Facile measurement of ¹H-¹5N residual dipolar couplings in larger perdeuterated proteins

We present a simple method, ARTSY, for extracting ¹J(NH) couplings and ¹H-¹⁵N RDCs from an interleaved set of two-dimensional ¹H-¹⁵N TROSY-HSQC spectra, based on the principle of quantitative J correlation. The primary advantage of the ARTSY method over other methods is the ability to measure couplings without scaling peak positions or altering the narrow line widths characteristic of TROSY spectra. Accuracy of the method is demonstrated for the model system GB3. Application to the catalytic core domain of HIV integrase, a 36 kDa homodimer with unfavorable spectral characteristics, demonstrates its practical utility. Precision of the RDC measurement is limited by the signal-to-noise ratio, S/N, achievable in the 2D TROSY-HSQC spectrum, and is approximately given by 30/(S/N) Hz.

Small molecules targeting the interaction between HIV-1 integrase and LEDGF/p75 cofactor

The search of small molecules as protein-protein interaction inhibitors represents a new attractive strategy to develop anti-HIV-1 agents. We previously reported a computational study that led to the discovery of new inhibitors of the interaction between enzyme HIV-1 integrase (IN) and the nuclear protein lens epithelium growth factor LEDGF/p75.(1) Herein, we describe new findings about the binding site of LEDGF/p75 on IN employing a different computational approach. In this way further structural requirements, helpful to disrupt LEDGF/p75-IN binding, have been identified. The main result of this work was the exploration of a relevant hydrophobic region. So we planned the introduction of suitable and simple chemical modifications on our previously reported 'hit' and the new synthesized compounds were subjected to biological tests. The results obtained demonstrate that the hydrophobic pocket could play a key role in improving inhibitory efficacy thus opening new suggestions to design active ligands.

Stimulation of the HIV-1 integrase enzymatic activity and cDNA integration by a peptide derived from the integrase protein

Here we describe the features of a peptide that was selected from the human immunodeficiency virus Type 1 (HIV-1) Integrase (IN) peptide library which interacts with both, the viral Rev and IN proteins. Because of its ability to stimulate the IN enzymatic activity this peptide was designated INS (IN stimulatory). Modification of its amino acid sequence revealed that replacement of its C-terminal lysine by glutamic acid (INS K188E) converts it from a stimulatory peptide to an inhibitory one. Both peptides promoted the dissociation of a previously described complex formed between Rev and IN whose formation results in IN inactivation. INS and INS K188E penetrated HIV-1-infected cells and caused stimulation and inhibition of viral genome integration, respectively. Using cultured cells infected with a DeltaRev HIV revealed that INS can directly activate the viral IN. These results suggest that the stimulatory effect of INS in wild-type virus-infected cells is due to a dual effect: it dissociates the inactive Rev-IN complex and directly activates the free IN.

Computer tools in the discovery of HIV-1 integrase inhibitors

Computer-aided drug design (CADD) methodologies have made great advances and contributed significantly to the discovery and/or optimization of many clinically used drugs in recent years. CADD tools have likewise been applied to the discovery of inhibitors of HIV-1 integrase, a difficult and worthwhile target for the development of efficient anti-HIV drugs. This article reviews the application of CADD tools, including pharmacophore search, quantitative structure-activity relationships, model building of integrase complexed with viral DNA and quantum-chemical studies in the discovery of HIV-1 integrase inhibitors. Different structurally diverse integrase inhibitors have been identified by, or with significant help from, various CADD tools.

[HIV-1 integrase inhibition by dimeric bisbenzimidazoles having different spacers]

HIV-1 integrase is responsible for one of the key steps of the viral replication, integration of the viral cDNA into the host cell genome. Integration inhibition leads to complete block of the virus replication. In this study inhibition of integration by dimeric bisbenzimidazoles DBBI(7) with heptamethylene and DBBI(8) with tri(ethylene glycol) spacers was examined, and it was learned out that IC50 for DBBI(7) was about 0.03 microM, and IC50 for DBBI(8) was about 10 microM. By using cross-linking assays, it was shown that both compounds impeded a proper disposition of DNA-substrate at the active centre of integrase. Dissociation constants for complexes between either DBBI and DNA-substrate of integrase were determined. Calculated Kd values were 270 nM and 140 nM for complexes formed by DBBI(7) and DBBI(8), respectively. Therefore, inhibition of integration does not directly result from the binding of DBBIs with DNA. The dependence of initial rates of enzymatic reaction on the DNA-substrate concentration in presence of different concentrations of inhibitors was found, and inhibition constants were determined. All the data obtained allow us to suppose that the different inhibition activity of DBBI(7) and DBBI(8) results from the different mechanism of their binding: DBBI(7) is a competitive inhibitor of integrase whereas DBBI(8) is assumed to show a more complex mechanism of inhibition.

