A 3D-QSAR Study of HIV-1 Integrase Inhibitors Using RASMS and Topomer CoMFA

Acquired Immunodeficiency Syndrome(AIDS) is a significant human health threat around the world. Therefore, the study of anti-human immunodeficiency virus(HIV) drug design has become an important task for today’s society. In this paper, a three-dimensional quantitative structure-activity relationships study(3 D-QSAR) was conducted on 53 HIV-1 integrase inhibitors(IN) using random sampling analysis on molecular surface(RASMS) and Topomer comparative molecular field analysis(Topomer CoMFA). The multiple correlation coefficients of fitting, cross-validation, and external validation of two models were 0.926, 0.815 and 0.908 and 0.930, 0.726 and 0.855, respectively. The results indicated that two models obtained had both favorable estimation stability and good prediction capability. Topomer Search was used to search appropriate R groups from ZINC database, and 28 new compounds were designed thereby. The Topomer CoMFA model was subsequently used to predict the biological activity of these compounds, showing that 24 of the new compounds were more active than the template molecule. Ligands of the template molecule and new designed compounds were used for molecular docking to study the interaction of these compounds with the protein receptor. The results show that the ligands would form hydrogen-bonding interactions with the residues LEU58, THR83, GLN62, MET155, LYS119 and ALA154 of the protein receptor generally, thereby providing additional insights for the design of even more effective HIV/AIDS drugs.

Building the Pharmacophore Model of HIV-1 Integrase Strand Transfer Inhibitors and Studying Their Inhibition Mechanism

The replication of HIV-1 requires the integration of its cyclic DNA into host DNA by HIV-1 integrase （IN）, which includes two important reactions, 3＇-processing and strand transfer, both catalyzed by HIV-1 IN. Disrupting either of the reactions will fulfill the purpose of inhibiting the replication of HIV-1. In this paper, pharmacophore modeling and molecular docking are employed to investigate the inhibition mechanism of the HIV-1 IN strand transfer inhibitors （INSTIs）. Based on the results, we suggest that the inhibition mechanism of INSTIs involves the inhibitor chelating the cofactors Mg2＋ and its forming hydrogen bonds with some crucial residues adjacent to the DDE active center.

Synthesis of 6-sulfamoyl-4-oxoquinoline-3-carboxylic acid derivatives as integrase antagonists with anti-HIV activity

A series of novel 6-sulfamoyl-4-oxoquinoline-3-carboxylic acids derivatives have been synthesized and screened for HIV integrase inhibition activity. Their structures were confirmed by ESI-MS, ^1H NMR and ^13C NMR. 2009 Li Ming Hu. Published by Elsevier B.V. on behalf of Chinese Chemical Society. All rights reserved.

Retroviral integrase protein and intasome nucleoprotein complex structures

Retroviral replication proceeds through the integration of a DNA copy of the viral RNA genome into the host cellular genome, a process that is mediated by the viral integrase(IN) protein. IN catalyzes two distinct chemical reactions: 3'-processing, whereby the viral DNA is recessed by a di- or trinucleotide at its 3'-ends, and strand transfer, in which the processed viral DNA ends are inserted into host chromosomal DNA. Although IN has been studied as a recombinant protein since the 1980 s, detailed structural understanding of its catalytic functions awaited high resolution structures of functional IN-DNA complexes or intasomes, initially obtained in 2010 for the spumavirus prototype foamy virus(PFV). Since then, two additional retroviral intasome structures, from the α-retrovirus Rous sarcoma virus(RSV) and β-retrovirus mouse mammary tumor virus(MMTV), have emerged. Here, we briefly review the history of IN structural biology prior to the intasome era, and then compare the intasome structures of PFV, MMTV and RSV in detail. Whereas the PFV intasome is characterized by a tetrameric assembly of IN around the viral DNA ends, the newer structures harbor octameric IN assemblies. Although the higher order architectures of MMTV and RSV intasomes differ from that of the PFV intasome, they possess remarkably similar intasomal core structures. Thus, retroviral integration machineries have adapted evolutionarily to utilize disparate IN elements to construct convergent intasome core structures for catalytic function.

