Two-carbon-elongated HIV-1 protease inhibitors with a tertiary-alcohol-containing transition-state mimic

2-Alkyl substituted benzimidazoles as a new class of selective AT2 receptor ligands

Ligands comprising a benzimidazole rather than the imidazole ring that is common in AT₂R ligands e.g. in the AT₂R agonist C21, can provide both high affinity and receptor selectivity. In particular, compounds encompassing benzimidazoles, substituted in the 2-position with small bulky groups such as an isopropyl (K_i = 4.0 nM) or a tert-butyl (K_i = 5.3 nM) or alternatively a thiazole heterocycle (K_i = 5.1 nM) demonstrate high affinity and AT₂R selectivity. An n-butyl chain, as found in the AT₁R selective sartans, makes the ligand less receptor selective. The isobutyl group on the biaryl scaffold present in most AT₂R selective ligands reported so far was originally derived from the nonselective potent AT₁R/AT₂R ligand L-162,313. Notably, in all ligands discussed herein, the isobutyl group was substituted by an n-propyl group and ligands with high affinity to AT₂R were provided and in addition the majority of them demonstrate a favorable AT₂R/AT₁R selectivity. The introduction of fluoro atoms in various positions had no pronounced effect on the affinity data. Ligands with a thiazole or a tert-butyl group attached to the 2-position and with a terminal trifluoromethyl butoxycarbonyl sidechain exhibited a similar stability as C21 in human liver microsomes, while other ligands examined were less stable in the microsome assay.

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.

Sensing HIV Protease and Its Inhibitor Using "Helical Epitope"-Imprinted Polymers

A helical epitope-peptide (lle⁸⁵-Gly⁹⁴) was selected from the α-helix structure of the HIV protease (PR) as the template, which represents an intricate interplay between structure conformation and dimerization. The peptide template was mixed with water, trifluoroethanol (TFE), and acetonitrile (ACN) at a certain ratio to enlarge the helical conformation in the solution for the fabrication of helical epitope-mediated molecularly imprinted polymers (HEMIPs) on a quartz crystal microbalance (QCM) chip. The template molecules were then removed under equilibrium batch rebinding conditions involving 5% acetic acid/water. The resulting HEMIPs chip exhibited a high affinity toward template peptide HIV PR_85-94, His-tagged HIV PR, and HIV PR, with dissociation constants (K_d) as 160, 43.3, and 78.5 pM, respectively. The detection limit of the developed HIV PR_85-94 QCM sensor is 0.1 ng/mL. The HEMIPs chip exhibited a high affinity and selectivity to bind HIV PR and subsequently to an inhibitor of HIV PR (nelfinavir). The HIV PR binding site was properly oriented on the HEMIPs-chip to develop a HIV PR/HEMIPs chip, which can effectively bind nelfinavir to establish a sandwich assay. The nelfinavir then attached to the HIV PR/HEMIPs chip, which can be easily removed involving 0.8% acetic acid/water. Therefore, HIV PR/HEMIPs chip can be useful to screen for other HIV PR inhibitors. This technique may improve drug targeting for HIV therapy and also strengthen investigations into other virus assays.

Beta-sitosterol attenuates insulin resistance in adipose tissue via IRS-1/Akt mediated insulin signaling in high fat diet and sucrose induced type-2 diabetic rats