[Advances in the study of HIV-1 integrase inhibitors of alpha, gamma-diketo compounds]

HIV-1 integrase (IN) is an essential enzyme for retroviral replication. There is no analogue for this enzyme in human cells so that inhibition of IN will not bring strong effect on human body. Thus, HIV-1 IN has become a rational target for therapy of AIDS. This review provides a comprehensive report of alpha, gamma-diketo IN inhibitors discovered in recent years. Compilation of such data will prove to be beneficial in developing QSAR, pharmacophore hypothesis generation and validation, virtual screening and synthesis of compounds with higher activity.

A dynamic model of HIV integrase inhibition and drug resistance

Human immunodeficiency virus type 1 (HIV-1) integrase is one of three virally encoded enzymes essential for replication and, therefore, a rational choice as a drug target for the treatment of HIV-1-infected individuals. In 2007, raltegravir became the first integrase inhibitor approved for use in the treatment of HIV-infected patients, more than a decade since the approval of the first protease inhibitor (saquinavir, Hoffman La-Roche, 1995) and two decades since the approval of the first reverse transcriptase inhibitor (retrovir, GlaxoSmithKline, 1987). The slow progress toward a clinically effective HIV-1 integrase inhibitor can at least in part be attributed to a poor structural understanding of this key viral protein. Here we describe the development of a restrained molecular dynamics protocol that produces a more accurate model of the active site of this drug target. This model provides an advance on previously described models as it ensures that the catalytic DDE motif makes correct, monodentate interactions with the two active-site magnesium ions. Dynamic restraints applied to this coordination state create models with the correct solvation sphere for the metal ion complex and highlight the coordination sites available for metal-binding ligands. Application of appropriate dynamic flexibility to the core domain allowed the inclusion of multiple conformational states in subsequent docking studies. These models have allowed us to (1) explore the effects of key drug resistance mutations on the dynamic flexibility and conformational preferences of HIV integrase and to (2) study raltegravir binding in the context of these dynamic models of both wild type and the G140S/Q148H drug-resistant enzyme.

Designed zinc finger protein interacting with the HIV-1 integrase recognition sequence at 2-LTR-circle junctions

Integration of HIV-1 cDNA into the host genome is a crucial step for viral propagation. Two nucleotides, cytosine and adenine (CA), conserved at the 3' end of the viral cDNA genome, are cleaved by the viral integrase (IN) enzyme. As IN plays a crucial role in the early stages of the HIV-1 life cycle, substrate blockage of IN is an attractive strategy for therapeutic interference. In this study, we used the 2-LTR-circle junctions of HIV-1 DNA as a model to design zinc finger protein (ZFP) targeting at the end terminal portion of HIV-1 LTR. A six-contiguous ZFP, namely 2LTRZFP was designed using zinc finger tools. The designed motif was expressed and purified from E. coli to determine its binding properties. Surface plasmon resonance (SPR) was used to determine the binding affinity of 2LTRZFP to its target DNA. The level of dissociation constant (K(d)) was 12.0 nM. The competitive SPR confirmed that 2LTRZFP specifically interacted with its target DNA. The qualitative binding activity was subsequently determined by EMSA and demonstrated the aforementioned correlation. In addition, molecular modeling and binding energy analyses were carried out to provide structural insight into the binding of 2LTRZFP to the specific and nonspecific DNA target. It is suggested that hydrogen-bonding interactions play a key role in the DNA recognition mechanisms of the designed ZFP. Our study suggested an alternative HIV therapeutic strategy using ZFP interference of the HIV integration process.

