Design, synthesis, and biological and structural evaluations of novel HIV-1 protease inhibitors to combat drug resistance

An end-to-end method for predicting compound-protein interactions based on simplified homogeneous graph convolutional network and pre-trained language model

Identification of interactions between chemical compounds and proteins is crucial for various applications, including drug discovery, target identification, network pharmacology, and elucidation of protein functions. Deep neural network-based approaches are becoming increasingly popular in efficiently identifying compound-protein interactions with high-throughput capabilities, narrowing down the scope of candidates for traditional labor-intensive, time-consuming and expensive experimental techniques. In this study, we proposed an end-to-end approach termed SPVec-SGCN-CPI, which utilized simplified graph convolutional network (SGCN) model with low-dimensional and continuous features generated from our previously developed model SPVec and graph topology information to predict compound-protein interactions. The SGCN technique, dividing the local neighborhood aggregation and nonlinearity layer-wise propagation steps, effectively aggregates K-order neighbor information while avoiding neighbor explosion and expediting training. The performance of the SPVec-SGCN-CPI method was assessed across three datasets and compared against four machine learning- and deep learning-based methods, as well as six state-of-the-art methods. Experimental results revealed that SPVec-SGCN-CPI outperformed all these competing methods, particularly excelling in unbalanced data scenarios. By propagating node features and topological information to the feature space, SPVec-SGCN-CPI effectively incorporates interactions between compounds and proteins, enabling the fusion of heterogeneity. Furthermore, our method scored all unlabeled data in ChEMBL, confirming the top five ranked compound-protein interactions through molecular docking and existing evidence. These findings suggest that our model can reliably uncover compound-protein interactions within unlabeled compound-protein pairs, carrying substantial implications for drug re-profiling and discovery. In summary, SPVec-SGCN demonstrates its efficacy in accurately predicting compound-protein interactions, showcasing potential to enhance target identification and streamline drug discovery processes.Scientific contributionsThe methodology presented in this work not only enables the comparatively accurate prediction of compound-protein interactions but also, for the first time, take sample imbalance which is very common in real world and computation efficiency into consideration simultaneously, accelerating the target identification and drug discovery process.

Oxazolidinones as versatile scaffolds in medicinal chemistry

Oxazolidinone is a five-member heterocyclic ring with several biological applications in medicinal chemistry. Among the three possible isomers, 2-oxazolidinone is the most investigated in drug discovery. Linezolid was pioneered as the first approved drug containing an oxazolidinone ring as the pharmacophore group. Numerous analogues have been developed since its arrival on the market in 2000. Some have succeeded in reaching the advanced stages of clinical studies. However, most oxazolidinone derivatives reported in recent decades have not reached the initial stages of drug development, despite their promising pharmacological applications in a variety of therapeutic areas, including antibacterial, antituberculosis, anticancer, anti-inflammatory, neurologic, and metabolic diseases, among other areas. Therefore, this review article aims to compile the efforts of medicinal chemists who have explored this scaffold over the past decades and highlight the potential of the class for medicinal chemistry.

Design, synthesis, and biological evaluation of novel HIV-1 protease inhibitors containing pyrrolidine-derived P2 ligands to combat drug-resistant variant

The design, synthesis, and biological evaluation of a novel series of HIV-1 protease inhibitors containing pyrrolidines with diverse linkers as the P2 ligands and various aromatic derivatives as the P2' ligands were described. A number of inhibitors demonstrated potent efficacy in both enzyme and cellular assays, as well as relatively low cytotoxicity. In particular, inhibitor 34b with a (R)-pyrrolidine-3-carboxamide P2 ligand and a 4-hydroxyphenyl P2' ligand displayed exceptional enzyme inhibitory activity with an IC₅₀ value of 0.32 nM. Furthermore, 34b also exhibited robust antiviral activity against both wild-type HIV-1 and drug-resistant variant with low micromolar EC₅₀ values. In addition, the molecular modelling studies revealed the extensive interactions between inhibitor 34b and the backbone residues of both wild-type and drug-resistant HIV-1 protease. These results suggested the feasibility of utilizing pyrrolidine derivatives as the P2 ligands and provided valuable information for further design and optimization of highly potent HIV-1 protease inhibitors.