Multifunctional facets of retrovirus integrase

The retrovirus integrase(IN) is responsible for integration of the reverse transcribed linear c DNA into the host DNA genome. First, IN cleaves a dinucleotide from the 3' OH blunt ends of the viral DNA exposing the highly conserved CA sequence in the recessed ends. IN utilizes the 3' OH ends to catalyze the concerted integration of the two ends into opposite strands of the cellular DNA producing 4 to 6 bp staggered insertions, depending on the retrovirus species. The staggered ends are repaired by host cell machinery that results in a permanent copy of the viral DNA in the cellular genome. Besides integration, IN performs other functions in the replication cycle of several studied retroviruses. The proper organization of IN within the viral internal core is essential for the correct maturation of the virus. IN plays a major role in reverse transcription by interacting directly with the reverse transcriptase and by binding to the viral capsid protein and a cellular protein. Recruitment of several other host proteins into the viral particle are also promoted by IN. IN assists with the nuclear transport of the preintegration complex across the nuclear membrane. With several retroviruses, IN specifically interacts with different host protein factors that guide the preintegration complex to preferentially integrate the viral genome into specific regions of the host chromosomal target. Human gene therapy using retrovirus vectors is directly affected by the interactions of IN with these host factors. Inhibitors directed against the human immunodeficiency virus(HIV) IN bind within the active site of IN containing viral DNA ends thus preventing integration and subsequent HIV/AIDS.

Synthesis and Biological Activities of Quinoline Derivatives as HIV-1 Integrase Inhibitors

Based on the structure of the integrase core domain and pharmacophore perception, the authors picked out the hit quinolone derivative 1 as the lead compound via virtual screen in ACD, MDDIL NCI and Chinese Herb three-dimensional database with the aid of DOCK4.0 program and synthesized a series of analogues of compound 1. Their primary anti-HIV properties against integrase reveal that 6-position methyl group on the benzene ring of quinolone plays a more important role than chlorine, 7-position methyl group or no substituted group. But the title compounds exhibit little difference When the substituted group was phenyl or thienyl on the pyridine ring of quinoline.

Synthesis and HIV-1 Integrase Inhibitory Activity of Furanone Derivatives

Twenty novel furanone derivatives, based on the structure of raltegravir which was the first HIV-1 inte- grase（IN） inhibitor approved by the United States Food and Drug Administration（US FDA）, were designed, synthesized and characterized by ^1H NMR, IR and MS. The biological activities of these compounds against HIV-1 IN in vitro were evaluated. The assay results indicate that the replacement of pyrimidinone with furanone decreased the inhibitory activity of the compounds to HIV-1 IN. Compounds 3i, 3j and 3t show moderate inhibitory activity against HIV-1 IN and selectively inhibit the strand transfer reaction.

Investigation of formation of dimeric G-quadruplex of HIV-1 integrase inhibitor by nuclear magnetic resonance

In this research, an unusually dimeric G-quadruplex of d（GGGTGGGTGGGTGGGT） （SI）, the potent nanomolar HIV-1 integrase inhibitor, was detected by nuclear magnetic resonance （NMR）. This result has been confirmed by electrospray ionization mass spectrometry （ESI-MS） and circular dichroism （CD）.

Synthesis, Crystal Structure and Anti-integrase Activity of 25,27-Bis[(Z)-4-(p-methoxyphenyl)-4-hydroxybut-3-en-2-one-1-methyl]-26,28-dihydroxycalix[4]arene

The title compound （C50H.44010） was synthesized and structurally determined by single-crystal X-ray diffraction method. It crystallizes in monoclinic, space group P21/c with a = 16.713（4）, b --- 13.189（3）, c = 19.434（5） A, β = 104.411（4）°, Mr = 804.85, Dc = 1.288 g/cm3, V = 4149.2（17） A3, Z = 4, F（000） = 1696, #（MoKa） = 0.089 mm-1T = 296（2） K, 7279 independent reflections with 3172 observed ones （I 〉 2δ（/））, R = 0.0520 and wR = 0.1203 with GOF = 0.928 （R = 0.1464 and wR = 0.1657 for all data）. The calixarene moiety maintains the symmetric cone conformation through intramolecular O-H…O hydrogen bonds. Preliminary bioassays indicated that the title compound has a potent inhibitory activity against the strand transfer process of HIV-1 integrase.