[Computer-assisted search and optimization of new integrase inhibitor of human immunodeficiency virus]

Finding and optimization of new HIV-1 integrase inhibitors is an important task due to the drawbacks of the existing antiretroviral therapy caused by the significant adverse effects, high cost of the treatment, and emerging resistance. In this study we used computer-assisted methods for finding and optimization of new HIV-1 integrase inhibitors blocking the 3'-processing reaction. Possibility of application of the specialized version of computer program PASS for searching original inhibitors of 3'-processing reaction among the commercially available samples of chemical compounds, belonging to a new chemical class, is shown. We compared the general pharmacological profiles calculated by PASS for the sets of original integrase inhibitors discovered in the study with those for known inhibitors published in literature. It was shown that the predicted average selectivity is close for the compounds from both sets, while the predicted adverse/toxic actions are less for the original compounds. Differences of pharmacological profiles of original compounds and known from literature inhibitors of 3'-processing pointed out to the essential novelty of our substances. Significantly less deviations from the recommended values for QikProp parameters, which characterized the ADME properties, have been observed for the original compounds than for the integrase inhibitors published in literature. Thus, one may come to the conclusion that the original compounds look more prospective comparing to the earlier known inhibitors of 3'-processing.

Impact of emission anisotropy on fluorescence spectroscopy and FRET distance measurements

The objective of this report is to provide a practical and improved method for estimating Förster resonance energy transfer distance measurement error due to unknown angles in the dipole orientation factor based on emission anisotropy measurements. We improve on the method of Dale et al. (1979), which has minor mistakes and is frequently interpreted in overly optimistic ways in the literature. To facilitate proper fluorescence intensity measurements, we also evaluated instrument parameters that could impact the measurement. The apparent fluorescence intensity of isotropic samples depends on the sample emission anisotropy, fluorometer geometry, and optical apertures. We separate parameters of the sample, and those of the cylindrically symmetric illumination source and detector in the equations describing results of unpolarized and polarized fluorescence intensity measurements. This approach greatly simplifies calculations compared with the more universal method of Axelrod (1989). We provide a full computational method for calculating the Förster resonance energy transfer distance error and present a graph describing distance error in the simplest case.

Docking-based 3D-QSAR study of HIV-1 integrase inhibitors

In this study, 3-aroyl-1,1-dioxo-1,4,2-benzodithiazine and 4-chloro-N-(4-oxopyrimidin-2-yl)-2-mercaptobenzenesulfonamide derivatives (HIV-1 integrase inhibitors) were used for CoMFA and CoMSIA to determine the substructures required for the activity of these molecules. To explore the binding mode of inhibitors, docking studies were done and docked conformation of highly active molecule was used as template for alignment. The best CoMFA model yielded the cross validation r(2)(cv)=0.728, non-cross validation r(2)(ncv)=0.934 and predictive r(2)(pred)=0.708. The best CoMSIA model yielded a cross validation r(2)(cv)=0.794, non-cross validation r(2)(ncv)=0.928 and predictive r(2)(pred)=0.59. It was found that steric (CoMFA) and hydrophobic fields (CoMSIA) have large contribution towards the inhibitory activity than the other fields. Docking and 3D-QSAR studies have provided clues to a better understanding of interaction between the inhibitors and HIV-1 integrase.

New approaches for inhibiting HIV integrase: a journey beyond the active site

Integrase (IN) inhibitors have proven to be highly beneficial in the treatment of HIV infection. The recently approved inhibitor, raltegravir, the phase III clinical trials compound elvitegravir, and all other agents reported to be in clinical trials bind to the active site of IN and share the same mechanism of action. There is a high probability for the development of cross resistance among these compounds. Therefore, drugs targeting alternative mechanisms and binding sites on IN are desired. Two potential sites for inhibiting the enzyme have been disclosed recently. The first site is located in the catalytic core domain and is used by the enzyme to bind the host protein lens epithelium-derived growth factor. The second site was identified by the selective covalent trapping of pyridoxal phosphate to the C-terminal domain of the enzyme. The targeting of these sites as a potential novel approach for inhibiting HIV IN is reviewed.

