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.

The Biochemical Impact by Covalent Shielding of the Anionic Oxygen of the Phosphate Group in DNA and RNA as Methylated Phosphotriester Linkage on the Inhibition of DNA Duplication and on HIV-1 RNA Viral Infectivity Has Been Seriously Overlooked

With the help of model experiments, we are able to offer a detailed proposal for the inhibition of DNA duplication and no inhibition of RNA viral infectivity. As a backbone, we introduced methyl phosphotriester (MPTE). Duplex formation according to the traditional Watson and Crick base-pairing: [(MPTE)n−1 DNA] * DNA and [(MPTE)n−1 DNA] * RNA, where n = number of DNA and RNA bases. However, in the latter case, inhibition is obtained by reduction of the number of MPTE linkages, as is confirmed with model experiments and under biological conditions with micro (mi)RNA substrates. The latter results have recently been published. One or more single MPTEs are disseminated over different places of DNA without neighbour MPTEs (Prof. Wen-Yih Chen and his group, Taiwan).

Nonlinear Uncertain HIV-1 Model Controller by Using Control Lyapunov Function

In this paper, we introduce a new Control Lyapunov Function (CLF) approach for controlling the behavior of nonlinear uncertain HIV-1 models. The uncertainty is in decay parameters and also external control setting. CLF is then applied to different strategies. One such strategy considers input into infected cells population stage and the other considers input into a virus population stage. Furthermore, by adding noise to the HIV-1 model a realistic comparison between control strategies is presented to evaluate the system’s dynamics. It has been demonstrated that nonlinear control has effectiveness and robustness, in reducing virus loading to an undetectable level.

一类具时滞与饱和发生率的HIV-1传染病模型的全局稳定性

提出了一类具时滞与饱和发生率的HIV-1传染病模型,分析讨论了无病平衡点E0(T0,0,0)和正平衡点E+(T*,I*,V*)的全局稳定性。通过构造Lyapunov函数和La Salle不变集原理,证明了当dμ>sγβ,对任意τ≥0,无病平衡点E0(T0,0,0)是全局渐近稳定的;当dμ<sγβ,对任意τ≥0,E+(T*,I*,V*)是全局渐近稳定的,并通过数值模拟验证了所得结论。

Computer-assisted anti-AIDS drug development: cyclophilin B against the HIV-1 subtype A V3 loop

Aim: The objects of this study originated from the experimental observations, whereby the HIV -1 gp120 V3 loop is a high-affinity ligand for immunophilins, and consisted in generating the structural complex of cyclophilin (Cyc) B belonging to immunophilins family with the virus subtype A V3 loop (SA-V3 loop) as well as in specifying the Cyc B segment forming the binding site for V3 synthetic copy of which, on the assumption of keeping the 3D peptide structure in the free state, may present a forwardlooking basic structure for anti-AIDS drug development. Methods: To reach the objects of view, molecular docking of the HIV-1 SA-V3 loop structure determined previously with the X-ray conformation of Cyc B was put into practice by Hex 4.5 program (http://www.loria.fr/~ritchied/ hex/) and the immunophilin stretch responsible for binding to V3 (Cyc B peptide) was identified followed by examination of its 3D structure and dynamic behavior in the unbound status. To design the Cyc B peptide, the X-ray conformation for the identical site of the native protein was involved in the calculations as a starting model to find its best energy structural variant. The search for this most preferable structure was carried out by consecutive use of the molecular mechanics and simulated annealing methods. The molecular dynamics computations were implemented for the Cyc B peptide by the GROMACS computer package (http:// www.gromacs.org/). Results: The overmolecular structure of Cyc B with V3 was built by computer modeling tools and the immunophilinderived peptide able to mask effectively the structurally invariant V3 segments embracing the functionally crucial amino acids of the HIV-1 gp120 envelope protein was constructed and analyzed. Conclusions: Starting from the joint analysis of the results derived with those of the literature, the generated peptide was suggested to offer a promising basic structure for making a reality of the protein engineering projects aimed at developing the anti-AIDS drugs able to stop the HIV’s spread.