In our previous study, we have shown that β-sitosterol (SIT) enhances glycemic control by increasing the activation of insulin receptor (IR) and glucose transporter 4 (GLUT4) proteins in adipose tissue. However, the possible role of SIT on the regulation of post-receptor insulin signal transduction is not known. Hence, the study was aimed to assess the effects of SIT on IRS-1/Akt mediated insulin signaling molecules in high-fat diet and sucrose induced type-2 diabetic rats. An oral effective dose of SIT (20 mg/kg b.wt) was given for 30 days to high fat-fed type-2 diabetic rats to find out whether SIT regulates IRS-1/Akt pathway of insulin signaling. The results showed that SIT attenuated the insulin receptor substrate-1 serine phosphorylation (p-IRS-1^Ser636) (P = 0.0003). However, it up-regulated the mRNA expression of IR (P = 0.0036) and post-receptor insulin signaling molecules such as IRS-1 (P < 0.0001), β-arrestin-2 (P < 0.0058), Akt (P = 0.0008), AS160 (P = 0.0030) and GLUT4 (P < 0.0001) with a concomitant increase in the levels of IRS-1(P < 0.0001), p-IRS1-1^Tyr632 (P = 0.0014), Akt (P < 0.0001), p-Akt^{Ser473/Thr308} (P = 0.0006; P < 0.0001), AS160 and p-AS160^Thr642 (P < 0.0001) compared with type-2 diabetic rats. In Silico analysis was also performed and it showed that SIT possesses the greater binding affinity with β-arrestin-2, c-Src, and IRS-1 as well as Akt proteins and proved to attenuate insulin resistance as this study coincides with in vivo findings. Our present study clearly shows that SIT attenuates high fat diet-induced detrimental changes in adipose tissue. Therefore, it is concluded from the present findings that, SIT could be used as potential therapeutic phytomedicine for the management of type-2 diabetes.

Structural insights on bioremediation of polycyclic aromatic hydrocarbons using microalgae: a modelling-based computational study

Research on bioremediation of polycyclic aromatic hydrocarbons (PAHs) has established that several remediating microbial species are capable of degrading only low molecular weight (LMW)-PAHs, whereas high molecular weight (HMW)-PAHs are hardly degradable. In the present study, the efficiency of degradation of both LMW and HMW-PAHs by cytochrome P450 monooxygenase (CYP) of microalgae was studied. CYP have a key role in the detoxification of xenobiotics. So far, the structure of CYP in microalgae is not predicted; the protein structure was constructed by molecular modelling in the current study using the available template of microalgal CYP. Modelled microalgae 3D structures were docked against 38 different PAH compounds, and the information regarding the interaction between protein and PAHs viz. binding sites along with mode of interactions was investigated. We report that CYP from the microalgae Haematococcus pluvialis and Parachlorella kessleri was found to possess broad oxidising capability towards both LMW and HMW-PAHs. P. kessleri showed a least value with extra precision glide score of - 10.23 and glide energy of - 23.48 kcal/mol. PAHs bind to CYP active sites at Lys ⁶⁹, Trp ⁹⁶, Gln ³⁹⁷ and Arg ³⁹⁸ through intermolecular hydrogen bonding. Also, study revealed that PAHs interacted with CYP active sites through intermolecular hydrogen bonding, hydrophobic bonding, π-π interactions and van der waals interactions. Thus, structural elucidation study confirms that microalgae Parachlorella kessleri have the capacity to remediate HMW more efficiently than other microorganisms. Our results provide a framework in understanding the structure and the possible binding sites of CYP protein for degradation of PAH and that could be a screening tool in identifying the phycoremediation potential.

Sequence, Structural Analysis and Metrics to Define the Unique Dynamic Features of the Flap Regions Among Aspartic Proteases

Aspartic proteases are a class of hydrolytic enzymes that have been implicated in a number of diseases such as HIV, malaria, cancer and Alzheimer's. The flap region of aspartic proteases is a characteristic unique structural feature of these enzymes; and found to have a profound impact on protein overall structure, function and dynamics. Flap dynamics also plays a crucial role in drug binding and drug resistance. Therefore, understanding the structure and dynamic behavior of this flap regions is crucial in the design of potent and selective inhibitors against aspartic proteases. Defining metrics that can describe the flap motion/dynamics has been a challenging topic in literature. This review is the first attempt to compile comprehensive information on sequence, structure, motion and metrics used to assess the dynamics of the flap region of different aspartic proteases in "one pot". We believe that this review would be of critical importance to the researchers from different scientific domains.

