Structure-based design of HIV protease inhibitors: sulfonamide-containing 5,6-dihydro-4-hydroxy-2-pyrones as non-peptidic inhibitors

Fluorine in anti-HIV drugs approved by FDA from 1981 to 2023

Human immunodeficiency virus (HIV) is the etiological agent of acquired immunodeficiency syndrome (AIDS). Nowadays, FDA has approved over thirty antiretroviral drugs grouped in six categories. Interestingly, one-third of these drugs contain different number of fluorine atoms. The introduction of fluorine to obtain drug-like compounds is a well-accepted strategy in medicinal chemistry. In this review, we summarized 11 fluorine-containing anti-HIV drugs, focusing on their efficacy, resistance, safety, and specific roles of fluorine in the development of each drug. These examples may be of help for the discovery of new drug candidates bearing fluorine in their structures.

Iridium-Catalyzed Asymmetric Allylic Substitution Reaction of 4-Hydroxypyran-2-one

Pyranones have raised great concerns owing to their considerable applications in a variety of sectors. However, the development of direct asymmetric allylation of 4-hydroxypyran-2-ones is still restricted. Herein, we present an effective iridium-catalyzed asymmetric functionalization technique for the synthesis of 4-hydroxypyran-2-one derivatives over direct and efficient catalytic asymmetric Friedel-Crafts-type allylation by using allyl alcohols. The allylation products could be obtained with good to high yields (up to 96%) and excellent enantioselectivities (>99% ee). Therefore, the disclosed technique provides a new asymmetric synthetic strategy to explore pyranone derivatives in depth, thus providing an interesting approach for global application and further utilization in organic synthesis and pharmaceutical chemistry.

Viral proteases as therapeutic targets

Some medically important viruses-including retroviruses, flaviviruses, coronaviruses, and herpesviruses-code for a protease, which is indispensable for viral maturation and pathogenesis. Viral protease inhibitors have become an important class of antiviral drugs. Development of the first-in-class viral protease inhibitor saquinavir, which targets HIV protease, started a new era in the treatment of chronic viral diseases. Combining several drugs that target different steps of the viral life cycle enables use of lower doses of individual drugs (and thereby reduction of potential side effects, which frequently occur during long term therapy) and reduces drug-resistance development. Currently, several HIV and HCV protease inhibitors are routinely used in clinical practice. In addition, a drug including an inhibitor of SARS-CoV-2 main protease, nirmatrelvir (co-administered with a pharmacokinetic booster ritonavir as Paxlovid®), was recently authorized for emergency use. This review summarizes the basic features of the proteases of human immunodeficiency virus (HIV), hepatitis C virus (HCV), and SARS-CoV-2 and discusses the properties of their inhibitors in clinical use, as well as development of compounds in the pipeline.

Oral administration of tipranavir with long-chain triglyceride results in moderate intestinal lymph targeting but no efficient delivery to HIV-1 reservoir in mesenteric lymph nodes

The introduction of combination antiretroviral therapy (cART) led to substantial improvement in mortality and morbidity of HIV-1 infection. However, the poor penetration of antiretroviral agents to HIV-1 reservoirs limit the ability of the antiretroviral agents to eliminate the virus. Mesenteric lymph nodes (MLNs) are one of the main HIV-1 reservoirs in patients under suppressive cART. Intestinal lymphatic absorption pathway substantially increases the concentration of lipophilic drugs in mesenteric lymph and MLNs when they are co-administered with long-chain triglyceride (LCT). Chylomicrons (CM) play a crucial role in the intestinal lymphatic absorption as they transport drugs to the lymph lacteals rather than blood capillary by forming CM-drug complexes in the enterocytes. Thus, lipophilic antiretroviral drugs could potentially be delivered to HIV-1 reservoirs in MLNs by LCT-based formulation approach. In this study, protease inhibitors (PIs) were initially screened for their potential for intestinal lymphatic targeting using a computational model. The candidates were further assessed for their experimental affinity to CM. Tipranavir (TPV) was the only-candidate with substantial affinity to both artificial and natural CM in vitro and ex vivo. Pharmacokinetics and biodistribution studies were then performed to evaluate the oral bioavailability and intestinal lymphatic targeting of TPV in rats. The results showed similar oral bioavailability of TPV with and without co-administration of LCT vehicle. Although LCT-based formulation led to 3-fold higher concentrations of TPV in mesenteric lymph compared to plasma, the levels of the drug in MLNs were similar to plasma in both LCT-based and lipid-free formulation groups. Thus, LCT-based formulation approach alone was not sufficient for effective delivery of TPV to MLNs. Future efforts should be directed to a combined highly lipophilic prodrugs/lipid-based formulation approach to target TPV, other PIs and potentially other classes of antiretroviral agents to viral reservoirs within the mesenteric lymphatic system.