Molecular Modeling of Quinoline-Based Compounds as Potential Dual Inhibitors of Reverse Transcriptase and Integrase of HIV

As follow-up of our past publication?[1], we propose that quinolones (as part of the pyridinone family) are capable to increase the number of interactions with HIV reverse transcriptase (RT) or integrase (IN) by adding a halogen in position C-8 of aromatic portion of the quinolones. This addition could help with the activity of dual inhibitors of RT and IN. In this work, we add a chlorine atom with the rationale to identify in the docking simulations a halogen interaction with the oxygen in the near aminoacids in the binding pockets of RT and IN enzymes. Our docking studies started with RT and 320 structures. Later, we took 73 structures with good results in docking with RT. The structures that we choose contain ester or acids groups in C-3 due the structural similarity with groups in charge to interact with the Mg++ ions in Elvitegravir. In conclusion, we obtained 14 structures that could occupy the allosteric pocket of RT and could inhibit the catalytic activity of IN, for this reason could be dual inhibitors. A major perspective of this work is the synthesis and testing of the potential dual inhibitors designed.

Multidrug Resistant <i>Shigella</i>Associated with Class 1 Integrase and Other Virulence Genes as a Cause of Diarrhea in Pediatric Patients

Background: Shigella is one of the most serious pathogens associated with bloody diarrhea in children. The empiric antibiotic therapy of enteric illness with blood streaked stool leads to emergence of multi drug resistant (MDR) Shigella. The condition gets exacerbated by presence of integrons that facilitate the horizontal spread. Virulence genes associated with MDR Shigella modulate the patient outcome, particularly in children. Objectives: The present study was aiming at isolation of MDR Shigella from children with diarrheal sickness and characterization of those isolates as regarding presence of class 1 integrase and other virulence genes. Methods: Four hundred and ninety patients under the age of five suffering from diarrheal illness were examined for presence of Shigella in their stool specimens. MDR Shigella was determined using the antibiotic susceptibility testing by disc diffusion method;those isolates were tested for presence of class 1 integrase by PCR. Multiplex PCR assay was used to determine the presence of virulence genes, virA, ial, sen, set1A, set1B, sat, ipaBCD, ipaH and stx in the MDR Shigella isolates. Results: The isolation rate of Shigella from pediatric patients was 5.3%. Most of the isolated Shigella (57.7%) were from infants between 12 and 23 month. 73.1% of the identified Shigella were MDR. intI1 gene was present in 78.9% of MDR isolates. Muliplex PCR revealed that ipaH and ipaBCD, virA, sat, ial, set1A and set1B, sen were detected in 94.7%, 78.9%, 73.7%, 68.4%, 42.1%, 36.8% of the MDR Shigella isolates respectively. Conclusion: The MDR isolates represented a considerable percentage of Shigella detected in pediatric patients. Presence of intI1 gene in most of MDR Shigella reflects the higher possibility of resistant strains spread. Existence of a variety of virulence genes in those isolates is an important indicator of serious disease outcome.