AgNO3 dependant modulation of glucose mediated respiration kinetics in Escherichia coli at different pH and temperature

The inhibitory role of AgNO₃ on glucose-mediated respiration in Escherichia coli has been investigated as a function of pH and temperature using Clark-type electrode, environmental scanning electron microscopy, and computational tools. In the given concentration of bacterial suspension (1 × 10⁸  CFU/ml), E. coli showed an increasing nonlinear trend of tetra-phasic respiration between 1-133 μM glucose concentration within 20 min. The glucose concentrations above 133 μM did not result any linear increment in respiration but rather showed a partial inhibition at higher glucose concentrations (266-1066 μM). In the presence of glucose, AgNO₃ caused a concentration-dependent (47-1960 μM) inhibition of the respiration rate within 4 min of its addition. The respiration rate was the highest at pH 7-8 and then was decreased on either side of this pH range. The inhibitory action of AgNO₃ upon bacterial respiration was the highest at 37 °C. The observations of the respiration data were well supported by the altered bacterial morphology as observed in electron microscopic study. Docking study indicated the AgNO₃ binding to different amino acids of all respiratory complex enzymes in E. coli and thereby explaining its interference with the respiratory chain. Copyright © 2016 John Wiley & Sons, Ltd.

Recent Progress in the Development of HIV-1 Protease Inhibitors for the Treatment of HIV/AIDS

HIV-1 protease inhibitors continue to play an important role in the treatment of HIV/AIDS, transforming this deadly ailment into a more manageable chronic infection. Over the years, intensive research has led to a variety of approved protease inhibitors for the treatment of HIV/AIDS. In this review, we outline current drug design and medicinal chemistry efforts toward the development of next-generation protease inhibitors beyond the currently approved drugs.

Crystal structure of 5-hy-droxy-methyl-2-meth-oxy-phenol

In the title compound, C8H10O3, the hy-droxy-methyl group is twisted by 74.51 (13)° from the plane of the benzene ring to which it is connected. By contrast, the benzene and meth-oxy groups are almost coplanar, making a dihedral angle of 4.0 (2)°. In the crystal, O-H⋯O hydrogen bonds link the mol-ecules into a three-dimensional network.

Molecular insights on analogs of HIV PR inhibitors toward HTLV-1 PR through QM/MM interactions and molecular dynamics studies: comparative structure analysis of wild and mutant HTLV-1 PR

Retroviruses HTLV-1 and HIV-1 are the primary causative agents of fatal adult T-cell leukemia and acquired immune deficiency syndrome (AIDS) disease. Both retroviruses are similar in characteristics mechanism, and it encodes for protease that mainly involved in the viral replication process. On the basis of the therapeutic success of HIV-1 PR inhibitors, the protease of HTLV-1 is mainly considered as a potential target for chemotherapy. At the same time, structural similarities in both enzymes that originate HIV PR inhibitors can also be an HTLV-1 PR inhibitor. But the expectations failed because of rejection of HIV PR inhibitors from the HTLV-1 PR binding pocket. In this present study, the reason for the HIV PR inhibitor rejection from the HTLV-1 binding site was identified through sequence analysis and molecular dynamics simulation method. Functional analysis of M37A mutation in HTLV PR clearly shows that the MET37 specificity and screening of potential inhibitors targeting MET37 is performed by using approved 90% similar HIV PR inhibitor compounds. From this approach, we report few compounds with a tendency to accept/donate electron specifically to an important site residue MET37 in HTLV-1 PR binding pocket.

Aspartic protease inhibitors containing tertiary alcohol transition-state mimics

Aspartic proteases (APs) are a class of enzymes engaged in the proteolytic digestion of peptide substrates. APs play important roles in physiological and infectious pathways, making them plausible drug targets. For instance in the treatment of HIV infections, access to an efficient combination of protease and reverse transcriptase inhibitors have changed a terminal illness to a chronic but manageable disease. However, the benefits have been limited due to the emergence of drug resistant viral strains, poor pharmacokinetic properties of peptidomimetic inhibitors and adverse effects associated with the treatment. In the 1980s, D. Rich and co-workers proposed a novel strategy for the development of AP inhibitors by replacing the secondary hydroxyl group with a tertiary alcohol as part of the transition state (TS) mimicking moiety. This strategy has been extensively explored over the last decade with a common belief that masking of the polar group, e.g. by intramolecular hydrogen bonding, has the potential to enhance transcellular transport. This is the first review presenting the advances of AP inhibitors comprising a tertiary hydroxyl group. The inhibitors have been classified into different tert-hydroxy TS mimics and their design strategies, synthesis, biological activities, structure-activity-relationships and X-ray structures are discussed.