Direct synthesis of 4-hydroxycoumarins and 4-hydroxy-6-methyl-2-pyrone containing chroman-4-ones via a silver catalyzed radical cascade cyclization reaction

A novel AgNO3/K2S2O8 catalyzed radical cascade cyclization reaction of 2-(allyloxy)arylaldehydes with 4-hydroxycoumarins and 4-hydroxy-6-methyl-2-pyrone produces two new series of chroman-2-ones.

Structure-activity relationship of natural and synthetic coumarin derivatives against Mycobacterium tuberculosis

Aim: Eight coumarin derivatives (1a-h) obtained from natural (-)-mammea A/BB (1) and 13 synthetic coumarins (2-14) had their cytotoxicity and biological activity evaluated against Mycobacterium tuberculosis H₃₇Rv reference strain and multidrug-resistant clinical isolates. Materials & methods: Anti-M. tuberculosis activity was evaluated by resazurin microtiter assay plate, and the cytotoxicity of natural and synthetic products using J774A.1 macrophages by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide. Results: Compounds 1g, 5, 6, 12 and 14 were more active against M. tuberculosis H₃₇Rv and multidrug-resistant clinical isolates with MIC values ranging from 15.6 to 62.5 μg/ml. Conclusion: These results demonstrate that the coumarin derivatives were active against multidrug-resistant clinical isolates, becoming potential candidates to be used in the treatment of resistant tuberculosis.

Accurate prediction of relative binding affinities of a series of HIV-1 protease inhibitors using semi-empirical quantum mechanical charge

A major challenge in computer-aided drug design is the accurate estimation of ligand binding affinity. Here, a new approach that combines the adaptive steered molecular dynamics (ASMD) and partial atomic charges calculated by semi-empirical quantum mechanics (SQMPC), namely ASMD-SQMPC, is suggested to predict the ligand binding affinities, with 24 HIV-1 protease inhibitors as testing examples. In the ASMD-SQMPC, the relative binding free energy (ΔG) is reflected by the average maximum potential of mean force (<PMF>_max ) between bound and unbound states. The correlation coefficient (R² ) between the <PMF>_max and experimentally determined ΔG is 0.86, showing a significant improvement compared with the conventional ASMD (R² = 0.52). Therefore, this study provides an efficient approach to predict the relative ΔG and reveals the significance of precise partial atomic charges in the theoretical simulations.

tert-Butylhydroperoxide (TBHP) mediated oxidative cross-dehydrogenative coupling of quinoxalin-2(1H)-ones with 4-hydroxycoumarins, 4-hydroxy-6-methyl-2-pyrone and 2-hydroxy-1,4-naphthoquinone under metal-free conditions

We report an efficient and atom-economical method of C-3 functionalization of quinoxalin-2(1H)-ones with 4-hydroxycoumarins, 4-hydroxy-6-methyl-2-pyrone, and 2-hydroxy-1,4-naphthoquinone via the free radical cross-coupling pathway under metal-free conditions. tert-Butylhydroperoxide (TBHP) smoothly promotes the reaction furnishing the cross-dehydrogenative coupling (CDC) products in very good to excellent yields. The protocol neither uses any toxic reagents nor metal catalysts to carry out the reaction, and all the products have been obtained without column chromatography purification. Different radical trapping experiments with 2,2,6,6-tetramethylpiperidine-1-oxyl, butylated hydroxytoluene, and diphenyl ethylene confirm the involvement of radicals.

