of membrane reorganizing unsaturation elements in the hydrophobic anchor of cationic lipids is not universal but cell dependent. The strength of the interaction of lipids 1-15 with DNA was assessed by their ability to exclude ethidium bromide bound to the DNA. Cationic lipids with long hydrophobic tails were found, in general, to be efficient in excluding EtBr from DNA. Gel to liquid crystalline transition temperatures of the lipids was measured by fluorescence anisotropy measurement technique. In general (lipid 2 being an exception), transfection efficient lipids were found to have their mid transition temperatures at or below physiological temperatures (37 degrees C).     

Hydrophobic core flexibility modulates enzyme activity in HIV-1 protease

Human immunodeficiency virus Type-1 (HIV-1) protease is crucial for viral maturation and infectivity. Studies of protease dynamics suggest that the rearrangement of the hydrophobic core is essential for enzyme activity. Many mutations in the hydrophobic core are also associated with drug resistance and may modulate the core flexibility. To test the role of flexibility in protease activity, pairs of cysteines were introduced at the interfaces of flexible regions remote from the active site. Disulfide bond formation was confirmed by crystal structures and by alkylation of free cysteines and mass spectrometry. Oxidized and reduced crystal structures of these variants show the overall structure of the protease is retained. However, cross-linking the cysteines led to drastic loss in enzyme activity, which was regained upon reducing the disulfide cross-links. Molecular dynamics simulations showed that altered dynamics propagated throughout the enzyme from the engineered disulfide. Thus, altered flexibility within the hydrophobic core can modulate HIV-1 protease activity, supporting the hypothesis that drug resistant mutations distal from the active site can alter the balance between substrate turnover and inhibitor binding by modulating enzyme activity.