Virtual screening of potential inhibitor against FtsZ protein from Staphylococcus aureus

The gram-positive bacterium Staphylococcus aureus, responsible for a wide variety of diseases in human involve all organ systems ranging from localized skin infections to life-threatening systemic infections. FtsZ, the key protein of bacterial cell division was selected as a potent anti bacterial target. In order to identify the new compounds structure based screening process was carried out. An enrichment study was performed to select a suitable scoring function and to retrieve potential candidates against FtsZ from a large chemical database. The docking score and docking energy values were compared and their atomic interaction was also evaluated. Furthermore molecular dynamics simulation were also been performed to check the stability and the amino acids interacted towards the FtsZ. Finally we selected C ID 16284, 25916, 15894, 13403 as better lead compounds. From these results, we conclude that our insilico results will provide a framework for the detailed in vitro and in vivo studies about the FtsZ protein activity in drug development process.

Synthesis of P1'-functionalized macrocyclic transition-state mimicking HIV-1 protease inhibitors encompassing a tertiary alcohol

Seven novel tertiary alcohol containing linear HIV-1 protease inhibitors (PIs), decorated at the para position of the benzyl group in the P1' side with (hetero)aromatic moieties, were synthesized and biologically evaluated. To study the inhibition and antiviral activity effect of P1-P3 macrocyclization, 14- and 15-membered macrocyclic PIs were prepared by ring-closing metathesis of the corresponding linear PIs. The macrocycles were more active than the linear precursors and compound 10f, with a 2-thiazolyl group in the P1' position, was the most potent PI of this new series (Ki 2.2 nM, EC50 0.2 μM). Co-crystallized complexes of both linear and macrocyclic PIs with the HIV-1 protease enzyme were prepared and analyzed.

Recent patents and emerging therapeutics for HIV infections: a focus on protease inhibitors

The inclusion of protease inhibitors (PIs) in highly active antiretroviral therapy has significantly improved clinical outcomes in HIV-1-infected patients. To date, PIs are considered to be the most important therapeutic agents for the treatment of HIV infections. Despite high anti-HIV-1 potency, poor oral bioavailability of PIs has been a major concern. For achieving therapeutic concentrations, large doses of PIs are administered, which results in unacceptable systemic toxicities. Such severe and long-term toxicities necessitate the development of safer and potentially promising PIs. Recently, considerable attention has been paid to the development of newer compounds capable of inhibiting wild-type and resistant HIV-1 protease. Some of these PIs have displayed potent HIV-1 protease inhibitory activity. In this review, we have made an attempt to provide an overview on clinically approved and newly developing PIs, and related recent patents in the development of novel PIs.

Molecular modeling studies and comparative analysis on structurally similar HTLV and HIV protease using HIV-PR inhibitors

Retroviruses are most perilous viral family, which cause much damage to the Homo sapiens. HTLV-1 mechanism found to more similar with HIV-1 and both retroviruses are causative agents of severe and fatal diseases including adult T-cell leukemia (ATL) and the acquired immune deficiency syndrome (AIDS). Both viruses code for a protease (PR) that is essential for replication and therefore represents a key target for drugs interfering with viral infection. In this work, the comparative study of HIV-1 and HTLV-1 PR enzymes through sequence and structural analysis is reported along with approved drugs of HIV-PR. Conformation of each HIV PR drugs have been examined with different parameters of interactions and energy scorings parameters. MD simulations with respect to timescale event of 20 ns favors that, few HIV-PR inhibitors can be more active inside the HTLV-1 PR binding pocket. Overall results suggest that, some of HIV inhibitors like Tipranavir, Indinavir, Darunavir and Amprenavir are having good energy levels with HTLV-1. Due to absence of interactions with MET37, here we report that derivatives of these compounds can be much better inhibitors for targeting HTLV-1 proteolytic activity.