Synthesis, antimicrobial evaluation and in silico studies of novel 3,4-disubstituted pyrrolidinesulfonamides

3,4-Disubstituted pyrrolidinesulfonamides were synthesized and screened for their antimicrobial activity. Title compounds were established as potent antibacterial and antifungal agents. Noteworthy antimicrobial activity was found for the title compounds against the tested microorganisms. They exhibit comparable results with standard drugs. Besides the in vitro antimicrobial activity, the synthesized compounds were evaluated for their in silico inhibitory activity on active site of β-glucosidase enzyme. In silico studies were done by GOLD docking method against β-glucosidase 3VKK (PDB Id). In silico studies were conducted to evaluate the ability of synthesized compounds to inhibit the β-glucosidase enzyme. The results revealed that 3,4-disubstitutedpyrrolidinesulfonamides are the potent β-glucosidase inhibitors by binding at the active site. A sensible inhibition against β-glucosidases was observed for the compound with 13,4-oxadizole ring has higher β-glucosidase inhibition activity than the other compounds. The free energy of binding and inhibition constant (Ki) of the docked compounds were evaluated and presented.

Synthesis of Polysubstituted Trifluoromethylpyridines from Trifluoromethyl-α,β-ynones

A novel and efficient method for synthesis of polysubstituted trifluoromethylpyridine derivatives by the Bohlmann-Rahtz heteroannulation reaction is described, which use trifluoromethyl-α,β-ynones as trifluoromethyl building blocks to react with β-enamino esters or β-enamino ketones in the presence of ZnBr₂ to form the trifluoromethylpyridine derivatives in good yields. The protocol has the advantages of readily available starting materials, mild reaction conditions, and high atom economy.

Synthesis of 2-amino-3-ethoxycarbonyl-4-aryl-4H,5H-pyrano-[3,2-c]benzopyran-5-one

A series of 2-amino-3-ethoxycarbonyl-4-aryl-4 H,5 H-pyrano-[3,2- c]benzopyran-5-ones have been were synthesised by the reaction of 4-hydroxycoumarin, an aromatic aldehyde and ethyl cyanoacetate under microwave irradiation with short times and high yields.

Unique Flap Conformation in an HIV-1 Protease with High-Level Darunavir Resistance

Darunavir (DRV) is one of the most powerful protease inhibitors (PIs) for treating human immunodeficiency virus type-1 (HIV-1) infection and presents a high genetic barrier to the generation of resistant viruses. However, DRV-resistant HIV-1 infrequently emerges from viruses exhibiting resistance to other protease inhibitors. To address this resistance, researchers have gathered genetic information on DRV resistance. In contrast, few structural insights into the mechanism underlying DRV resistance are available. To elucidate this mechanism, we determined the crystal structure of the ligand-free state of a protease with high-level DRV resistance and six DRV resistance-associated mutations (including I47V and I50V), which we generated by in vitro selection. This crystal structure showed a unique curling conformation at the flap regions that was not found in the previously reported ligand-free protease structures. Molecular dynamics simulations indicated that the curled flap conformation altered the flap dynamics. These results suggest that the preference for a unique flap conformation influences DRV binding. These results provide new structural insights into elucidating the molecular mechanism of DRV resistance and aid to develop PIs effective against DRV-resistant viruses.

Drug resistance mechanisms of three mutations V32I, I47V and V82I in HIV-1 protease toward inhibitors probed by molecular dynamics simulations and binding free energy predictions

Molecular dynamics simulation and binding free energy calculations were used to probe drug resistance of HIV-1 protease mutations toward inhibitors.

Amidine Sulfonamides and Benzene Sulfonamides: Synthesis and Their Biological Evaluation

New amidine and benzene sulfonamide derivatives were developed and structures of the new products were confirmed by elemental and spectral analysis (FT-IR, ESI-MS,1HNMR, and13CNMR). In vitro, developed compounds were screened for their antibacterial and antifungal activities against medically important bacterial strains, namely,S. aureus, B. subtilis, andE. coli, and fungi, namely,A. flavus, A. parasiticus, andA.sp. The antibacterial and antifungal activities have been determined by measuring MIC values (μg/mL) and zone of inhibitions (mm). Among the tested compounds, it was found that compounds3b,9a, and9bhave most potent activity againstS. aureus, A. flavus, and A. parasiticus, respectively, and were found to be more active than sulfamethoxazole and itraconazole with MIC values 40 μg/mL. In contrast, all the compounds were totally inactive against theA.sp. except10band15bto show activity to some extent.