Design and Evaluation of Novel HIV-1 Protease Inhibitors Containing Phenols or Polyphenols as P2 Ligands with High Activity against DRV-Resistant HIV-1 Variants

With the increasing prevalence of drug-resistant variants, novel potent HIV-1 protease inhibitors with broad-spectrum antiviral activity against multidrug-resistant causative viruses are urgently needed. Herein, we designed and synthesized a new series of HIV-1 protease inhibitors with phenols or polyphenols as the P2 ligands and a variety of sulfonamide analogs as the P2' ligands. A number of these new inhibitors showed superb enzymatic inhibitory activity and antiviral activity. In particular, inhibitors 15d and 15f exhibited potent enzymatic inhibitory activity in the low picomolar range, and the latter showed excellent activity against the Darunavir-resistant HIV-1 variant. Furthermore, the molecular modeling studies provided insight into the ligand-binding site interactions between inhibitors and the enzyme cavity, and they sparked inspiration for the further optimization of potent inhibitors.

Decoding molecular mechanism underlying binding of drugs to HIV-1 protease with molecular dynamics simulations and MM-GBSA calculations

HIV-1 protease (PR) is thought to be efficient targets of anti-AIDS drug design. Molecular dynamics (MD) simulations and multiple post-processing analysis technologies were applied to decipher molecular mechanism underlying binding of three drugs Lopinavir (LPV), Nelfinavir (NFV) and Atazanavir (ATV) to the PR. Binding free energies calculated by molecular mechanics generalized Born surface area (MM-GBSA) suggest that compensation between binding enthalpy and entropy plays a vital role in binding of drugs to PR. Dynamics analyses show that binding of LPV, NFV and ATV highly affects structural flexibility, motion modes and dynamics behaviour of the PR, especially for two flaps. Computational alanine scanning and interaction network analysis verify that although three drugs have structural difference, they share similar binding modes to the PR and common interaction clusters with the PR. The current findings also confirm that residues located interaction clusters, such as Asp25/Asp25', Gly27/Gly27', Ala28/Ala28', Asp29, Ile47/Ile47', Gly49/Gly49', Ile50/Ile50', Val82/Val82' and Ile84/Ile84, can be used as efficient targets of clinically available inhibitors towards the PR.

Insights into effect of the Asp25/Asp25' protonation states on binding of inhibitors Amprenavir and MKP97 to HIV-1 protease using molecular dynamics simulations and MM-GBSA calculations

The protonation states of two aspartic acids in the catalytic strands of HIV-1 protease (PR) remarkably affect bindings of inhibitors to PR. It is requisite for the design of potent inhibitors towards PR to investigate the influences of Asp25/Asp25' protonated states on dynamics behaviour of PR and binding mechanism of inhibitors to PR. In this work, molecular dynamics (MD) simulations, MM-GBSA method and principal component (PC) analysis were coupled to explore the effect of Asp25/Asp25' protonation states on conformational changes of PR and bindings of Amprenavir and MKP97 to PR. The results show that the Asp25/Asp25' protonation states exert different impacts on structural fluctuations, flexibility and motion modes of PR. Dynamics analysis verifies that Asp25/Asp25' protonated states highly affect conformational dynamics of two flaps in PR. The binding free energy calculations results suggest that the Asp25/Asp25' protonated states obviously strengthen bindings of inhibitors to PR compared to the non-protonation state. Calculations of residue-based free energy decomposition indicate that the Asp25/Asp25' protonation not only disturbs the interaction network of inhibitors with PR but also stabilizes bindings of inhibitors to PR by cancelling the electrostatic repulsive interaction. Therefore, special attentions should be paid to the Asp25/Asp25' protonation in the design of potent inhibitors towards PR.