Validation of potential inhibitors for SrtA against Bacillus anthracis by combined approach of ligand-based and molecular dynamics simulation

The development of SrtA inhibitors targeting the biothreat organism namely Bacillus anthracis was achieved by the combined approach of pharmacophore modeling, binding interactions, electron transferring capacity, ADME, and Molecular dynamics studies. In this study, experimentally reported Ba-SrtA inhibitors (pyridazinone and pyrazolethione derivatives) were considered for the development of enhanced pharmacophoric model. The obtained AAAHR hypothesis was a pure theoretical concept that accounts for common molecular interaction network present in experimentally active pyridazinone and pyrazolethione derivatives. Pharmacophore-based screening of AAAHR hypothesis provides several new compounds, and those compounds were treated with four phases of docking protocols with combined Glide-QPLD docking approach. In this approach, scoring and charge accuracy variations were seen to be dominated by QM/MM approach through the allocation of partial charges. Finally, we reported the best compounds from binding db, Chembridge db, and Toslab based on scoring values, energy parameters, electron transfer reaction, ADME, and cell adhesion inhibition activity. The dynamic state of interaction and binding energy assess that new compounds are more active inside the binding pocket and these compounds on experimental validations will survive as better inhibitors for targeting the cell adhesion mechanism of Ba-SrtA.

Synthesis, X-ray analysis, and biological evaluation of a new class of stereopure lactam-based HIV-1 protease inhibitors

In an effort to identify a new class of druglike HIV-1 protease inhibitors, four different stereopure β-hydroxy γ-lactam-containing inhibitors have been synthesized, biologically evaluated, and cocrystallized. The impact of the tether length of the central spacer (two or three carbons) was also investigated. A compound with a shorter tether and (3R,4S) absolute configuration exhibited high activity with a K_i of 2.1 nM and an EC₅₀ of 0.64 μM. Further optimization by decoration of the P1′ side chain furnished an even more potent HIV-1 protease inhibitor (K_i = 0.8 nM, EC₅₀ = 0.04 μM). According to X-ray analysis, the new class of inhibitors did not fully succeed in forming two symmetric hydrogen bonds to the catalytic aspartates. The crystal structures of the complexes further explain the difference in potency between the shorter inhibitors (two-carbon spacer) and the longer inhibitors (three-carbon spacer).

Synthesis, 2D-NMR and molecular modelling studies of pentacycloundecane lactam-peptides and peptoids as potential HIV-1 wild type C-SA protease inhibitors

In this study, eight non-natural peptides and peptoids incorporating the pentacycloundecane (PCU) lactam were designed and synthesized as potential inhibitors of the wild type C-SA HIV-protease. Five of these inhibitors gave IC(50) values ranging from 0.5 up to 0.75 µM against the resistance-prone wild type C-South African HIV-protease. NMR EASY-ROESY studies enabled us to describe the secondary structure of three of these compounds in solution. The 3D structures of the selected cage peptides were also modelled in solution using QM/MM/MD simulations. Satisfactory agreement between the NMR observations and the low energy calculated structures exists. Only one of these inhibitors (11 peptoid), which showed the best IC(50)(0.5 µM), exhibited a definable 3-D structure in solution. Autodock4 and AutodockVina were used to model the potential interaction between these inhibitors and the HIV-PR. It appears that the docking results are too crude to be correlated with the relative narrow range of experimental IC(50) values (0.5-10 µM). The PCU-peptides and peptoides were several orders less toxic (145 μM for 11 and 102 μM for 11 peptoid) to human MT-4 cells than lopinavir (0.025 μM). This is the first example of a polycyclic cage framework to be employed as an HIV-PR transition state analogue inhibitor and can potentially be utilized for other diseases related proteases. [Figure: see text].