Peptides derived from HIV-1 integrase that bind Rev stimulate viral genome integration

Background

The human immunodeficiency virus type 1 (HIV-1) integrase protein (IN), catalyzes the integration of viral DNA into the host cell genome. IN catalyzes the first step of the integration process, namely the 3′-end processing in which IN removes a pGT dinucleotide from the 3′ end of each viral long terminal repeat (LTR). Following nuclear import of the viral preintegration complex, the host chromosomal DNA becomes accessible to the viral cDNA and the second step of the integration process, namely the strand-transfer step takes place. This ordered sequence of events, centered on integration, is mandatory for HIV replication.

Methodology/Principal Findings

Using an integrase peptide library, we selected two peptides, designated INr-1 and INr-2, which interact with the Rev protein and probably mediate the Rev-integrase interaction. Using an in-vitro assay system, we show that INr-1 and INr-2 are able to abrogate the inhibitory effects exerted by Rev and Rev-derived peptides on integrase activity. Both INr-1 and INr-2 were found to be cell-permeable and nontoxic, allowing a study of their effect in HIV-1-infected cultured cells. Interestingly, both INr peptides stimulated virus infectivity as estimated by production of the viral P24 protein, as well as by determination of the appearance of newly formed virus particles. Furthermore, kinetics studies revealed that the cell-permeable INr peptides enhance the integration process, as was indeed confirmed by direct determination of viral DNA integration by real-time PCR.

Conclusions/Significance

The results of the present study raise the possibility that in HIV-infected cells, the Rev protein may be involved in the integration of proviral DNA by controlling/regulating the activity of the integrase. Release from such inhibition leads to stimulation of IN activity and multiple viral DNA integration events.

An unusual helix turn helix motif in the catalytic core of HIV-1 integrase binds viral DNA and LEDGF

Background

Integrase (IN) of the type 1 human immunodeficiency virus (HIV-1) catalyzes the integration of viral DNA into host cellular DNA. We identified a bi-helix motif (residues 149–186) in the crystal structure of the catalytic core (CC) of the IN-Phe185Lys variant that consists of the α₄ and α₅ helices connected by a 3 to 5-residue turn. The motif is embedded in a large array of interactions that stabilize the monomer and the dimer.

Principal Findings

We describe the conformational and binding properties of the corresponding synthetic peptide. This displays features of the protein motif structure thanks to the mutual intramolecular interactions of the α₄ and α₅ helices that maintain the fold. The main properties are the binding to: 1- the processing-attachment site at the LTR (long terminal repeat) ends of virus DNA with a K_d (dissociation constant) in the sub-micromolar range; 2- the whole IN enzyme; and 3- the IN binding domain (IBD) but not the IBD-Asp366Asn variant of LEDGF (lens epidermal derived growth factor) lacking the essential Asp366 residue. In our motif, in contrast to the conventional HTH (helix-turn-helix), it is the N terminal helix (α₄) which has the role of DNA recognition helix, while the C terminal helix (α₅) would rather contribute to the motif stabilization by interactions with the α₄ helix.

Conclusion

The motif, termed HTHi (i, for inverted) emerges as a central piece of the IN structure and function. It could therefore represent an attractive target in the search for inhibitors working at the DNA-IN, IN-IN and IN-LEDGF interfaces.

Study on the binding mode of the integrase with DNA via steered molecular dynamics simulation

Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme in the lifecycle of this virus and also an important target for the study of anti-HIV drugs. In the current work, a model for the active site of IN and viral DNA was built by combining experimental data with the results of steered molecular dynamics simulation. The model was then taken into a series automatic molecular docking calculations with two groups of inhibitors. According to the results of molecular docking, the inhibitors of the second group share a similar binding model with those of the first group, though they have no common scaffold. The newly built model of the IN-DNA complex is helpful for our subsequent research on the design of IN inhibitors.