Piperidine scaffold as the novel P2-ligands in cyclopropyl-containing HIV-1 protease inhibitors: Structure-based design, synthesis, biological evaluation and docking study

A series of potent HIV-1 protease inhibitors, containing diverse piperidine analogues as the P2-ligands, 4-substituted phenylsulfonamides as the P2'-ligands and a hydrophobic cyclopropyl group as the P1'-ligand, were designed, synthesized and evaluated in this work. Among these twenty-four target compounds, many of them exhibited excellent activity against HIV-1 protease with half maximal inhibitory concentration (IC50) values below 20 nM. Particularly, compound 22a containing a (R)-piperidine-3-carboxamide as the P2-ligand and a 4-methoxylphenylsulfonamide as the P2'-ligand exhibited the most effective inhibitory activity with an IC50 value of 3.61 nM. More importantly, 22a exhibited activity with inhibition of 42% and 26% against wild-type and Darunavir (DRV)-resistant HIV-1 variants, respectively. Additionally, the molecular docking of 22a with HIV-1 protease provided insight into the ligand-binding properties, which was of great value for further study.

Design and biological evaluation of novel HIV-1 protease inhibitors with isopropanol as P1' ligand to enhance binding with S1' subsite

Newly designed HIV-1 protease inhibitors that maximize interactions with the protein backbone, especially in the form of hydrogen bonds, may enhance the antiviral potency of these compounds and minimize acquisition of drug-resistant mutations. Herein, we described a series of new HIV-1 PIs containing phenols as the P2 ligands and chiral isopropanol as the P1' ligands, in combination with 4-trifluoromethylphenylsulfonamide or 4-nitrophenylsulfonamide as the P2' ligands. And most of these compounds exhibited nanomolar inhibitory potency. In particular, inhibitors 13c and 13e with 4-trifluoromethylphenylsulfonamide as the P2' ligand and (R) - isopropanol as the P1' ligand, exhibited antiviral IC₅₀ values of 1.64 nM and 2.33 nM, respectively. Furthermore, they also showed remarkable activity against wild-type and DRV-resistant HIV-1 variants that raised the prospect of designing more effective PIs further.

Synthesis and evaluation of potent human immunodeficiency virus 1 protease inhibitors with epimeric isopropanol as novel P1' ligands

Aim: HIV-1 protease inhibitors regimens suffered from a number of drawbacks, among which, the most egregious issue was the growing emergence of drug-resistant strains. Materials & methods: The design strategy of maximizing the protease active site interactions with the inhibitor, especially promoting extensive hydrogen bonding with the protein backbone atoms, might be in favor of combating drug resistance. A series of HIV-1 protease inhibitors that incorporated enantiomeric isopropanols as the P1' ligands in combination with phenols as the P2 ligands were reported herein. Results: A number of inhibitors displayed potent protease enzyme inhibition activity. In particular, inhibitor 14c showed comparable potency as darunavir with IC₅₀ value of 1.91 nM and activity against darunavir-resistant HIV-1 variants. Conclusion: The new kind of HIV-1 protease inhibitors deserves further study.

Syntheses and Biological Activities of triazole-based Sulfonamides

:

The triazole and sulfonamide compounds are known as biologically active agents that were employed for medicinal applications. These compounds were obtained in different forms by a variety of techniques to vast ranges of applications. The broad biological properties of these compounds have encouraged researchers to design and synthesize triazole-based sulfonamide derivatives as compounds with potential biological activity. In this review, we summarized the synthetic procedures of triazole-based sulfonamide compounds together with their biological activities during the last two decades.

Effective estimation of the inhibitor affinity of HIV-1 protease via a modified LIE approach

The inhibition of the Human Immunodeficiency Virus Type 1 Protease (HIV-1 PR) can prevent the synthesis of new viruses. Computer-aided drug design (CADD) would enhance the discovery of new therapies, through which the estimation of ligand-binding affinity is critical to predict the most efficient inhibitor. A time-consuming binding free energy method would reduce the usefulness of CADD. The modified linear interaction energy (LIE) approach emerges as an appropriate protocol that performs this task. In particular, the polar interaction free energy, which is obtained via numerically resolving the linear Poisson–Boltzmann equation, plays as an important role in driving the binding mechanism of the HIV-1 PR + inhibitor complex. The electrostatic interaction energy contributes to the attraction between two molecules, but the vdW interaction acts as a repulsive factor between the ligand and the HIV-1 PR. Moreover, the ligands were found to adopt a very strong hydrophobic interaction with the HIV-1 PR. Furthermore, the results obtained corroborate the high accuracy and precision of computational studies with a large correlation coefficient value R = 0.83 and a small RMSE δ_RMSE = 1.25 kcal mol⁻¹. This method is less time-consuming than the other end-point methods, such as the molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and free energy perturbation (FEP) approaches. Overall, the modified LIE approach would provide ligand-binding affinity with HIV-1 PR accurately, precisely, and rapidly, resulting in a more efficient design of new inhibitors.