QSAR analysis on benzodithiazine derivatives as HIV-1 integrase inhibitors

Objective:Inhibition of HIV-1 integrase is an important strategy for the treatment of HIV and AIDS.There-fore, HIV-1 integrase inhibitory activity of 3-aroyl-1,1-dioxo-1,4,2-benzodithiazines has been analyzed with different physicochemical parameters.Methods:In the present work,quantitative structure activity relationship studies were performed on a series of benzodithiazines as HIV-1 integrase inhibitors using the modeling software Win CAChe version 6.1.Multiple linear regression analysis was performed to derive quantitative structure activity relationship models which were further evaluated for statistical significance and predictive power by internal and external validation.Results:The best QSAR models were having good correlation coefficient (r) with low standard error of estimation(SEE) and cross validated square of correlation coefficient (q^2 ).The robustness of the models was checked by Y-randomization test and they were identified as good predictive models.The model for HIV integrase(wt) inhibitory activity of benzodithiazines suggest that the increase of dipole moment(Z) of molecules leads to reduce 3’processing and strand transfer inhibitory activity, substitution with high electro positive groups is conducive for the 3’processing inhibitory activity,and the increase in heat of formation is favorable for 3 -processing and strand transfer inhibitory activity.Conclusion: The model for HIV integrase(C65s) inhibitory activity of benzodithiazines suggest that the increase of dipole moment(X) of molecules leads to reduce 3’processing and strand transfer inhibitory activity,and the substitution with high hydrophobic groups is conducive for the 3’processing and strand transfer inhibitory.

Three-dimensional Quantitative Structure-activity Relationship Models of HIV-1 Integrase Inhibitors of DKAs

As one of the three viral encoded enzymes of HIV-1 infection, HIV-1 integrase has become an attractive drug target for the treatment. Diketoacid compounds （DKAs） are one kind of potent and selective inhibitors of HIV-1 IN. In the present work, two three-dimensional QSAR techniques （CoMFA and CoMSIA） were employed to correlate the molecular structure with the activity of inhibiting the strand transfer for 147 DKAs. The all-oritation search （AOS） and all-placement search （APS） were used to optimize the CoMFA model. The diketo and keto-enol tautomers of DKAs were also used to establish the CoMFA models. The results indicated that the enol was the dominant conformation in the HIV-1 IN and DKAs complexes. It can provide a new method and reference to identify the bioactive conformation of drugs by using QSAR analysis. The best CoMSIA model, with five fields combined, implied that the hydrophobic field is very important as well as the steric and electrostatic fields. All models indicated favorable internal validation. A comparative analysis with the three models demonstrated that the CoMFA model seems to be more predictive. The contour maps could afford steric, electrostatic, hydrophobic and H-bond information about the interaction of ligand-receptor complex visually. The models would give some useful guidelines for designing novel and potent HIV-1 integrase inhibitors.

Estimated Binding Energies of Drug-Like and Nondrug-Like Molecules in the Active Site of HIV-1 Integrase, 1BIS.pdb, and Two Mutant Models: Y143R and N155H

Lipinski’s “Rule of Five” was introduced for predicting oral bioavailability to describe drug-like molecules. For the purpose of this research the rules were used to separate potential inhibitors of HIV-1 integrase (1BIS.pdb) into two groups: drug-like and nondrug-like. If one of Lipinski’s “Rule of Five” was not followed the potential inhibitor was classified as nondrug-like. Thirty molecules were identified from the literature, twenty-four drug-like and six nondrug-like, that were docked into the active site of 1BIS.pdb (considered the non-mutated protein) and two mutant models, Y143R and N155H. These are two of the mutations that have led to increased resistance to HIV-1 integrase drugs such as raltegravir and elvitegravir. The computational software, ICM-Pro (Molsoft L.L.C.), was used to determine the estimated binding energy (EBE) of the drug/protein complex. It was found that the nondrug-like molecules generally had a more negative EBE, that is, tighter binding with 1BIS. pdb, though there were several exceptions in the drug-like group. With the protein mutant model Y143R, the majority of drug-like (58%) and nondrug-like molecules (67%) had tighter binding. However, for the mutant model N155H, there was the same percent (46%) of drug-like molecules with tighter binding with the mutant model as with 1BIS.pdb. The drug-like molecules were used when there was a ≥1 kcal/mole difference between 1BIS.pdb and either of the two mutant models to suggest a pharmacophore with structural characteristics for an HIV-1 integrase inhibitor.