Characterization and structural analysis of HIV-1 integrase conservation

The HIV-1 integrase, responsible for the chromosomal integration of the newly synthesized double-stranded viral DNA into the host genomic DNA, represents a new and important target of potential clinical relevance. For instance, two integrase inhibitors, raltegravir and elvitegravir, have been shown to be promising in clinical trials, and the first has been recently made available for clinical practice. As is the case for other antiviral drugs, drug resistance to integrase inhibitors occurs both in vitro and/or in vivo through the selection of mutations within the HIV genome. Indeed, many integrase mutations have already been associated with resistance to all the different integrase inhibitors tested in in vitro and/or in vivo studies. Among them, about 40 substitutions have been specifically associated with the development of resistance to raltegravir and/or elvitegravir; some of them were also found in vivo in patients failing such integrase inhibitors. The relevance of integrase mutations in clinical practice has yet to be defined, in light of the lack of long-term follow-up of treated patients and the limited data about the prevalence of integrase inhibitor-associated mutations in integrase inhibitor-naive patients (either untreated, or treated with antiretrovirals not containing integrase inhibitors). Therefore, by structural analysis elaboration and literature discussion, the aim of this review is to characterize the conserved residues and regions of HIV-1 integrase and the prevalence of mutations associated with integrase inhibitor resistance, by matching data originated from a well-defined cohort of HIV-1 B subtype-infected individuals (untreated and antiretroviral-treated) and data originated from the public Los Alamos Database available in the literature (all patients integrase inhibitor-naive by definition). In integrase inhibitor-naive patients, 180 out of 288 HIV-1 integrase residues (62.5%) are conserved (< 1% variability). Residues involved in protein stability, multimerization, DNA binding, catalytic activity, and in the binding with the human cellular cofactor LEDGF/p75 are fully conserved. Some of these residues clustered into large defined regions of consecutive invariant amino acids, suggesting that consecutive residues in specific structural domains are required for the correct performance of HIV-1 integrase functions. All primary signature mutations emerging in patients failing raltegravir (Y143R, Q148H/K/R, N155H) or elvitegravir (T66I, E92Q, S147G, Q148H/K/R, N155H), as well as secondary mutations (H51Y, T66A/K, E138K, G140S/A/C, Y143C/H, K160N, R166S, E170A, S230R, D232N, R263K) were completely absent or highly infrequent (< 0.5%) in integrase inhibitor-naive patients, either infected with HIV-1 B subtype (drug-naive or antiretroviral-treated), or non-B subtypes/group N and O. Differently, other mutations (L74M, T97A, S119G/R, V151I, K156N, E157Q, G163K/R, V165I, I203M, T206S, S230N) occurred as natural polymorphisms with a different prevalence according to different HIV-1 subtype/circulating recombinant form/group. In conclusion, the HIV-1 integrase in vivo is an enzyme requiring the full preservation of almost two-thirds of its amino acids in the absence of specific integrase inhibitor pressure. Primary mutations associated with resistance to integrase inhibitors clinically relevant today are absent or highly infrequent in integrase inhibitor-naive patients. The characterization of the highly conserved residues (involved in protein stability, multimerization, DNA binding, catalytic activity, LEDGF binding, and some with still poorly understood function) could help in the rational design of new HIV-1 inhibitors with alternative mechanisms of action and more favorable resistance profiles.

Surface plasmon resonance study on HIV-1 integrase strand transfer activity

Understanding the molecular mechanism of HIV-1 integrase (IN) activity is critical to find functional inhibitors for an effective AIDS therapy. A robust, fast, and sensitive method for studying IN activity is required. In this work, an assay for real-time label-free monitoring of the IN activity based on surface plasmon resonance was developed. This assay enabled direct monitoring of the integration of a viral doubled-stranded (ds) DNA into the host genome. The strand transfer reaction was detected by using two different DNA targets: supercoiled plasmid (pUC 19) and short palindrome oligonucleotide. The effect of the length of the DNA target on the possibility to monitor the actual process of the strand transfer reaction is discussed. The surface density of integrated ds-DNA was determined. IN binding to the oligonucleotide complexes and model DNA triplexes in the presence of various divalent ions as metal cofactors was investigated as well. The assay developed can serve as an important analytical tool to search for potential strand transfer reaction inhibitors as well as for the study of compounds interfering with the binding of ds long terminal repeats-IN complexes with the host DNA.

Symmetrical 1-pyrrolidineacetamide showing anti-HIV activity through a new binding site on HIV-1 integrase

AIM

To characterize the functional and pharmacological features of a symmetrical 1-pyrrolidineacetamide, N,N'-(methylene-di-4,1-phenylene) bis-1-pyrrolidineacetamide, as a new anti-HIV compound which could competitively inhibit HIV-1 integrase (IN) binding to viral DNA.

