HIV-1 Integrase Pharmacophore:  Discovery of Inhibitors through Three-Dimensional Database Searching

Nicklaus, Marc C.; Neamati, Nouri; Hong, Huasheng; Mazumder, Abhijit; Sunder, Sanjay; Chen, Julie; Milne, G. W. A.; Pommier, ﻿Yves

doi:10.1021/jm960596u

Cited by 165 publications

(147 citation statements)

References 60 publications

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“…Knowledge of key amino acid residues involved in the binding of potential drugs, and therefore which residues are likely to mutate under therapeutic pressure, would inevitably help researchers stay one step ahead of drug-resistant viral strains. A co-crystal structure of one of our inhibitors was previously solved with the ASV-IN (4,5). This complex was subsequently used as a surrogate structure to discover IN inhibitors through highthroughput docking studies (6).…”

mentioning

confidence: 99%

Discovery of a small-molecule HIV-1 integrase inhibitor-binding site

Al‐Mawsawi

Fikkert

Dayam

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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Herein, we report the identification of a unique HIV-1 integrase (IN) inhibitor-binding site using photoaffinity labeling and mass spectrometric analysis. We chemically incorporated a photo-activatable benzophenone moiety into a series of coumarin-containing IN inhibitors. A representative of this series was covalently photocrosslinked with the IN core domain and subjected to HPLC purification. Fractions were subsequently analyzed by using MALDI-MS and electrospray ionization (ESI)-MS to identify photo-crosslinked products. In this fashion, a single binding site for an inhibitor located within the tryptic peptide 128 AACWWAGIK 136 was identified. Site-directed mutagenesis followed by in vitro inhibition assays resulted in the identification of two specific amino acid residues, C130 and W132, in which substitutions resulted in a marked resistance to the IN inhibitors. Docking studies suggested a specific disruption in functional oligomeric IN complex formation. The combined approach of photo-affinity labeling͞MS analysis with site-directed mutagenesis͞molecular modeling is a powerful approach for elucidating inhibitor-binding sites of proteins at the atomic level. This approach is especially important for the study of proteins that are not amenable to traditional x-ray crystallography and NMR techniques. This type of structural information can help illuminate processes of inhibitor resistance and thereby facilitate the design of more potent second-generation inhibitors.drug design ͉ mass spectrometry ͉ photoaffinity labeling H IV-1 integrase (IN) mediates the insertion of viral DNA into the host genome. This process occurs through two separate events, both catalyzed by IN. In the 3Ј-processing reaction, IN cleaves a dinucleotide adjacent to a conserved CA on each terminus of the reverse-transcribed viral DNA. This cleavage results in two 3Ј hydroxyl groups that are used for a subsequent nucleophilic attack. IN then inserts this DNA product into the host genome in the second reaction, termed strand transfer (1, 2). IN reactions can be carried out in vitro by using purified protein, a DNA substrate with ends mimicking the U3 or U5 viral DNA termini, and Mg 2ϩ or Mn 2ϩ as a cofactor (3).Structural information detailing the association between IN and inhibitors under development is of enormous therapeutic importance. Knowledge of key amino acid residues involved in the binding of potential drugs, and therefore which residues are likely to mutate under therapeutic pressure, would inevitably help researchers stay one step ahead of drug-resistant viral strains. A co-crystal structure of one of our inhibitors was previously solved with the ASV -IN (4, 5). This complex was subsequently used as a surrogate structure to discover IN inhibitors through highthroughput docking studies (6). Thus far, only two examples of co-crystal structures of HIV-1 IN core in complex with inhibitors have been reported (7,8). Despite our own repeated attempts, solving co-crystal structures of IN with our potent inhibitors has failed. This pauc...

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mentioning

confidence: 99%

Discovery of a small-molecule HIV-1 integrase inhibitor-binding site

Al‐Mawsawi

Fikkert

Dayam

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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“…The underlying methodology of pharmacophore model was defined by different researchers [33]. Recently, this model was successfully applied in mesangial cell proliferation inhibitor discovery and virtual screening of potential ligands for many targets such as HIV integrase and CCR5 antagonist [34][35][36][37]. In 3D pharmacophore model, the molecular spatial features and volume constraints represent the intrinsic interactions of small bioactive ligands with protein receptors.…”

Section: Ligand-based Approachmentioning

confidence: 99%

Exploring the Ligand-Protein Networks in Traditional Chinese Medicine: Current Databases, Methods and Applications

Zhao

Wei

2014

Advances in Experimental Medicine and Biology

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The traditional Chinese medicine (TCM), which has thousands of years of clinical application among China and other Asian countries, is the pioneer of the "multicomponent-multitarget" and network pharmacology. Although there is no doubt of the efficacy, it is difficult to elucidate convincing underlying mechanism of TCM due to its complex composition and unclear pharmacology. The use of ligand-protein networks has been gaining significant value in the history of drug discovery while its application in TCM is still in its early stage. This paper firstly surveys TCM databases for virtual screening that have been greatly expanded in size and data diversity in recent years. On that basis, different screening methods and strategies for identifying active ingredients and targets of TCM are outlined based on the amount of network information available, both on sides of ligand bioactivity and the protein structures. Furthermore, applications of successful in silico target identification attempts are discussed in detail along with experiments in exploring the ligand-protein networks of TCM. Finally, it will be concluded that the prospective application of ligand-protein networks can be used not only to predict protein targets of a small molecule, but also to explore the mode of action of TCM.

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“…Tang and co-workers utilized ligand-based pharmacophore modelling techniques to identify two non-planar alkaloids as groove binders of the parallel G-quadruplex (Li et al 2009). In their report, the representative pharmacophore was constructed using the CATALYST software package (version 4.11, Accelrys Inc.) (Nicklaus et al 1997). A total of 38 1,4-disubstituted anthraquinone derivatives comprised the training set, with IC50 values against rat glioma C6 cells spanning three orders of magnitudes (from 0.07 mM to 103 mM).…”

Section: Discovery Of Oncogenic Promoter G-quadruplex-stabilizing Ligmentioning

confidence: 99%