Microwave-assisted synthesis of small molecules targeting the infectious diseases tuberculosis, HIV/AIDS, malaria and hepatitis C

The unique properties of microwave in situ heating offer unparalleled opportunities for medicinal chemists to speed up lead optimisation processes in early drug discovery. The technology is ideal for small-scale discovery chemistry because it allows full reaction control, short reaction times, high safety and rapid feedback. To illustrate these advantages, we herein describe applications and approaches in the synthesis of small molecules to combat four of the most prevalent infectious diseases; tuberculosis, HIV/AIDS, malaria and hepatitis C, using dedicated microwave instrumentation.

Synthesis, characterization, anti-inflammatory and in vitro antimicrobial activity of some novel alkyl/aryl substituted tertiary alcohols

The synthesis of some novel alkyl/aryl substituted tertiary alcohols was accomplished in two steps. The synthetic route involves preparation of Grignard reagents by treating alkyl/aryl bromides with magnesium turnings in dry ether. Then substituted chalcones were reacted with the Grignard reagents to afford alkyl/aryl substituted tertiary alcohols 1-10. The structures of the synthesized compounds were assigned on the basis of FT-IR, 1H-NMR, 13C-NMR and mass spectroscopic data. The in vivo anti-inflammatory activity of the synthesized compounds was evaluated using the carrageenan-induced hind paw edema method and was compared with that of ibuprofen. Some of the newly synthesized compounds showed promising anti-inflammatory activity. The tertiary alcohols 1-10 were also screened for antibacterial activity against ten bacterial strains using seven Gram-positive and three Gram-negative bacteria and for antifungal activity against Aspergillus Flavus, Aspergillus Niger and Aspergillus pterus. Tertiary alcohols 1-10 were found to exhibit good to excellent antimicrobial activities compared to levofloxacin and fluconazole used as standard drugs.

Ionic derivatives of betulinic acid as novel HIV-1 protease inhibitors

Betulinic acid is a natural product possessing abundant and favourable biological activity, including anti-cancer, anti-malarial, anti-inflammatory and anti-HIV properties, while causing minimal toxicity to unaffected cells. The full biological potency of betulinic acid cannot be fully unlocked, however, for a number of reasons, a primary one being its limited solubility in aqueous and biologically pertinent organic media. Aiming to improve the water solubility of betulinic acid without disrupting its structurally related bioactivity, we have prepared different ionic derivatives of betulinic acid. Inhibition bioassays on HIV-1 protease-catalysed peptide hydrolysis indicate significantly improved performance resulting from converting the betulinic acid to organic salt form. Indeed, for one particular cholinium-based derivative, its water solubility is improved more than 100 times and the half maximal inhibitory concentration (IC(50)) value (22 μg mL(-1)) was one-third that of wide-type betulinic acid (60 μg mL(-1)). These encouraging results advise that additional studies of ionic betulinic acid derivatives as a therapeutic solution against HIV-1 infection are warranted.

Structural features determining the intestinal epithelial permeability and efflux of novel HIV-1 protease inhibitors

The primary aim of this study was to identify structural features that alter the intestinal epithelial permeability and efflux in a series of novel HIV-1 protease inhibitors (PIs). Eleven PIs were selected containing a tertiary alcohol in a transition-state mimicking scaffold, in which two substituents (R₁ and R₂) were varied systematically. Indinavir was selected as a reference compound. The apical-to-basolateral permeability was investigated in 2/4/A1 and Caco-2 monolayers. In addition, the basolateral-to-apical permeability was investigated in the Caco-2 monolayers and the efflux ratios were calculated. The absence of active drug transport processes in 2/4/A1 cells allowed identification and modeling of structural elements affecting the passive permeability. For instance, small aromatic R₁ substituents and a small (bromo-) R₂ substituent were associated with a high passive permeability. Efflux studies in Caco-2 cells indicated that amide-substituted neutral hydrophobic amino acids, such as valine and leucine, in the R₁ position, reduced the apical-to-basolateral transport and enhanced the efflux. We conclude that our investigation revealed structural features that alter the intestinal epithelial permeability and efflux in the series of PIs and hope that these results can contribute to the synthesis of PIs with improved permeability and limited efflux properties. © 2010 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 100:3763–3772, 2011