METHODS

A surface plasma resonance (SPR)-based competitive assay was employed to determine the compound's inhibitory activity, and the 3-(4,5-dimethylthiazol- 2-yl)-2,5-diphenyltetrazolium bromide cell assay was used to qualify the antiviral activity. The potential binding sites were predicted by molecular modeling and determined by site-directed mutagenesis and a SPR binding assay.

RESULTS

1-pyrrolidineacetamide, N,N'-(methylene-di-4,1-phenylene) bis-1-pyrrolidineacetamide could competitively inhibit IN binding to viral DNA with a 50% inhibitory concentration (IC(50)) value of 7.29+/-0.68 micromol/L as investigated by SPR-based investigation. Another antiretroviral activity assay showed that this compound exhibited inhibition against HIV-1(IIIB) replication with a 50% effective concentration (EC(50)) value of 40.54 micromol/L in C8166 cells, and cytotoxicity with a cytotoxic concentration value of 173.84 micromol/L in mock-infected C8166 cells. Molecular docking predicted 3 potential residues as 1-pyrrolidineacetamide, N,N'-(methylene-di-4,1-phenylene)bis-1- pyrrolidineacetamide binding sites. The importance of 3 key amino acid residues (Lys103, Lys173, and Thr174) involved in the binding was further identified by site-directed mutagenesis and a SPR binding assay.

CONCLUSION

This present work identified a new anti-HIV compound through a new IN-binding site which is expected to supply new potential drug-binding site information for HIV-1 integrase inhibitor discovery and development.

Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors

HIV-1 integrase is the third enzymatic target of antiretroviral (ARV) therapy. However, few data have been published on the distribution of naturally occurring amino acid variation in this enzyme. We therefore characterized the distribution of integrase variants among more than 1,800 published group M HIV-1 isolates from more than 1,500 integrase inhibitor (INI)-naïve individuals. Polymorphism rates equal or above 0.5% were found for 34% of the central core domain positions, 42% of the C-terminal domain positions, and 50% of the N-terminal domain positions. Among 727 ARV-naïve individuals in whom the complete pol gene was sequenced, integrase displayed significantly decreased inter- and intra-subtype diversity and a lower Shannon's entropy than protease or RT. All primary INI-resistance mutations with the exception of E157Q--which was present in 1.1% of sequences--were nonpolymorphic. Several accessory INI-resistance mutations including L74M, T97A, V151I, G163R, and S230N were also polymorphic with polymorphism rates ranging between 0.5% to 2.0%.

HIV type 1 integrase inhibitors: from basic research to clinical implications

Similar to other retroviruses, productive infection with HIV-1 requires three key steps in the viral replication: (i) reverse transcription of viral genomic RNA into viral cDNA by the viral reverse transcriptase; (ii) integration of viral cDNA into host cell genome using the viral integrase; and (iii) cleavage of newly synthesized viral polypeptide by the viral protease into individual viral proteins during new virion assembly. Following their discovery, all three viral enzymes were considered as targets for antiretroviral drugs. However, while multiple reverse transcriptase and protease inhibitors have been used for more than 12 years to treat HIV-infected individuals, only recently has the viral integrase enzyme emerged as an alternative, clinically validated target to block HIV-1 replication. Here we review the biology of HIV-1 integration, the mechanisms of action and development of resistance to integrase inhibitors, and the latest data on the most recent clinical trials involving this promising, novel class of antiretroviral drugs.

HIV integrase: a target for drug discovery

Current antiviral strategies against HIV rely on structure-function analysis of HIV reverse transcriptase (RT) and protease (PR). The third viral pol gene product, HIV integrase (IN), is also a good target for drug discovery, since IN is essential for retroviral replication and, moreover, it has no obvious functional analogue in the host. IN forms a ternary complex with metal ions and DNA and has a mechanism of catalysis common with other polynucleotidyl transferases. Although there is no structural information for full-length IN available, structures of all three functional IN domains have been determined by X-ray crystallography and NMR spectroscopy. The N-terminal domain has a novel zinc-binding fold, the catalytic domain shares a common structural motif with other polynucleotidyl transferases, and the C-terminal DNA-binding domain has a Src-homology-3-like fold. This structural information provides the basis for drug development. In turn, increasing numbers of IN inhibitors identified so far may serve structure-function analysis of IN. The final goal is the development of new classes of anti-HIV drugs, which can be added to the repertoire of anti-RT and anti-PR drugs.