The inhibition of the Human Immunodeficiency Virus Type 1 Protease (HIV-1 PR) can prevent the synthesis of new viruses.

Preliminary SAR and biological evaluation of potent HIV-1 protease inhibitors with pyrimidine bases as novel P2 ligands to enhance activity against DRV-resistant HIV-1 variants

Introducing pyrimidine bases, the basic components of nucleic acid, to P2 ligands might enhance the potency of Human Immunodeficiency Virus-1 (HIV-1) protease inhibitors because of the carbonyl and amino groups promoting the formation of extensive hydrogen bonding interactions. In this work, we provide evidence that inhibitor 10e, with N-2-(2,4-Dioxo-3,4-dihydropyrimidin-1(2H)-yl) acetamide as the P2 ligand and a 4-methoxylphenylsulfonamide as the P2' ligand, displayed remarkable enzyme inhibitory and antiviral activity, with the IC₅₀ 2.53 nM in vitro and a promising inhibition ratio with 68% against wild-type HIV-1 in vivo, with low cytotoxicity. This inhibitor also exhibited appreciable antiviral activity against DRV-resistant HIV-1 variants, which was of great value for further study.

Structural exploration of hydroxyethylamines as HIV-1 protease inhibitors: new features identified

The current study deals with chemometric modelling strategies (Naïve Bayes classification, hologram-based quantitative structure-activity relationship (HQSAR), comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA)) to explore the important features of hydroxylamine derivatives for exerting potent human immunodeficiency virus-1 (HIV-1) protease inhibition. Depending on the statistically validated reliable and robust quantitative structure-activity relationship (QSAR) models, important and crucial structural features have been identified that may be responsible for enhancing the activity profile of these hydroxylamine compounds. Arylsulfonamide function along with methoxy or fluoro substitution is important for enhancing activity. Bulky steric substitution at the sulfonamide nitrogen disfavours activity whereas smaller hydrophobic substitution at the same position is found to be favourable. Apart from the crucial oxazolidinone moiety, pyrrolidine, cyclic urea and methyl ester functions are also responsible for increasing the HIV-1 protease inhibitory profile. Observations derived from these modelling studies may be utilized further in designing promising HIV-1 protease inhibitors of this class.

Hydroxyethylamine derivatives as HIV-1 protease inhibitors: a predictive QSAR modelling study based on Monte Carlo optimization

Application of HIV-1 protease inhibitors (as an anti-HIV regimen) may serve as an attractive strategy for anti-HIV drug development. Several investigations suggest that there is a crucial need to develop a novel protease inhibitor with higher potency and reduced toxicity. Monte Carlo optimized QSAR study was performed on 200 hydroxyethylamine derivatives with antiprotease activity. Twenty-one QSAR models with good statistical qualities were developed from three different splits with various combinations of SMILES and GRAPH based descriptors. The best models from different splits were selected on the basis of statistically validated characteristics of the test set and have the following statistical parameters: r² = 0.806, Q² = 0.788 (split 1); r² = 0.842, Q² = 0.826 (split 2); r² = 0.774, Q² = 0.755 (split 3). The structural attributes obtained from the best models were analysed to understand the structural requirements of the selected series for HIV-1 protease inhibitory activity. On the basis of obtained structural attributes, 11 new compounds were designed, out of which five compounds were found to have better activity than the best active compound in the series.

