Stapled SC34EK fusion inhibitors with high potency against HIV-1 and improved protease resistance

A single all-hydrocarbon staple introduction in SC34EK can afford a potent HIV inhibitor with high protease resistance for ADIS treatment.     

Support Vector Machines for predicting HIV protease cleavage sites in protein

Knowledge of the polyprotein cleavage sites by HIV protease will refine our understanding of its specificity, and the information thus acquired is useful for designing specific and efficient HIV protease inhibitors. The pace in searching for the proper inhibitors of HIV protease will be greatly expedited if one can find an accurate, robust, and rapid method for predicting the cleavage sites in proteins by HIV protease. In this article, a Support Vector Machine is applied to predict the cleavability of oligopeptides by proteases with multiple and extended specificity subsites. We selected HIV-1 protease as the subject of the study. Two hundred ninety-nine oligopeptides were chosen for the training set, while the other 63 oligopeptides were taken as a test set. Because of its high rate of self-consistency (299/299 = 100%), a good result in the jackknife test (286/299 = 95%) and correct prediction rate (55/63 = 87%), it is expected that the Support Vector Machine method can be referred to as a useful assistant technique for finding effective inhibitors of HIV protease, which is one of the targets in designing potential drugs against AIDS. The principle of the Support Vector Machine method can also be applied to analyzing the specificity of other multisubsite enzymes.     

Computational simulations of HIV-1 proteases--multi-drug resistance due to nonactive site mutation L90M

Human immunodeficiency virus type 1 protease (HIV-1 PR) is one of the proteins that currently available anti-HIV-1 drugs target. Inhibitors of HIV-1 PR have become available, and they have lowered the rate of mortality from acquired immune deficiency syndrome (AIDS) in advanced countries. However, the rate of emergence of drug-resistant HIV-1 variants is quite high because of their short retroviral life cycle and their high mutation rate. Serious drug-resistant mutations against HIV-1 PR inhibitors (PIs) frequently appear at the active site of PR. Exceptionally, some other mutations such as L90M cause drug resistance, although these appear at nonactive sites. The mechanism of resistance due to nonactive site mutations is difficult to explain. In this study, we carried out computational simulations of L90M PR in complex with each of three kinds of inhibitors and one typical substrate, and we clarified the mechanism of resistance. The L90M mutation causes changes in interaction between the side chain atoms of the 90th residue and the main chain atoms of the 25th residue, and a slight dislocation of the 25th residue causes rotation of the side chain at the 84th residue. The rotation of the 84th residue leads to displacement of the inhibitor from the appropriate binding location, resulting in a collision with the flap or loop region. The difference in levels of resistance to the three inhibitors has been explained from energetic and structural viewpoints, which provides the suggestion for promising drugs keeping its efficacy even for the L90M mutant.     

Anti-cancer activity of novel dibenzo[b,f]azepine tethered isoxazoline derivatives

Background  

Nef is an HIV-1 accessory protein essential for viral replication and AIDS progression. Nef interacts with a multitude of host cell signaling partners, including members of the Src kinase family. Nef preferentially activates Hck, a Src-family kinase (SFK) strongly expressed in macrophages and other HIV target cells, by binding to its regulatory SH3 domain. Recently, we identified a series of kinase inhibitors that preferentially inhibit Hck in the presence of Nef. These compounds also block Nef-dependent HIV replication, validating the Nef-SFK signaling pathway as an antiretroviral drug target. Our findings also suggested that by binding to the Hck SH3 domain, Nef indirectly affects the conformation of the kinase active site to favor inhibitor association.     

Computer-aided design and discovery of protein–protein interaction inhibitors as agents for anti-HIV therapy

Protein–protein interactions (PPI) are involved in most of the essential processes that occur in organisms. In recent years, PPI have become the object of increasing attention in drug discovery, particularly for anti-HIV drugs. Although the use of combinations of existing drugs, termed highly active antiretroviral therapy (HAART), has revolutionized the treatment of HIV/AIDS, problems with these agents, such as the rapid emergence of drug-resistant HIV-1 mutants and serious adverse effects, have highlighted the need for further discovery of new drugs and new targets. Numerous investigations have shown that PPI play a key role in the virus’s life cycle and that blocking or modulating them has a significant therapeutic potential. Here we summarize the recent progress in computer-aided design of PPI inhibitors, mainly focusing on the selection of the drug targets (HIV enzymes and virus entry machinery) and the utilization of peptides and small molecules to prevent a variety of protein–protein interactions (viral–viral or viral–host) that play a vital role in the progression of HIV infection.     