Detection of integron integrase genes on King George Island, Antarctica

The presence and diversity of class 1 integrase gene （intl） sequences were evaluated by PCR using previously designed primers. Two clone libraries were constructed from DNA in sediment and microbial mat samples collected on Fildes Peninsula, King George Island, Antarctica.The libraries constructed from samples collected at Halfthree Point （HP） and Norma Cove （NC） contained 62 and 36 partial intl sequences, respectively. These sequences clustered into 10 different groups with 〈 95% amino acid identity. Alignment of the deduced amino acid sequences with those from recognized integron-encoded integrases demonstrated the presence of highly conserved motifs characteristic of intl integrases. The HP library contained 42 nucleotide sequences identical to the class 1 intl gene found in a collection of trimethoprim-resistant （Tmpr） Antarctic Enterobacter sp. isolates, previously collected in the same area. These integrons, located on plasmids, had a genetic organization similar to that of pKOX105 from Klebsiella oxytoca. The 20 remaining HP and NC library sequences were similar to integrase sequences previously determined in a metagenomic analysis of environmental samples. We have demonstrated the presence of integron integrase genes in Antarctic sediment samples. About half these genes were very similar to the class 1 integrons found in human- associated microbiota, suggesting that they originated from human-dominated ecosystems. The remaining integrase genes were probably associated with endemic bacteria.

Increasing Deaths Due to Malignancy in HIV＋ Patients is Associated with Integrase Inhibitor Therapy

Despite reductions in AIDS-related deaths, registries show HIV＋ patients are still dying at a younger age than HIV-peers. Although overall mortality has declined in this population, a growing percent of deaths are due to malignancy. Since the data demonstrating the growing percentage of deaths due to malignancy in the HIV＋ population is derived from registries, the study explores whether the subset dying from malignancy has particular characteristics that can be seen in a well-characterized cohort. In the well-characterized HIV＋ cohort, the percentage of deaths due to cancer was seen to increase over four years （2010-2013） from 21% to 24% to 38% to 40%. The mean CD4-count of those who died from malignancy was 252＋/-42 and 333＋/-36 in patients with death from other causes. The viral load was not suppressed in 26% of patients dying from malignancy. Of patients on integrase inhibitor therapy, 48% of deaths were due to malignancy while in patients not on this therapy, 10% of deaths were due to malignancy （relative risk = 4.8）. In HIV＋ patients, a low CD4-count, failure to achieve viral suppression, and use of integrase inhibitors were associated with malignancy as the cause of death. The association of a specific therapy, integrase inhibition, with malignancy is seen in the study.

The differential effects of integrase strand transfer inhibitors and efavirenz on neuropsychiatric conditions and brain imaging in HIV-positive men who have sex with men

Integrase strand transfer inhibitors(INSTIs)have emerged as the first‐line choice for treating human immunodeficiency virus(HIV)infection due to their superior efficacy and safety.However,the impact of INSTIs on the development of neuropsychiatric conditions in people living with HIV(PLWH)is not fully understood due to limited data.In this study,we conducted a cross‐sectional examination of PLWH receiving antiretroviral therapy,with a specific focus on HIV‐positive men who have sex with men(MSM)on INSTI‐based regimens(n=61)and efavirenz(EFV)‐based regimens(n=28).Participants underwent comprehensive neuropsychiatric evaluations and multimodal magnetic resonance imaging(MRI)scans,including T1‐weighted images and resting‐state functional MRI.Compared to the EFV group,the INSTI group exhibited primarily reduced gray matter volume(GMV)in the right superior parietal gyrus,higher regional homogeneity(ReHo)in the left postcentral gyrus,lower ReHo in the right orbital part of the inferior frontal gyrus,and increased voxel‐wise functional connectivity for the seed region in the left inferior temporal gyrus with clusters in the right cuneus.Furthermore,the analysis revealed a main effect of antiretroviral drugs on GMV changes,but no main effect of neuropsychiatric disorders or their interaction.The repeated analysis of participants who did not switch regimens confirmed the GMV changes in the INSTI group,validating the initial findings.Our study demonstrated gray matter atrophy and functional brain changes in PLWH on INSTI‐based regimens compared to those on EFV‐based regimens.These neuroimaging results provide valuable insights into the characteristics of brain network modifications in PLWH receiving INSTI‐based regimens。