Insight into binding mechanisms of inhibitors MKP56, MKP73, MKP86, and MKP97 to HIV-1 protease by using molecular dynamics simulation

HIV-1 protease (PR) has been a significant target for design of potent inhibitors curing acquired immunodeficiency syndrome. Molecular dynamics simulations coupled with molecular mechanics Poisson-Boltzmann surface area method were performed to study interaction modes of four inhibitors MKP56, MKP73, MKP86, and MKP97 with PR. The results suggest that the main force controlling interactions of inhibitors with PR should be contributed by van der Waals interactions between inhibitors and PR. The cross-correlation analyses based on MD trajectories show that inhibitor binding produces significant effect on the flap dynamics of PR. Hydrogen bond analyses indicate that inhibitors can form stable hydrogen bonding interactions with the residues from the catalytic strands of PR. The contributions of separate residues to inhibitor bindings are evaluated by using residue-based free energy decomposition method and the results demonstrate that the CH-π and CH-CH interactions between the hydrophobic groups of inhibitors with residues drive the associations of inhibitors with PR. We expect that this study can provide a significant theoretical aid for design of potent inhibitors targeting PR.

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.

Anti-HIV Drug Discovery and Development: Current Innovations and Future Trends

The early effectiveness of combinatorial antiretroviral therapy (cART) in the treatment of HIV infection has been compromised to some extent by rapid development of multidrug-resistant HIV strains, poor bioavailability, and cumulative toxicities, and so there is a need for alternative strategies of antiretroviral drug discovery and additional therapeutic agents with novel action modes or targets. From this perspective, we first review current strategies of antiretroviral drug discovery and optimization, with the aid of selected examples from the recent literature. We highlight the development of phosphate ester-based prodrugs as a means to improve the aqueous solubility of HIV inhibitors, and the introduction of the substrate envelope hypothesis as a new approach for overcoming HIV drug resistance. Finally, we discuss future directions for research, including opportunities for exploitation of novel antiretroviral targets, and the strategy of activation of latent HIV reservoirs as a means to eradicate the virus.

Fast gap-free enumeration of conformations and sequences for protein design

Despite significant successes in structure-based computational protein design in recent years, protein design algorithms must be improved to increase the biological accuracy of new designs. Protein design algorithms search through an exponential number of protein conformations, protein ensembles, and amino acid sequences in an attempt to find globally optimal structures with a desired biological function. To improve the biological accuracy of protein designs, it is necessary to increase both the amount of protein flexibility allowed during the search and the overall size of the design, while guaranteeing that the lowest-energy structures and sequences are found. DEE/A*-based algorithms are the most prevalent provable algorithms in the field of protein design and can provably enumerate a gap-free list of low-energy protein conformations, which is necessary for ensemble-based algorithms that predict protein binding. We present two classes of algorithmic improvements to the A* algorithm that greatly increase the efficiency of A*. First, we analyze the effect of ordering the expansion of mutable residue positions within the A* tree and present a dynamic residue ordering that reduces the number of A* nodes that must be visited during the search. Second, we propose new methods to improve the conformational bounds used to estimate the energies of partial conformations during the A* search. The residue ordering techniques and improved bounds can be combined for additional increases in A* efficiency. Our enhancements enable all A*-based methods to more fully search protein conformation space, which will ultimately improve the accuracy of complex biomedically relevant designs.

Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions

Protein-protein interactions (PPIs) underlie the majority of biological processes, signaling, and disease. Approaches to modulate PPIs with small molecules have therefore attracted increasing interest over the past decade. However, there are a number of challenges inherent in developing small-molecule PPI inhibitors that have prevented these approaches from reaching their full potential. From target validation to small-molecule screening and lead optimization, identifying therapeutically relevant PPIs that can be successfully modulated by small molecules is not a simple task. Following the recent review by Arkin et al., which summarized the lessons learnt from prior successes, we focus in this article on the specific challenges of developing PPI inhibitors and detail the recent advances in chemistry, biology, and computation that facilitate overcoming them. We conclude by providing a perspective on the field and outlining four innovations that we see as key enabling steps for successful development of small-molecule inhibitors targeting PPIs.