Tipranavir: a novel second-generation nonpeptidic protease inhibitor

Tipranavir is a new nonpeptidic protease inhibitor and belongs to the class of 4-hydroxy-5, 6-dihydro-2-pyrones. Chemically, tipranavir is based on coumarin and sulfonamide compounds, amongst others. It exhibits potent and specific activity against both HIV-1 and -2. Tipranavir 500 mg in combination with ritonavir 200 mg twice daily results in optimum viral load reduction and suppresses both wild-type and protease inhibitor-resistant virus. It is metabolized by the cytochrome P4503A4 enzyme and its pharmacokinetic parameters are enhanced when combined with ritonavir. Tipranavir is excreted primarily in the feces, with minimal excretion in urine. In early trials, tipranavir/ritonavir was demonstrated to be safe and well tolerated, with mild gastrointestinal side effects. Preliminary data indicate pharmacokinetic interaction with nucleotide reverse transcriptase inhibitors; however, no dose adjustments are recommended at this time. Virologic response is not adequate when combined with other ritonavir-boosted protease inhibitors, and is currently not recommended. As with other protease inhibitors, tipranavir interacts with fluconazole, atorvastatin, clarithromycin and rifabutin and absorption is reduced when taken with antacids and didanosine (enteric coated formulation). Phase III trials are underway to compare the efficacy of tipranavir/ritonavir with other antiretroviral agents.

Rhodium-catalysed asymmetric hydrogenation as a valuable synthetic tool for the preparation of chiral drugs

During the last few decades, rhodium-catalysed asymmetric hydrogenation of diverse alkene classes has emerged as a powerful synthetic tool in the pharmaceutical industry, contributing to the manufacturing of chiral drugs, recent drug candidates for clinical trials, and major synthetic precursors of drugs. Numerous efficient chiral rhodium complexes, most of which are derived from enantiopure phosphorus ligands, have been employed for the preparation of chiral drugs and intermediates thereof. This review article is intended to provide an updated overview of the most striking contributions in this field, organised according to substrate class: acrylate derivatives, itaconate derivatives, α-substituted enamides, α-arylenol acetates, and minimally functionalised olefins.

[Bioinformatics studies on drug resistance against anti-HIV-1 drugs]

More than 20 drugs have been available for anti-HIV-1 treatment in Japan. Combination therapy with these drugs dramatically decreases in morbidity and mortality of AIDS. However, due to high mutation rate of HIV-1, treatment with ineffective drugs toward patients infected with HIV-1 causes accumulation of mutations in the virus, and emergence of drug resistant viruses. Thus, to achieve appropriate application of the drugs toward the respective patients living with HIV-1, methods for predicting the level of drug-resistance using viral sequence information has been developed on the basis of bioinformatics. Furthermore, ultra-deep sequencing by next-generation sequencer whose data analysis is also based on bioinformatics, or in silico structural modeling have been achieved to understand drug resistant mechanisms. In this review, I overview the bioinformatics studies about drug resistance against anti-HIV-1 drugs.

Rationale for more diverse inhibitors in competition with substrates in HIV-1 protease

The structural fluctuations of HIV-1 protease in interaction with its substrates versus inhibitors were analyzed using the anisotropic network model. The directions of fluctuations in the most cooperative functional modes differ mainly around the dynamically key regions, i.e., the hinge axes, which appear to be more flexible in substrate complexes. The flexibility of HIV-1 protease is likely optimized for the substrates' turnover, resulting in substrate complexes being dynamic. In contrast, in an inhibitor complex, the inhibitor should bind and lock down to inactivate the active site. Protease and ligands are not independent. Substrates are also more flexible than inhibitors and have the potential to meet the dynamic distributions that are inherent in the protease. This may suggest a rationale and guidelines for designing inhibitors that can better fit the ensemble of binding sites that are dynamically accessible to the protease.