Solution structure of HIV-1 protease flaps probed by comparison of molecular dynamics simulation ensembles and EPR experiments

The introduction of multidrug treatment regimens has dramatically prolonged the progression and survival of AIDS patients. However, the success of the long-term treatment has been hindered by strains of HIV that are increasingly resistant to inhibitors of targets such as HIV protease (HIV PR). Therefore, the need for a thorough understanding of the structure and dynamics of HIV PR and how these are altered in resistant mutants is crucial for the design of more effective treatments. Crystal structures of unbound HIV PR show significant heterogeneity and often have extensive crystal packing interactions. Recent site-directed spin labeling (SDSL) and double electron-electron resonance (DEER) spectroscopy studies characterized flap conformations in HIV-1 protease in an inhibited and uninhibited form and distinguished the extent of flap opening in an unbound form. However, the correlation between EPR-measured interspin distances and structural/dynamic features of the flaps has not been established. In this report, we link EPR-based data and 900 ns of MD simulation in explicit water to gain insight into the ensemble of conformations sampled by HIV PR flaps in solution, both in the presence and in the absence of an FDA-approved HIV PR inhibitor.     

The anti-HIV potential of imidazole,oxazole and thiazole hybrids: A mini-review

Human immunodeficiency virus (HIV) especially HIV-1 infection and its progression to acquired immune deficiency syndrome (AIDS) remains a significant global health challenge. The advent of the highly active antiretroviral therapy (HAART) has greatly extended the life expectancy of patients living with HIV, but it has become evident that long-term HAART will not eliminate the HIV reservoir and cure the infection. Moreover, the drug resistance and undesirable side effects hamper efficacious therapy, creating an urgent need to develop novel, more effective and less toxic anti-HIV therapeutics. Imidazole, oxazole and thiazole with two heteroatoms at meta-position of five-membered rings are fascinating structures and constitute an important class of heterocycles in drug discovery. Their derivatives could exert the anti-HIV activity through diverse mechanisms and possess promising antiviral activity against both drug-sensitive and drug-resistant HIV strains. This review summarizes the research progress made regarding the anti-HIV potential of imidazole, oxazole and thiazole hybrids, and the structure–activity relationships (SARs) are also discussed to facilitate further rational design of more effective candidates, covering articles published from 2012 to 2022.     

Understanding the basis of I50V‐induced affinity decrease in HIV‐1 protease via molecular dynamics simulations using polarized force field

Human immunodeficiency virus (HIV)‐1 protease is one of the most promising drug target commonly utilized to combat Acquired Immune Deficiency Syndrome (AIDS). However, with the emergence of drug resistance arising from mutations, the efficiency of protease inhibitors (PIs) as a viable treatment for AIDS has been greatly reduced. I50V mutation as one of the most significant mutations occurring in HIV‐1 protease will be investigated in this study. Molecular dynamics (MD) simulation was utilized to examine the effect of I50V mutation on the binding of two PIs namely indinavir and amprenavir to HIV‐1 protease. Prior to the simulations conducted, the electron density distributions of the PI and each residue in HIV‐1 protease are derived by combining quantum fragmentation approach molecular fractionation with conjugate caps and Poisson–Boltzmann solvation model based on polarized protein‐specific charge scheme. The atomic charges of the binding complex are subsequently fitted using delta restrained electrostatic potential (delta‐RESP) method to overcome the poor charge determination of buried atom. This way, both intraprotease polarization and the polarization between protease and the PI are incorporated into partial atomic charges. Through this study, the mutation‐induced affinity variations were calculated and significant agreement between experiments and MD simulations conducted was observed for both HIV‐1 protease‐drug complexes. In addition, the mechanism governing the decrease in the binding affinity of PI in the presence of I50V mutation was also explored to provide insights pertaining to the design of the next generation of anti‐HIV drugs. © 2015 Wiley Periodicals, Inc.     