Communication: Chemical functionality of interfacial water enveloping nanoscale structural defects in proteins

Building upon a non-Debye multiscale treatment of water dielectrics, this work reveals the biochemical role of interfacial water enveloping nanoscale structural defects in soluble proteins, asserting its role as a chemical base. This quasi-reactant status is already implied by the significant concentration of structural defects in the vicinity of an enzymatically active site, delineating their role as promoters or enhancers of catalytic activity.

On the Molecular Modeling Analyses of Novel HIV-1 Protease Inhibitors Based on Modified Chitosan Dimer

The molecular modeling studies include quantitative structure activity relationship, IR spectra, and docking calculations, occurring for novel inhibitors based on chitosan dimer which were tried as HIV protease. The inhibitors were investigated with molecular modeling calculations at different level of theories. Each compound has phenol with hydroxymethylcarbonyl (HMC) group which added to chitosan in positions 2, 3, 2′, or 3′. The geometry of studied compounds is optimized with semiempirical PM3 method. Quantitative structure activity relationship (QSAR) properties of the suggested compounds are calculated at the same level of theory. Depending on QSAR calculations, the compounds with positions 2 and 2′ are less hydrophilic. The position 2′ compound makes good docking interaction into HIV protease active site. Calculated IR spectra indicate that the interaction through hydrogen bonding through the hydrogen of OH at positions 3 and 3′ gives rise to two OH bands one for chitosan and the other for phenol and HMC group. While at position 3′ CH band starts to appear.

The QSAR and docking calculations of fullerene derivatives as HIV-1 protease inhibitors

The inhibition of HIV-1 protease is considered as one of the most important targets for drug design and the deactivation of HIV-1. In the present work, the fullerene surface (C60) is modified by adding oxygen atoms as well as hydroxymethylcarbonyl (HMC) groups to form 6 investigated fullerene derivative compounds. These compounds have one, two, three, four or five O atoms+HMC groups at different positions on phenyl ring. The effect of the repeating of these groups on the ability of suggested compounds to inhibit the HIV protease is studied by calculating both Quantitative Structure Activity Relationship (QSAR) properties and docking simulation. Based on the QSAR descriptors, the solubility and the hydrophilicity of studied fullerene derivatives increased with increasing the number of oxygen atoms+HMC groups in the compound. While docking calculations indicate that, the compound with two oxygen atoms+HMC groups could interact and binds with HIV-1 protease active site. This is could be attributed to the active site residues of HIV-1 protease are hydrophobic except the two aspartic acids. So that, the increase in the hydrophilicity and polarity of the compound is preventing and/or decreasing the hydrophobic interaction between the compound and HIV-1 protease active site.

QSAR prediction of HIV-1 protease inhibitory activities using docking derived molecular descriptors

In this study, application of a new hybrid docking-quantitative structure activity relationship (QSAR) methodology to model and predict the HIV-1 protease inhibitory activities of a series of newly synthesized chemicals is reported. This hybrid docking-QSAR approach can provide valuable information about the most important chemical and structural features of the ligands that affect their inhibitory activities. Docking studies were used to find the actual conformations of chemicals in active site of HIV-1 protease. Then the molecular descriptors were calculated from these conformations. Multiple linear regression (MLR) and least square support vector machine (LS-SVM) were used as QSAR models, respectively. The obtained results reveal that statistical parameters of the LS-SVM model are better than the MLR model, which indicate that there are some non-linear relations between selected molecular descriptors and anti-HIV activities of interested chemicals. The correlation coefficient (R), root mean square error (RMSE) and average absolute error (AAE) for LS-SVM are: R=0.988, RMSE=0.207 and AAE=0.145 for the training set, and R=0.965, RMSE=0.403 and AAE=0.338 for the test set. Leave one out cross validation test was used for assessment of the predictive power and validity of models which led to cross-validation correlation coefficient QUOTE of 0.864 and 0.850 and standardized predicted relative error sum of squares (SPRESS) of 0.553 and 0.581 for LS-SVM and MLR models, respectively.

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.