Prediction of potency of protease inhibitors using free energy simulations with polarizable quantum mechanics-based ligand charges and a hybrid water model

Reliable and robust prediction of the binding affinity for drug molecules continues to be a daunting challenge. We simulated the binding interactions and free energy of binding of nine protease inhibitors (PIs) with wild-type and various mutant proteases by performing GBSA simulations in which each PI's partial charge was determined by quantum mechanics (QM) and the partial charge accounts for the polarization induced by the protease environment. We employed a hybrid solvation model that retains selected explicit water molecules in the protein with surface-generalized Born (SGB) implicit solvent. We examined the correlation of the free energy with the antiviral potency of PIs with regard to amino acid substitutions in protease. The GBSA free energy thus simulated showed strong correlations (r > 0.75) with antiviral IC(50) values of PIs when amino acid substitutions were present in the protease active site. We also simulated the binding free energy of PIs with P2-bis-tetrahydrofuranylurethane (bis-THF) or related cores, utilizing a bis-THF-containing protease crystal structure as a template. The free energy showed a strong correlation (r = 0.93) with experimentally determined anti-HIV-1 potency. The present data suggest that the presence of selected explicit water in protein and protein polarization-induced quantum charges for the inhibitor, compared to lack of explicit water and a static force-field-based charge model, can serve as an improved lead optimization tool and warrants further exploration.

Computational multiscale modeling in protein--ligand docking

In biological systems, the binding of small molecule ligands to proteins is a crucial process for almost every aspect of biochemistry and molecular biology. Enzymes are proteins that function by catalyzing specific biochemical reactions that convert reactants into products. Complex organisms are typically composed of cells in which thousands of enzymes participate in complex and interconnected biochemical pathways. Some enzymes serve as sequential steps in specific pathways (such as energy metabolism), while others function to regulate entire pathways and cellular functions [1]. Small molecule ligands can be designed to bind to a specific enzyme and inhibit the biochemical reaction. Inhibiting the activity of key enzymes may result in the entire biochemical pathways being turned on or off [2], [3]. Many small molecule drugs marketed today function in this generic way as enzyme inhibitors. If research identifies a specific enzyme as being crucial to the progress of disease, then this enzyme may be targeted with an inhibitor, which may slow down or reverse the progress of disease. In this way, enzymes are targeted from specific pathogens (e.g., virus, bacteria, fungi) for infectious diseases [4], [5], and human enzymes are targeted for noninfectious diseases such as cardiovascular disease, cancer, diabetes, and neurodegenerative diseases [6].

Assessment of QM/MM scoring functions for molecular docking to HIV-1 protease

We explore the ability of four quantum mechanical (QM)/molecular mechanical (MM) models to accurately identify the native pose of six HIV-1 protease inhibitors and compare them with the AMBER force field and ChemScore and GoldScore scoring functions. Three QM/MM scoring functions treated the ligand at the HF/6-31G*, AM1d, and PM3 levels; the fourth QM/MM function modeled the ligand and active site at the PM3-D level. For the discrimination of native from non-native poses, solvent-corrected HF/6-31G*:AMBER and AMBER functions exhibited the best overall performance. While the electrostatic component of the MM and QM/MM functions appears important for discriminating the native pose of the ligand, the polarization contribution in the QM/MM functions was relatively insensitive to a ligand's binding mode and, for one ligand, actually hindered discrimination. The inclusion of a desolvation penalty, here using a generalized Born solvent model, improved discrimination for the MM and QM/MM methods. There appeared to be no advantage to binding mode prediction by incorporating active site polarization at the PM3-D level. Finally, we found that choice of the protonation state of the aspartyl dyad in the HIV-1 protease active site influenced the ability of scoring methods to determine the native binding pose.

Predicting drug resistance of the HIV-1 protease using molecular interaction energy components

Drug resistance significantly impairs the efficacy of AIDS therapy. Therefore, precise prediction of resistant viral mutants is particularly useful for developing effective drugs and designing therapeutic regimen. In this study, we applied a structure-based computational approach to predict mutants of the HIV-1 protease resistant to the seven FDA approved drugs. We analyzed the energetic pattern of the protease-drug interaction by calculating the molecular interaction energy components (MIECs) between the drug and the protease residues. Support vector machines (SVMs) were trained on MIECs to classify protease mutants into resistant and nonresistant categories. The high prediction accuracies for the test sets of cross-validations suggested that the MIECs successfully characterized the interaction interface between drugs and the HIV-1 protease. We conducted a proof-of-concept study on a newly approved drug, darunavir (TMC114), on which no drug resistance data were available in the public domain. Compared with amprenavir, our analysis suggested that darunavir might be more potent to combat drug resistance. To quantitatively estimate binding affinities of drugs and study the contributions of protease residues to causing resistance, linear regression models were trained on MIECs using partial least squares (PLS). The MIEC-PLS models also achieved satisfactory prediction accuracy. Analysis of the fitting coefficients of MIECs in the regression model revealed the important resistance mutations and shed light into understanding the mechanisms of these mutations to cause resistance. Our study demonstrated the advantages of characterizing the protease-drug interaction using MIECs. We believe that MIEC-SVM and MIEC-PLS can help design new agents or combination of therapeutic regimens to counter HIV-1 protease resistant strains.