Four-tiered pi interaction at the dimeric interface of HIV-1 integrase critical for DNA integration and viral infectivity

HIV-1 integrase (IN) is an essential enzyme for viral infection. Here, we report an extensive pi electron orbital interaction between four amino acids, W132, M178, F181 and F185, located at the dimeric interface of IN that is critical for the strand transfer activity alone. Catalysis of nine different mutant IN proteins at these positions were evaluated. Whereas the 3'-processing activity is predominantly strong, the strand transfer activity of each enzyme was completely dependent on an intact pi electron orbital interaction at the dimeric interface. Four representative IN mutants were constructed in the context of the infectious NL4.3 HIV-1 viral clone. Whereas viruses with an intact pi electron orbital interaction at the IN dimeric interface replicated comparable to wild type, viruses containing an abolished pi interaction were non-infectious. Q-PCR analysis of viral DNA forms during viral replication revealed pleiotropic effects of most mutations. We hypothesize that the pi interaction is a critical contact point for the assembly of functional IN multimeric complexes, and that IN multimerization is required for a functional pre-integration complex. The rational design of small molecule inhibitors targeting the disruption of this pi-pi interaction should lead to powerful anti-retroviral drugs.

Integrase, LEDGF/p75 and HIV replication

HIV integrates a DNA copy of its genome into a host cell chromosome in each replication cycle. The essential DNA cleaving and joining chemistry of integration is known, but there is less understanding of the process as it occurs in a cell, where two complex and dynamic macromolecular entities are joined: the viral pre-integration complex and chromatin. Among implicated cellular factors, much recent attention has coalesced around LEDGF/p75, a nuclear protein that may act as a chromatin docking factor or receptor for lentiviral pre-integration complexes. LEDGF/p75 tethers HIV integrase to chromatin, protects it from degradation, and strongly influences the genome-wide pattern of HIV integration. Depleting the protein from cells and/or over-expressing its integrase-binding domain blocks viral replication. Current goals are to establish the underlying mechanisms and to determine whether this knowledge can be exploited for antiviral therapy or for targeting lentiviral vector integration in human gene therapy.

Tn5 transposase as a useful platform to simulate HIV-1 integrase inhibitor binding mode

The targeting of HIV-1 integrase (IN) for the design of novel antiviral compounds has until now proceeded slowly, mainly due to the lack of three-dimensional structures reporting detail interactions between IN and its DNA substrates as well as the complete enzyme with its three domains. Recently, we have proposed that Tn5 transposase (Tnp) can be used as a useful surrogate model for IN in attempt to address the potential binding modes of Integrase Strand Transfer Inhibitors. In order to strengthen our hypothesis, molecular dynamics simulations of IN inhibitors bound to Tn5 Tnp active site are now reported. A comparison of the obtained results with well documented specific mutations associated with resistance to HIV-1 IN inhibitors confirmed that Tn5 Tnp can provide a valuable platform for the structure-based discovery of new ligands.

Design, synthesis, and antiviral evaluation of some 3'-carboxymethyl-3'-deoxyadenosine derivatives

3'-Carboxymethyl-3'-deoxyadenosine derivatives were prepared from 2'-O-TBDMS-3'-[(ethoxycarbonyl)methyl]-3'-deoxyadenosine (1) via simple and efficient procedures. Conversion of 1 to its 5'-azido-5'-deoxy derivative 5 was accomplished via a novel one-pot method employing 5'-activation (TosCl) followed by efficient nucleophilic displacement with tetramethylguanidinium azide. Compound 5 was converted to 5'-[(N-methylcarbamoyl)amino] derivative 8 via one-pot reduction/acylation employing H(2)/Pd-C followed by treatment with p-nitrophenyl N-methylcarbamate. N(6)-phenylcarbamoyl groups were introduced by treatment with phenylisocyanate, and an efficient new method for lactonization of 2'-O-TBDMS-3'-[(ethoxycarbonyl)methyl]-3'-deoxyadenosines to give corresponding 2',3'-lactones was also developed. Target compounds were evaluated for anti-HIV and anti-HIV integrase activities, but were not active at the concentrations tested.