Testing the substrate-envelope hypothesis with designed pairs of compounds

Acquired resistance to therapeutic agents is a significant barrier to the development of clinically effective treatments for diseases in which evolution occurs on clinical time scales, frequently arising from target mutations. We previously reported a general strategy to design effective inhibitors for rapidly mutating enzyme targets, which we demonstrated for HIV-1 protease inhibition [Altman et al. J. Am. Chem. Soc. 2008, 130, 6099–6113]. Specifically, we developed a computational inverse design procedure with the added constraint that designed inhibitors bind entirely inside the substrate envelope, a consensus volume occupied by natural substrates. The rationale for the substrate-envelope constraint is that it prevents designed inhibitors from making interactions beyond those required by substrates and thus limits the availability of mutations tolerated by substrates but not by designed inhibitors. The strategy resulted in subnanomolar inhibitors that bind robustly across a clinically derived panel of drug-resistant variants. To further test the substrate-envelope hypothesis, here we have designed, synthesized, and assayed derivatives of our original compounds that are larger and extend outside the substrate envelope. Our designs resulted in pairs of compounds that are very similar to one another, but one respects and one violates the substrate envelope. The envelope-respecting inhibitor demonstrates robust binding across a panel of drug-resistant protease variants, whereas the envelope-violating one binds tightly to wild type but loses affinity to at least one variant. This study provides strong support for the substrate-envelope hypothesis as a design strategy for inhibitors that reduce susceptibility to resistance mutations.

Computational study on the drug resistance mechanism against HCV NS3/4A protease inhibitors vaniprevir and MK-5172 by the combination use of molecular dynamics simulation, residue interaction network, and substrate envelope analysis

Hepatitis C virus (HCV) NS3/4A protease is an important and attractive target for anti-HCV drug development and discovery. Vaniprevir (phase III clinical trials) and MK-5172 (phase II clinical trials) are two potent antiviral compounds that target NS3/4A protease. However, the emergence of resistance to these two inhibitors reduced the effectiveness of vaniprevir and MK-5172 against viral replication. Among the drug resistance mutations, three single-site mutations at residues Arg155, Ala156, and Asp168 in NS3/4A protease are especially important due to their resistance to nearly all inhibitors in clinical development. A detailed understanding of drug resistance mechanism to vaniprevir and MK-5172 is therefore very crucial for the design of novel potent agents targeting viral variants. In this work, molecular dynamics (MD) simulation, binding free energy calculation, free energy decomposition, residue interaction network (RIN), and substrate envelope analysis were used to study the detailed drug resistance mechanism of the three mutants R155K, A156T, and D168A to vaniprevir and MK-5172. MD simulation was used to investigate the binding mode for these two inhibitors to wild-type and resistant mutants of HCV NS3/4A protease. Binding free energy calculation and free energy decomposition analysis reveal that drug resistance mutations reduced the interactions between the active site residues and substituent in the P2 to P4 linker of vaniprevir and MK-5172. Furthermore, RIN and substrate envelope analysis indicate that the studied mutations of the residues are located outside the substrate (4B5A) binding site and selectively decrease the affinity of inhibitors but not the activity of the enzyme and consequently help NS3/4A protease escape from the effect of the inhibitors without influencing the affinity of substrate binding. These findings can provide useful information for understanding the drug resistance mechanism against vaniprevir and MK-5172. The results can also provide some potential clues for further design of novel inhibitors that are less susceptible to drug resistance.

The nucleoside reverse transcriptase inhibitors, nonnucleoside reverse transcriptase inhibitors, and protease inhibitors in the treatment of HIV infections (AIDS)

The majority of the drugs currently used for the treatment of HIV infections (AIDS) belong to either of the following three classes: nucleoside reverse transcriptase inhibitors (NRTIs), nonnucleoside reverse transcriptase inhibitors (NNRTIs), and protease inhibitors (PIs). At present, there are 7 NRTIs, 5 NNRTIs, and 10 PIs approved for clinical use. They are discussed from the following viewpoints: (i) chemical formulae; (ii) mechanism of action; (iii) drug combinations; (iv) clinical aspects; (v) preexposure prophylaxis; (vi) prevention of mother-to-child transmission; (vii) their use in children; (viii) toxicity; (ix) adherence (compliance); (x) resistance; (xi) new NRTIs, NNRTIs, or PIs in (pre)clinical development; and (xii) the prospects for a "cure" of the disease.