Flux Balance Analysis Reveals Potential Anti-HIV-1 Metabolic Targets

Background:Human immunodeficiency virus type 1(HIV-1)remains a persistent global health challenge.Therefore,a continuous exploration of novel therapeutic strategies is essential.A comprehensive understanding of how HIV-1 utilizes the cellular metabolism machinery for replication can provide insights into new therapeutic approaches.Methods:In this study,we performed a flux balance analysis using a genome-scale metabolic model(GEM)integrated with an HIV-1 viral biomass objective function to identify potential targets for anti–HIV-1 interventions.We generated a GEM by integrating an HIV-1 production reaction into CD4+T cells and optimized for both host and virus optimal states as objective functions to depict metabolic profiles of cells in the status for optimal host biomass maintenance or for optimal HIV-1 virion production.Differential analysis was used to predict biochemical reactions altered optimal for HIV-1 production.In addition,we conducted in silico simulations involving gene and reaction knock-outs to identify potential anti–HIV-1 targets,which were subsequently validated by human phytohemagglutinin(PHA)blasts infected with HIV-1.Results:Differential analysis identified several altered biochemical reactions,including increased lysine uptake and oxidative phosphorylation(OXPHOS)activities in the virus optima compared with the host optima.In silico gene and reaction knock-out simulations revealed de novo pyrimidine synthesis,and OXPHOS could serve as potential anti–HIV-1 metabolic targets.In vitro assay confirmed that targeting OXPHOS using metformin could suppress the replication of HIV-1 by 56.6%(385.4±67.5 pg/mL in the metformintreated group vs.888.4±32.3 pg/mL in the control group,P<0.001).Conclusion:Our integrated host-virus genome-scale metabolic study provides insights on potential targets(OXPHOS)for anti-HIV therapies.

Current humanized mouse models for studying human immunology and HIV-1 immuno-pathogenesis

A robust animal model for "hypothesis-testing/mechanistic" research in human immunology and immuno-pathology should meet the following criteria.First,it has well-studied hemato-lymphoid organs and target cells similar to those of humans.Second,the human pathogens establish infection and lead to relevant diseases.Third,it is genetically inbred and can be manipulated via genetic,immunological and pharmacological means.Many human-tropic pathogens such as HIV-1 fail to infect murine cells due to the blocks at multiple steps of their life cycle.The mouse with a reconstituted human immune system and other human target organs is a good candidate.A number of human-mouse chimeric models with human immune cells have been developed in the past 20 years,but most with only limited success due to the selective engraftment of xeno-reactive human T cells in hu-PBL-SCID mice or the lack of significant human immune responses in the SCID-hu Thy/Liv mouse.This review summarizes the current understanding of HIV-1 immuno-pathogenesis in human patients and in SIV-infected primate models.It also reviews the recent progress in the development of humanized mouse models with a functional human immune system,especially the recent progress in the immunodeficient mice that carry a defective gammaC gene.NOD/SCID/gammaC-/(NOG or NSG) or the Rag2-/-/gammaC-/double knockout (DKO) mice,which lack NK as well as T and B cells (NTB-null mice),have been used to reconstitute a functional human immune system in central and peripheral lymphoid organs with human CD34+ HSC.These NTB-hu HSC humanized models have been used to investigate HIV-1 infection,immuno-pathogenesis and therapeutic interventions.Such models,with further improvements,will contribute to study human immunology,human-tropic pathogens as well as human stem cell biology in the tissue development and function in vivo.

The Establishment of an In Vivo HIV-1 Infection Model in Humanized B-NSG Mice

Suitable animal models for human immunodeficiency virus type 1(HIV-1)infection are important for elucidating viral pathogenesis and evaluating antiviral strategies in vivo.The B-NSG(NOD-PrkdcscidIl2rgtm1/Bcge)mice that have severe immune defect phenotype are examined for the suitability of such a model in this study.Human peripheral blood mononuclear cells(PBMCs)were engrafted into B-NSG mice via mouse tail vein injection,and the repopulated human T-lymphocytes were observed at as early as 3-weeks post-transplantation in mouse peripheral blood and several tissues.The humanized mice could be infected by HIV-1,and the infection recapitulated features of T-lymphocyte dynamic observed in HIV-1 infected humans,meanwhile the administration of combination antiretroviral therapy(cART)suppressed viral replication and restored T lymphocyte abnormalities.The establishment of HIV-1 infected humanized B-NSG mice not only provides a model to study virus and T cell interplays,but also can be a useful tool to evaluate antiviral strategies.