HIV-1 protease cleavage site prediction based on amino acid property

Knowledge of the polyprotein cleavage sites by HIV protease will refine our understanding of its specificity, and the information thus acquired is useful for designing specific and efficient HIV protease inhibitors. Recently, several works have approached the HIV-1 protease specificity problem by applying a number of classifier creation and combination methods. The pace in searching for the proper inhibitors of HIV protease will be greatly expedited if one can find an accurate, robust, and rapid method for predicting the cleavage sites in proteins by HIV protease. In this article, we selected HIV-1 protease as the subject of the study. 299 oligopeptides were chosen for the training set, while the other 63 oligopeptides were taken as a test set. The peptides are represented by features constructed by AAIndex (Kawashima et al., Nucleic Acids Res 1999, 27, 368; Kawashima and Kanehisa, Nucleic Acids Res 2000, 28, 374). The mRMR method (Maximum Relevance, Minimum Redundancy; Ding and Peng, Proc Second IEEE Comput Syst Bioinformatics Conf 2003, 523; Peng et al., IEEE Trans Pattern Anal Mach Intell 2005, 27, 1226) combining with incremental feature selection (IFS) and feature forward search (FFS) are applied to find the two important cleavage sites and to select 364 important biochemistry features by jackknife test. Using KNN (K-nearest neighbors) to combine the selected features, the prediction model obtains high accuracy rate of 91.3% for Jackknife cross-validation test and 87.3% for independent-set test. It is expected that our feature selection scheme can be referred to as a useful assistant technique for finding effective inhibitors of HIV protease, especially for the scientists in this field.     

Mangiferin, an anti-HIV-1 agent targeting protease and effective against resistant strains

The anti-HIV-1 activity of mangiferin was evaluated. Mangiferin can inhibit HIV-1(Ⅲ)(B) induced syncytium formation at non-cytotoxic concentrations, with a 50% effective concentration (EC??) at 16.90 μM and a therapeutic index (TI) above 140. Mangiferin also showed good activities in other laboratory-derived strains, clinically isolated strains and resistant HIV-1 strains. Mechanism studies revealed that mangiferin might inhibit the HIV-1 protease, but is still effective against HIV peptidic protease inhibitor resistant strains. A combination of docking and pharmacophore methods clarified possible binding modes of mangiferin in the HIV-1 protease. The pharmacophore model of mangiferin consists of two hydrogen bond donors and two hydrogen bond acceptors. Compared to pharmacophore features found in commercially available drugs, three pharmacophoric elements matched well and one novel pharmacophore element was observed. Moreover, molecular docking analysis demonstrated that the pharmacophoric elements play important roles in binding HIV-1 protease. Mangiferin is a novel nonpeptidic protease inhibitor with an original structure that represents an effective drug development strategy for combating drug resistance.     

Combating susceptibility to drug resistance: lessons from HIV-1 protease

Drug resistance is a major obstacle in modern medicine. However, resistance is rarely considered in drug development and may inadvertently be facilitated, as many designed inhibitors contact residues that can mutate to confer resistance, without significantly impairing function. Contemporary drug design often ignores the detailed atomic basis for function and primarily focuses on disrupting the target's activity, which is necessary but not sufficient for developing a robust drug. In this study, we examine the impact of drug-resistant mutations in HIV-1 protease on substrate recognition and demonstrate that most primary active site mutations do not extensively contact substrates, but are critical to inhibitor binding. We propose a general, structure-based strategy to reduce the probability of drug resistance by designing inhibitors that interact only with those residues that are essential for function.     

An insight to the molecular interactions of the FDA approved HIV PR drugs against L38L↑N↑L PR mutant

The aspartate protease of the human immune deficiency type-1 virus (HIV-1) has become a crucial antiviral target in which many useful antiretroviral inhibitors have been developed. However, it seems the emergence of new HIV-1 PR mutations enhances drug resistance, hence, the available FDA approved drugs show less activity towards the protease. A mutation and insertion designated L38L↑N↑L PR was recently reported from subtype of C-SA HIV-1. An integrated two-layered ONIOM (QM:MM) method was employed in this study to examine the binding affinities of the nine HIV PR inhibitors against this mutant. The computed binding free energies as well as experimental data revealed a reduced inhibitory activity towards the L38L↑N↑L PR in comparison with subtype C-SA HIV-1 PR. This observation suggests that the insertion and mutations significantly affect the binding affinities or characteristics of the HIV PIs and/or parent PR. The same trend for the computational binding free energies was observed for eight of the nine inhibitors with respect to the experimental binding free energies. The outcome of this study shows that ONIOM method can be used as a reliable computational approach to rationalize lead compounds against specific targets. The nature of the intermolecular interactions in terms of the host–guest hydrogen bond interactions is discussed using the atoms in molecules (AIM) analysis. Natural bond orbital analysis was also used to determine the extent of charge transfer between the QM region of the L38L↑N↑L PR enzyme and FDA approved drugs. AIM analysis showed that the interaction between the QM region of the L38L↑N↑L PR and FDA approved drugs are electrostatic dominant, the bond stability computed from the NBO analysis supports the results from the AIM application. Future studies will focus on the improvement of the computational model by considering explicit water molecules in the active pocket. We believe that this approach has the potential to provide information that will aid in the design of much improved HIV-1 PR antiviral drugs.     