On the orientation of the catalytic dyad in aspartic proteases

The recent re-refinement of the X-ray structure of apo plasmepsin II from Plasmodium falciparum suggests that the two carboxylate groups in the catalytic dyad are noncoplanar, (Robbins et al., Acta Crystallogr D Biol Crystallogr 2009;65: 294-296) in remarkable contrast with the vast majority of structures of aspartic proteases. Here, evidence for the noncoplanarity of the catalytic aspartates is provided by analysis of multiple explicit water molecular dynamics (MD) simulations of plasmepsin II, human beta-secretase, and HIV-protease. In the MD runs of plasmepsin II, the angle between the planes of the two carboxylates of the catalytic dyad is almost always in the range 60 degrees -120 degrees , in agreement with the perpendicular orientation in the re-refined X-ray structure. The noncoplanar arrangement is prevalent also in the beta-secretase simulations, as well as in the runs with the inhibitor-bound proteases. Quantum-mechanics calculations provide further evidence that before catalysis the noncoplanar arrangement is favored energetically in eukaryotic aspartic proteases. Remarkably, the coplanar orientation of the catalytic dyad is observed in MD simulations of HIV-protease at 100 K but not at 300 K, which indicates that the noncoplanar arrangement is favored by conformational entropy. This finding suggests that the coplanar orientation in the crystal structures of apo aspartic proteases is promoted by the very low temperature used for data collection (usually around 100 K).

HIV-1 protease inhibitors with a transition-state mimic comprising a tertiary alcohol: improved antiviral activity in cells

By a small modification in the core structure of the previously reported series of HIV-1 protease inhibitors that encompasses a tertiary alcohol as part of the transition-state mimicking scaffold, up to 56 times more potent compounds were obtained exhibiting EC(50) values down to 3 nM. Three of the inhibitors also displayed excellent activity against selected resistant isolates of HIV-1. The synthesis of 25 new and optically pure HIV-1 protease inhibitors is reported, along with methods for elongation of the inhibitor P1' side chain using microwave-accelerated, palladium-catalyzed cross-coupling reactions, the biological evaluation, and X-ray data obtained from one of the most potent analogues cocrystallized with both the wild type and the L63P, V82T, I84 V mutant of the HIV-1 protease.

Approaches to the design of HIV protease inhibitors with improved resistance profiles

PURPOSE OF REVIEW

This review describes current approaches to HIV protease inhibitor design, with a focus on improving their profile against drug-resistant mutants. Potential explanations for the flat resistance profile of some potent protease inhibitors and discrepancies between the apparent fold change of potency at the enzyme level and in cell-based assays are discussed.

RECENT FINDINGS

Despite new ideas and a clear rationale for designing inhibitors that bind outside the enzyme active site, all current protease inhibitors with potent antiviral activity target this site. Several bis-tetrahydrofuran-containing compounds including darunavir, brecanavir, GS-8374, and Sequoia protease inhibitors exhibit excellent potency against mutant HIV strains that are resistant to clinically used protease inhibitors. The apparently flat resistance profiles of these and some other protease inhibitors may, at least in part, be explained by their high potency against wild-type enzyme. The substrate envelope and solvent-anchoring hypotheses have been used to design and/or rationalize improved resistance profiles. Traditional approaches yielded a lysine sulfonamide PL-100 with a unique resistance profile.

SUMMARY

Several theories on how to design HIV protease inhibitors with improved resistance profiles have been proposed during the review period. The general concepts that are incorporated into most design strategies include maximizing the interactions with the backbone and conserved side chains of the enzyme while minimizing inhibitor size and maintaining conformational flexibility to allow for modified binding modes.