Evaluating the potency of HIV-1 protease drugs to combat resistance

HIV-1 protease has been an important drug target for the antiretroviral treatment of HIV infection. The efficacy of protease drugs is impaired by the rapid emergence of resistant virus strains. Understanding the molecular basis and evaluating the potency of an inhibitor to combat resistance are no doubt important in AIDS therapy. In this study, we first identified residues that have significant contributions to binding with six substrates using molecular dynamics simulations and Molecular Mechanics Generalized Born Surface Area calculations. Among the critical residues, Asp25, Gly27, Ala28, Asp29, and Gly49 are well conserved, with which the potent drugs should form strong interactions. We then calculated the contribution of each residue to binding with eight FDA approved drugs. We analyzed the conservation of each protease residue and also compared the interaction between the HIV protease and individual residues of the drugs and substrates. Our analyses showed that resistant mutations usually occur at less conserved residues forming more favorable interactions with drugs than with substrates. To quantitatively integrate the binding free energy and conservation information, we defined an empirical parameter called free energy/variability (FV) value, which is the product of the contribution of a single residue to the binding free energy and the sequence variability at that position. As a validation, the FV value was shown to identify single resistant mutations with an accuracy of 88%. Finally, we evaluated the potency of a newly approved drug, darunavir, to combat resistance and predicted that darunavir is more potent than amprenavir but may be susceptible to mutations on Val32 and Ile84.

Novel method for probing the specificity binding profile of ligands: applications to HIV protease

A detailed understanding of factors influencing the binding specificity of a ligand to a set of desirable targets and undesirable decoys is a key step in the design of potent and selective therapeutics. We have developed a general method for optimizing binding specificity in ligand-receptor complexes based on the theory of electrostatic charge optimization. This methodology can be used to tune the binding of a ligand to a panel of potential targets and decoys, along the continuum from narrow binding to only one partner to broad binding to the entire panel. Using HIV-1 protease as a model system, we probe specificity in three distinct ways. First, we probe interactions that could make the promiscuous protease inhibitor pepstatin more selective toward HIV-1 protease. Next, we study clinically approved HIV-1 protease inhibitors and probe ways to broaden the binding profiles toward both wild-type HIV-1 protease and drug-resistant mutants. Finally, we study a conformational ensemble of wild-type HIV-1 protease to 'design in' broad specificity to known drugs before resistance mutations arise. The results from this conformational ensemble were similar to those from the drug-resistant ensemble, suggesting the use of a conformational wild-type ensemble as a tool to develop escape-mutant-resistant inhibitors.

A New Strategy for the Synthesis of Benzylic Sulfonamides: Palladium-Catalyzed Arylation and Sulfonamide Metathesis

An efficient two-step strategy has been developed to access diversely functionalized benzylic sulfonamides. Execution of this strategy required the development of two reaction methods: the palladium-catalyzed cross-coupling of aryl halides with CH-acidic methanesulfonamides and a metathesis reaction between the resulting alpha-arylated sulfonamides and diverse amines. The broad scope of the cross-coupling process combined with a versatile sulfonamide metathesis constitutes an efficient strategy for the synthesis of various benzylic sulfonamides.

