Virtual Screening, Identification, and Biochemical Characterization of Novel Inhibitors of the Reverse Transcriptase of Human Immunodeficiency Virus Type-1

The reverse transcriptase (RT) of human immunodeficiency virus type-1 (HIV-1) is a leading target in current antiretroviral therapy. Unfortunately, drug-resistant RT mutants evolve under the pressure of these drugs, and therefore, new anti-RT inhibitors are constantly required for HIV-1/AIDS treatment. We virtually screened a large chemical library of compounds against two crystal structures of HIV-1 … Continued

Selective Structure-based Virtual Screening for Full and Partial Agonists of the ß2 Adrenergic Receptor

The recently solved high-resolution X-ray structure of the ß2 adrenergic receptor has been challenged for its ability to discriminate inverse agonists/antagonists from partial/full agonists. Whereas the X-ray structure of the ground state receptor was unsuitable to distinguish true ligands with different functional effects, modifying this structure to reflect early conformational events in receptor activation led … Continued

De Novo Parallel Design, Synthesis, and Evaluation of Inhibitors Against the Reverse Transcriptase of Human Immunodeficiency Virus Type-1 and Drug-resistant Variants

We used molecular modeling to design de novo broad-range inhibitors against wild type and drug-resistant variants of the reverse transcriptase (RT) of human immunodeficiency virus type-1 (HIV-1). First, we screened for small fragments that would interact with each one of four RT structures (one wild type and three mutants). Then, these fragments were linked to … Continued

Identification of Nonpeptide CCR5 Receptor Agonists by Structure-based Virtual Screening

A three-dimensional model of the chemokine receptor CCR5 has been built to fulfill structural peculiarities of its α-helix bundle and to distinguish known CCR5 antagonists from randomly chosen drug-like decoys. In silico screening of a library of 1.6 million commercially available compounds against the CCR5 model by sequential filters (drug-likeness, 2-D pharmacophore, 3-D docking, scaffold … Continued

Parameter Estimation for Scoring Protein-ligand Interactions Using Negative Training Data

Surflex-Dock employs an empirically derived scoring function to rank putative protein-ligand interactions by flexible docking of small molecules to proteins of known structure. The scoring function employed by Surflex was developed purely on the basis of positive data, comprising noncovalent protein-ligand complexes with known binding affinities. Consequently, scoring function terms for improper interactions received little … Continued

Virtual Screening for Aryl Hydrocarbon Receptor Binding Prediction

The overall goal of this study has been to validate computational models for predicting aryl hydrocarbon receptor (AhR) binding. Due to the unavailability of the AhR X-ray crystal structure we have decided to use QSARs models for the binding prediction virtual screening. We have built up CoMFA, Volsurf, and HQSAR models using as a training … Continued

N1-benzoyl-N2-[1-(1-naphthyl)ethyl]-trans-1,2-diaminocyclohexanes: Development of 4-chlorophenylcarboxamide (calhex 231) as a New Calcium Sensing Receptor Ligand Demonstrating Potent Calcilytic Activity

A structure-activity relationship (SAR) study was performed principally at the N1 position of N1-arylsulfonyl-N2-[1-(1-naphthyl)ethyl]-trans-1,2-diaminocyclohexanes, a new family of calcilytics acting at the calcium sensing receptor (CaSR). The most active compound in this series was the 4-(trifluoromethoxy)benzenesulfonyl derivative 7e, which displayed an IC50 of 5.4 ± 0.5 µM with respect to the inhibition of calcium-induced tritiated … Continued

Robust Ligand-based Modeling of the Biological Targets of Known Drugs

Systematic annotation of the primary targets of roughly 1000 known therapeutics reveals that over 700 of these modulate approximately 85 biological targets. We report the results of three analyses. In the first analysis, drug/drug similarities and target/target similarities were computed on the basis of three-dimensional ligand structures. Drug pairs sharing a target had significantly higher … Continued

Structure-based Design, Synthesis, and Biological Evaluation of Novel Inhibitors of Human Cyclophilin A

Cyclophilin A is involved in many cellular processes, including protein folding and intracellular transports. Because cyclophilin A has been shown to interact with HIV-1 gag proteins and to enhance the viral infectivity, nonimmunosuppressive cyclophilin A ligands may represent a new class of therapeutic agents against HIV. Here, we report a virtual screening using structure- and … Continued

Angiotensin II Pseudopeptides Containing 1,3,5-trisubstituted Benzene Scaffolds with High AT2 Receptor Affinity

Two 1,3,5-trisubstituted aromatic scaffolds intended to serve as γ-turn mimetics have been synthesized and incorporated in five pseudopeptide analogues of angiotensin II (Asp-Arg-Val-Tyr-Ile-His-Pro-Phe), replacing Val-Tyr-Ile, Val-Tyr, or Tyr-Ile. All the tested compounds exhibited nanomolar affinity for the AT2 receptor with the best compound (3) having a KI of 1.85 nM. Four pseudopeptides were AT2 selective, … Continued

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