The increasing incidence of resistance to current HIV-1 therapy underscores the need to develop antiretroviral agents with new mechanisms of action. Integrase, one of three viral enzymes essential for HIV-1 replication, presents an important yet unexploited opportunity for drug development. We describe here the identification and characterization of L-870,810, a small-molecule inhibitor of HIV-1 integrase with potent antiviral activity in cell culture and good pharmacokinetic properties. L-870,810 is an inhibitor with an 8-hydroxy-(1,6)-naphthyridine-7-carboxamide pharmacophore. The compound inhibits HIV-1 integrase-mediated strand transfer, and its antiviral activity in vitro is a direct consequence of this ascribed effect on integration. L-870,810 is mechanistically identical to previously described inhibitors from the diketo acid series; however, viruses selected for resistance to L-870,810 contain mutations (integrase residues 72, 121, and 125) that uniquely confer resistance to the naphthyridine. Conversely, mutations associated with resistance to the diketo acid do not engender naphthyridine resistance. Importantly, the mutations associated with resistance to each of these inhibitors map to distinct regions within the integrase active site. Therefore, we propose a model of the two inhibitors that is consistent with this observation and suggests specific interactions with discrete binding sites for each ligand. These studies provide a structural basis and rationale for developing integrase inhibitors with the potential for unique and nonoverlapping resistance profiles.A gents for the treatment of HIV-1 infection target two of the three virally encoded enzymes and belong to three mechanistic classes known as nucleoside reverse transcriptase, nonnucleoside reverse transcriptase (NNRTI), and protease inhibitors. Although treatment regimens comprising combinations of these agents have significantly reduced AIDS-related morbidity and mortality, it is estimated that 78% of treatment-naive patients harbor viruses that have evolved resistance to at least one of these drug classes (1, 2). The emergence of HIV-1 strains resistant to reverse transcriptase and protease inhibitors highlights the need to develop antiviral agents with novel mechanisms of action.Integrase (3, 4), one of the three virally encoded enzymes required for HIV-1 replication, catalyses the integration of viral DNA into the genome of the host cell. The integration reaction requires three discrete steps: assembly of a stable preintegration complex at the termini of the viral DNA and two sequential transesterification reactions. In the first reaction, 3Ј-end processing, endonucleolytic cleavage of the two 3Ј nucleotides at each DNA end generates 3Ј-hydroxyl groups that function as nucleophiles in the second reaction. The strand breakage of the cellular DNA and concomitant covalent linkage to the viral DNA is a consequence of the second transesterification reaction, strand transfer.The discovery of a series of diketo acids containing HIV-1 integrase i...

We describe the development of cell-permeable beta-secretase inhibitors that demonstratively inhibit the production of the secreted amino terminal fragment of an artificial amyloid precursor protein in cell culture. In addition to potent inhibition in a cell-based assay (IC50 < 100 nM), these inhibitors display impressive selectivity against other biologically relevant aspartyl proteases.

Colonization of the upper respiratory tract by pneumococcus is important both as a determinant of disease and for transmission into the population. The immunological mechanisms that contain pneumococcus during colonization are well studied in mice but remain unclear in humans. Loss of this control of pneumococcus following infection with influenza virus is associated with secondary bacterial pneumonia. We used a human challenge model with type 6B pneumococcus to show that acquisition of pneumococcus induced early degranulation of resident neutrophils and recruitment of monocytes to the nose. Monocyte function was associated with the clearance of pneumococcus. Prior nasal infection with live attenuated influenza virus induced inflammation, impaired innate immune function and altered genome-wide nasal gene responses to the carriage of pneumococcus. Levels of the cytokine CXCL10, promoted by viral infection, at the time pneumococcus was encountered were positively associated with bacterial load.

b S Supporting Information T he primary goal of any drug discovery effort is to increase the potency of prospective compounds to the greatest degree possible while also optimizing the many other physical properties necessary for drug development. In most cases, little effort is invested in understanding the underlying thermodynamic quantities of enthalpy and entropy that are responsible for determining free energy. More recently, it has become common to recast binding free energies in terms of ligand efficiency, that is, the potency per heavy atom.1À5 Ligand efficiency and the thermodynamic properties (ΔH and ΔS) can provide insights into ligand binding that go beyond simple comparisons of potency. It has been suggested that more efficient ligands and ligands with more negative enthalpies of binding 6À8 provide better starting points for lead optimization. While these two concepts have generally been considered independently, an argument will be provided here that they are related.With regard to enthalpy and entropy of binding, Friere and others 6,9 have presented an intriguing argument that drugs (ligands) that bind predominantly due to favorable enthalpies enjoy certain advantages over drugs where binding is driven predominantly by entropy. Some of the arguments in favor of enthalpy are that enthalpic interactions improve selectivity due to their geometric specificity, and they are inherently more efficient since they tend to be larger in magnitude than entropic effects. The second point already hints to an effect on overall ligand efficiency. The case for ligand efficiency has been made extensively in the literature and is now well accepted. Recent work 4,8,10,11 has shown that the standard definition of ligand efficiency is problematic for comparing ligands of disparate size because ligand efficiency is itself a function of molecular size. One question that arises in this connection is the degree to which enthalpy and entropy contribute to the observed decrease in average efficiencies as ligands become larger. Entropy is commonly regarded as a problem for larger ligands since presumably more conformational degrees of freedom should be lost upon binding. Indeed, this was the logic employed by Andrews 2 for including a correction factor in his group additivity scheme based on the number of rotatable bonds. In a previous paper, computational analysis of the contribution of conformational entropy showed no discernible trend 4 with respect to ligand size. The experimental measurement of the thermodynamics of ligand binding can be routinely accomplished through techniques such as isothermal titration calorimetry (ITC).12 However, because of the complexity, quantity of protein required, and lowthroughput of ITC experiments, the enthalpy and entropy of ligand binding are not routinely measured. Through the work of a number of primarily academic laboratories, there has been a steady growth in the availability of this data for a variety of protein targets. Some of this data has been archived in the publicly available ...

We have observed a high correlation between the intermolecular interaction energy (Einter) calculated for HIV-1 protease inhibitor complexes and the observed in vitro enzyme inhibition. A training set of 33 inhibitors containing modifications in the P1' and P2' positions was used to develop a regression equation which relates Einter and pIC50. This correlation was subsequently employed to successfully predict the activity of proposed HIV-1 protease inhibitors in advance of synthesis in a structure-based design program. This included a precursor, 47, to the current phase II clinical candidate, L-735,524 (51). The development of the correlation, its applications, and its limitations are discussed, and the force field (MM2X) and host molecular mechanics program (OPTIMOL) used in this work are described.