Potent Inhibition of HIV-1 Replication by Novel Non-peptidyl Small Molecule Inhibitors of Protease Dimerization

Dimerization of HIV-1 protease subunits is essential for its proteolytic activity, which plays a critical role in HIV-1 replication. Hence, the inhibition of protease dimerization represents a unique target for potential intervention of HIV-1. We developed an intermolecular fluorescence resonance energy transfer-based HIV-1-expression assay employing cyan and yellow fluorescent protein-tagged protease monomers. Using this assay, we identified non-peptidyl small molecule inhibitors of protease dimerization. These inhibitors, including darunavir and two experimental protease inhibitors, blocked protease dimerization at concentrations of as low as 0.01 microm and blocked HIV-1 replication with IC(50) values of 0.0002-0.48 microm. These agents also inhibited the proteolytic activity of mature protease. Other approved anti-HIV-1 agents examined except tipranavir, a CCR5 inhibitor, and soluble CD4 failed to block the dimerization event. Once protease monomers dimerize to become mature protease, mature protease is not dissociated by this dimerization inhibition mechanism, suggesting that these agents block dimerization at the nascent stage of protease maturation. The proteolytic activity of mature protease that managed to undergo dimerization despite the presence of these agents is likely to be inhibited by the same agents acting as conventional protease inhibitors. Such a dual inhibition mechanism should lead to highly potent inhibition of HIV-1.

Tipranavir: a new option for the treatment of drug-resistant HIV infection

Tipranavir is a recently approved nonpeptidic protease inhibitor specifically developed for the management of human immunodeficiency virus (HIV) infection in treatment-experienced patients with protease inhibitor-resistant infection. It is active against a wide range of drug-resistant laboratory- and patient-derived isolates. Tipranavir requires pharmacokinetic boosting by ritonavir (200 mg) to achieve therapeutic levels with twice-daily dosing and must be administered with food for optimal absorption. It is a potent protease inhibitor with a unique drug-resistance profile that offers advantages in the management of cases of multidrug-resistant HIV infection. Tipranavir (in combination with ritonavir) is both an inhibitor and inducer of cytochrome p450, with significant potential for drug-drug interactions, and therefore, it must be used cautiously when administered to patients who are receiving other drugs. Evolution of drug resistance after treatment failure with tipranavir is complex and is not yet fully understood. There is limited overlap in the resistance mutations that predict response to tipranavir and another new protease inhibitor, darunavir, which is active against drug-resistant isolates. Tipranavir is associated with elevations in alanine aminotransferase and aspartate aminotransferase levels, as well as elevated cholesterol and triglyceride levels, and can cause the typical gastrointestinal adverse effects associated with all protease inhibitors.

Synthesis of thiazolone-based sulfonamides as inhibitors of HCV NS5B polymerase

Several thiazolone-based sulfonamides were prepared, utilizing various hetero-aryl sulfonyl chlorides and different aldehydes, as inhibitors of NS5B polymerase, to target HCV. The best compound showed 0.6 microM [corrected] of IC50 inhibitory activity.

Genotypic changes in human immunodeficiency virus type 1 protease associated with reduced susceptibility and virologic response to the protease inhibitor tipranavir

Tipranavir is a novel, nonpeptidic protease inhibitor of human immunodeficiency virus type 1 (HIV-1) with activity against clinical HIV-1 isolates from treatment-experienced patients. HIV-1 genotypic and phenotypic data from phase II and III clinical trials of tipranavir with protease inhibitor-experienced patients were analyzed to determine the association of protease mutations with reduced susceptibility and virologic response to tipranavir. Specific protease mutations were identified based on stepwise multiple-regression analyses of phase II study data sets. Validation included analyses of phase III study data sets to determine if the same mutations would be selected and to assess how these mutations contribute to multiple-regression models of tipranavir-related phenotype and of virologic response. A tipranavir mutation score was developed from these analyses, which consisted of a unique string of 16 protease positions and 21 mutations (10V, 13V, 20M/R/V, 33F, 35G, 36I, 43T, 46L, 47V, 54A/M/V, 58E, 69K, 74P, 82L/T, 83D, and 84V). HIV-1 isolates displaying an increasing number of these tipranavir resistance-associated mutations had a reduced phenotypic susceptibility and virologic response to tipranavir. Regression models for predicting virologic response in phase III trials revealed that each point in the tipranavir score was associated with a 0.16-log10 copies/ml-lower virologic response to tipranavir at week 24 of treatment. A lower number of points in the tipranavir score and a greater number of active drugs in the background regimen were predictive of virologic success. These analyses demonstrate that the tipranavir mutation score is a potentially valuable tool for predicting the virologic response to tipranavir in protease inhibitor-experienced patients.