Automated molecular simulation based binding affinity calculator for ligand-bound HIV-1 proteases

The successful application of high throughput molecular simulations to determine biochemical properties would be of great importance to the biomedical community if such simulations could be turned around in a clinically relevant timescale. An important example is the determination of antiretroviral inhibitor efficacy against varying strains of HIV through calculation of drug-protein binding affinities. We describe the Binding Affinity Calculator (BAC), a tool for the automated calculation of HIV-1 protease-ligand binding affinities. The tool employs fully atomistic molecular simulations alongside the well established molecular mechanics Poisson-Boltzmann solvent accessible surface area (MMPBSA) free energy methodology to enable the calculation of the binding free energy of several ligand-protease complexes, including all nine FDA approved inhibitors of HIV-1 protease and seven of the natural substrates cleaved by the protease. This enables the efficacy of these inhibitors to be ranked across several mutant strains of the protease relative to the wildtype. BAC is a tool that utilizes the power provided by a computational grid to automate all of the stages required to compute free energies of binding: model preparation, equilibration, simulation, postprocessing, and data-marshaling around the generally widely distributed compute resources utilized. Such automation enables the molecular dynamics methodology to be used in a high throughput manner not achievable by manual methods. This paper describes the architecture and workflow management of BAC and the function of each of its components. Given adequate compute resources, BAC can yield quantitative information regarding drug resistance at the molecular level within 96 h. Such a timescale is of direct clinical relevance and can assist in decision support for the assessment of patient-specific optimal drug treatment and the subsequent response to therapy for any given genotype.     

Drug-resistant molecular mechanism of CRF01_AE HIV-1 protease due to V82F mutation

Human immunodeficiency virus type 1 protease (HIV-1 PR) is one of the major targets of anti-AIDS drug discovery. The circulating recombinant form 01 A/E (CRF01_AE, abbreviated AE) subtype is one of the most common HIV-1 subtypes, which is infecting more humans and is expanding rapidly throughout the world. It is, therefore, necessary to develop inhibitors against subtype AE HIV-1 PR. In this work, we have performed computer simulation of subtype AE HIV-1 PR with the drugs lopinavir (LPV) and nelfinavir (NFV), and examined the mechanism of resistance of the V82F mutation of this protease against LPV both structurally and energetically. The V82F mutation at the active site results in a conformational change of 79′s loop region and displacement of LPV from its proper binding site, and these changes lead to rotation of the side-chains of residues D25 and I50′. Consequently, the conformation of the binding cavity is deformed asymmetrically and some interactions between PR and LPV are destroyed. Additionally, by comparing the interactive mechanisms of LPV and NFV with HIV-1 PR we discovered that the presence of a dodecahydroisoquinoline ring at the P1′ subsite, a [2-(2,6-dimethylphenoxy)acetyl]amino group at the P2′ subsite, and an N2 atom at the P2 subsite could improve the binding affinity of the drug with AE HIV-1 PR. These findings are helpful for promising drug design. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Novel Antiretroviral Therapeutic Strategies for HIV

When the first cases of HIV infection appeared in the 1980s, AIDS was a deadly disease without any therapeutic alternatives. Currently, there is still no cure for most cases mainly due to the multiple tissues that act as a reservoir for this virus besides the high viral mutagenesis that leads to an antiretroviral drug resistance. Throughout the years, multiple drugs with specific mechanisms of action on distinct targets have been approved. In this review, the most recent phase III clinical studies and other research therapies as advanced antiretroviral nanodelivery systems will be here discussed. Although the combined antiretroviral therapy is effective in reducing viral loading to undetectable levels, it also presents some disadvantages, such as usual side effects, high frequency of administration, and the possibility of drug resistance. Therefore, several new drugs, delivery systems, and vaccines have been tested in pre-clinical and clinical trials. Regarding drug delivery, an attempt to change the route of administration of some conventional antiretrovirals has proven to be successful and surpassed some issues related to patient compliance. Nanotechnology has brought a new approach to overcoming certain obstacles of formulation design including drug solubility and biodistribution. Overall, the encapsulation of antiretroviral drugs into nanosystems has shown improved drug release and pharmacokinetic profile.