Development of a high-throughput assay for the HIV-1 integrase disintegration reaction

Both HIV-1 integrase (IN) and the central catalytic domain of IN (IN-CCD) catalyze the disintegration reaction in vitro.In this study,IN and IN-CCD proteins were expressed and purified,and a high-throughput format enzyme-linked immunosorbent assay (ELISA) was developed for the disintegration reaction.IN exhibited a marked preference for Mn2+ over Mg2+ as the divalent cation cofactor in disintegration.Baicalein,a known IN inhibitor,was found to be an IN-CCD inhibitor.The assay is sensitive and specific for the study of disintegration reaction as well as for the in vitro identification of antiviral drugs targeting IN,especially targeting IN-CCD.

Wikstroelide M potently inhibits HIV replication by targeting reverse transcriptase and integrase nuclear translocation

AIM： To evaluate the anti-HIV activity and mechanism of action of wikstroelide M, a daphnane diterpene from Daphne acutiloba Rehder （Thymelaeaceae）. METHOD： The anti-HIV activities of wikstroelide M against different HIV strains were evaluated by cytopathic effect assay and p24 quantification assay with ELISA. The inhibitory effect of wikstroelide M on HIV reverse transcription was analyzed by real-time PCR and ELISA. The effect of wikstroelide M on HIV-1 integrase nuclear translocation was observed with a cell-based imaging assay. The effect of wikstroelide M on LEDGF/p75-IN interaction was assayed by molecular docking. RESULTS： Wikstroelide M potently inhibited different HIV-1 strains, including HIV-lmn, HIV-1AI7, and HIV-19495, induced a cytopathic effect, with ECs0 values ranging from 3.81 to 15.65 ng.mL-I. Wikstroelide M also had high inhibitory activities against HIV-2noD and HIV-2cBL_20-induced cytopathic effects with ECs0 values of 18.88 and 31.90 ng.mL 1. The inhibitory activities of wikstroelide M on the three HIV-1 strains were further confirmed by p24 quantification assay, with ECs0 values ranging from 15.16 to 35.57 ng.mL-1. Wikstroelide M also potently inhibited HIV-lnm induced cytolysis in MT-4 cells, with an ECs0 value of 9.60 ng.mL ~. The mechanistic assay showed that wikstroelide M targeted HIV-I reverse transcriptase and nuclear translocation of integrase through disrupting the interaction between integrase and LEDGF/p75. CONCLUSION： Wikslroelide M may be a potent HIV-1 and HIV-2 inhibitor, the mechanisms of action may include inhibition of reverse trascriptase activity and inhibition of integrase nuclear Iranslocation through dismpting the interaction between integrase and LEDGF/p75.

Application of serine integrases for secondary metabolite pathway assembly in Streptomyces

Serine integrases have been shown to be efficient tools for metabolic pathway assembly.To further improve the flexibility and efficiency of pathway engineering via serine integrases,we explored how multiple orthogonally active serine integrases can be applied for use in vitro for the heterologous expression of complex biosynthesis pathways in Streptomyces spp.,the major producers of useful bioactive natural products.The results show that multiple orthogonal serine integrases efficiently assemble the genes from a complex biosynthesis pathway in a single in vitro recombination reaction,potentially permitting a versatile combinatorial assembly approach.Furthermore,the assembly strategy also permitted the incorporation of a well-characterised promoter upstream of each gene for expression in a heterologous host.The results demonstrate how site-specific recombination based on orthogonal serine integrases can be applied in Streptomyces spp.