Optimization and computational evaluation of a series of potential active site inhibitors of the V82F/I84V drug-resistant mutant of HIV-1 protease: an application of the relaxed complex method of structure-based drug design

The Relaxed Complex method, an approach to structure-based drug design that incorporates the flexibilities of both the ligand and target protein, was applied to the immunodeficiency virus protease system. The control cases used AutoDock3.0.5 to dock a fully flexible version of the prospective drug JE-2147 (aka SM-319777 or KNI-764) to large ensembles of conformations extracted from conventional, all atom, explicitly solvated molecular dynamic simulations of the wild type, and the V82F/I84V drug-resistant mutant of HIV-1 protease. The best set of run parameters from the control cases produced robust results when used against 2200 different conformations of the wild-type HIV-1 protease or against 2200 conformations of the mutant. The results of the control cases, the published advice from experts, and structural intuition were used to design a new series of 23 potential active site inhibitors. The compounds were evaluated by docking them against 700 different conformations of the V82F/I84V mutant. The results of this first round of lead optimization were quite promising. Approximately one-third of that series performed at least slightly better than the parent compound, and four of those compounds displayed significantly better binding affinities against that drug-resistant mutant (within our computational model).

Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug design

To test the anticorrelated relationship that was recently displayed in conventional molecular dynamics (MD) simulations, several different restrained MD simulations on a wild type and on the V82F/I84V drug-resistant mutant of HIV-1 protease were performed. This anticorrelated relationship refers to the observation that compression of the peripheral ear-to-cheek region of HIV protease (i.e., the elbow of the flap to the fulcrum and the cantilever) occurred as the active site flaps were opening, and, conversely, expansion of that ear-to-cheek region occurred as both flaps were closing. An additional examination of this anticorrelated relationship was necessary to determine whether it can be harnessed in a useful manner. Consequently, six different MD experiments were performed that incorporated pairwise distance restraints in that ear-to-cheek region (i.e., the distance between the alpha-carbons of Gly40 and Gln61 was restrained to either 7.7 or 10.5 A, in both monomers). Pushing the backbones of the ear and the cheek regions away from each other slightly did force the flaps that guard the active site to remain closed in both the wild type and the mutant systems-even though there were no ligands in the active sites. Thus, these restrained MD simulations provided evidence that the anticorrelated relationship can be exploited to affect the dynamic behavior of the flaps that guard the active site of HIV-1 protease. These simulations supported our hypothesis of the mechanism governing flap motion, and they are the first step towards validating that peripheral surface as a new target for drug design.

Drug Resistance of HIV-1 Protease Against JE-2147: I47V Mutation Investigated by Molecular Dynamics Simulation

Anti-retroviral therapies for acquired immunodeficiency syndrome (AIDS) patients are at risk because of drug resistance that has been identified with a number of currently marketed drugs. HIV-1 protease (HIV-pr), a well-validated AIDS therapeutic target, undergoes various mutations leading to resistance such existing drugs. However, the molecular basis of drug resistance of HIV-pr is still not fully understood. JE-2147, an experimental inhibitor of HIV-pr, shows a resistance profile different from that of known drugs. Noteworthy, it is less susceptible to several common mutations, but it is still susceptible to a few mutations, including I47V which appears to be specific for JE-2147. In this work, the molecular details of the effect of I47V mutation is investigated using molecular dynamics simulation. Four simulations of apo and complexed proteins in their wild type (WT) and mutant forms have been performed. It is found that the mobility of the side chain of mutant Val47 in chain B of HIV-pr about the inhibitor increases significantly relative to WT Ile47 in chain B. This is due to loss of optimized packing of the inhibitor to the residue 47 in chain B of the mutant when compared with WT enzyme. There also are subtle differences in motion involving residues in the flap region, which are more prominent in the apo form.

2-Pyrone natural products and mimetics: isolation, characterisation and biological activity

The review summarises natural products containing the 2-pyrone moiety. An emphasis has been placed upon the biological activity associated with 2-pyrones, particularly with respect to potential therapeutic or anti-microbial agents. Where appropriate, non-natural 2-pyrone analogues are discussed, particularly those derived from natural product lead compounds.