Improving the positional adaptability:structurebased design of biphenyl-substituted diaryltriazines as novel non-nucleoside HIV-1 reverse transcriptase inhibitors

In order to improve the positional adaptability of our previously reported naphthyl diaryltriazines(NP-DATAs),synthesis of a series of novel biphenyl-substituted diaryltriazines(BP-DATAs)with a flexible side chain attached at the C-6 position is presented.These compounds exhibited excellent potency against wild-type(WT)HIV-1 with EC50 values ranging from 2.6 to 39 nmol/L and most of them showed low nanomolar anti-viral potency against a panel of HIV-1 mutant strains.Compounds 5 j and 6 k had the best activity against WT,single and double HIV-1 mutants and reverse transcriptase(RT)enzyme comparable to two reference drugs(EFV and ETR)and our lead compound NP-DATA(1).Molecular modeling disclosed that the side chain at the C-6 position of DATAs occupied the entrance channel of the HIV-1 reverse transcriptase non-nucleoside binding pocket(NNIBP)attributing to the improved activity.The preliminary structure-activity relationship and PK profiles were also discussed.

Synthesis and biological evaluation of a series of2-(((5-akly/aryl-1H-pyrazol-3-yl)methyl)thio)-5-alkyl-6-(cyclohexylmethyl)-pyrimidin-4(3H)-ones as potential HIV-1 inhibitors

A series of 2-(((5-akly/aryl-1 H-pyrazol-3-yl)methyl)thio)-5-alkyl-6-(cyclohexylmethyl)-pyrimidin-4(3 H)-ones were synthesized and their anti-HIV-1 activities were evaluated.Most of these compounds were highly active against wild-type(WT)HIV-1 strain(ⅢB)with EC50 values in the range of0.0038-0.4759μmol/L.Among those compounds,I-11 had an EC50 value of 3.8 nmol/L and SI(selectivity index)of up to 25,468 indicating excellent activity against WT HIV-1.In vitro anti-HIV-1 activity and resistance profile studies suggested that compounds 1-11 and 1-12 displayed potential anti-HIV-1 activity against laboratory adapted strains and primary isolated strains including different subtypes and tropism strains(EC50s range from 4.3 to 63.6 nmol/L and 18.9-219.3 nmol/L,respectively).On the other hand,it was observed that those two compounds were less effective with EC50 values of 2.77 and4.87μmol/L for HIV-1 A17(K103 N+Y181 C).The activity against reverse transcriptase(RT)was also evaluated for those compounds.Both I-11 and 1-12 obtained sub-micromolar IC50 values showing their potential in RT inhibition.The pharmacokinetics examination in rats indicated that compound 1-11 has acceptable pharmacokinetic properties and bioavailability.Preliminary structure-activity relationships and molecular modeling studies were also discussed.

Conformational analysis on anti-HIV-1 peptide T22 ([Tyr^(5,12),Lys^7]-polyphemusinⅡ)

The conformational scan of anti-HIV peptide T22 ([Tyr5,12, Lys7]-polyphemusin II) backbone on a deformed potential energy surface (PES) was performed using the potential smoothing searching (PSS) protocol. All located minima were then transferred to the original PES using undeformed optimized potentials for liquid simulations (OPLS) potential function, and minimized by multi-con-former minimization (MCM). For solution-phase calculations, the GB/SA continuum model for water was used. This application of PSS integrated with MCM is proved a feasible method for solving the multiple-minimum problem in the conformational analysis of flexible molecules with cyclic structure.

A systematic analysis of intrinsic regulators for HIV-1 R5 to X4 phenotypic switch

Background： Human immunodeficiency virus isolates most often use chemokine receptor CCR5 or CXCR4 as a coreceptor to enter target cells. During early stages of HIV-1 infection, CCR5-tropic viruses are the predominant species. The CXCR4-tropic viruses may emerge late in infection. Recognition of factors influencing this phenotypic switch may give some hints on the antiviral strategies like anti-H1V/AIDS drugs, gene therapy and vaccines. Methods： To investigate the mechanism that triggers R5 to X4 phenotypic switch, we performed a systematic sensitivity analysis based on a five-dimensional model with time-varying parameters. We studied the sensitivity of each factor to the CCR5-to-CXCR4 tropism switch and acquired some interesting outcomes beyond expectation. Results： The death rate of free virus （dv）, rate that uninfected CD4＋ T cells arise from precursors （s） and proliferate as stimulated by antigens （r）, and in vivo viral burst size （N） are four robust factors which are constantly observed to have a strong correlation with the evolution of viral phenotype for most patients longitudinally. Conclusions： Crucial factors, which are essential to phenotypie switch and disease progression, are almost the same for different patients at different time points, including the production of both virus and CD4＋ T cells and the decay of virion. It is also worth mentioning that although the sequence of factors sorted by the influence varies between patients, the trends of influences engendered by most factors as disease progresses are similar inter-patients.