Structure-activity relationships of carbocyclic influenza neuraminidase inhibitors

Umbrella Sampling-Based Method to Compute Ligand-Binding Affinity

Many proteins have a solvent-exposed binding cleft, which permits their inhibitors to bind and unbind without significant protein conformation transforms. The binding/unbinding pathways of these protein-inhibitor complexes can be rather straightforwardly sampled by using umbrella sampling (US) simulation methods. During a US simulation, the C_α atoms of the protein are restrained via a harmonic force. The potential of mean force (PMF) along the binding pathway can be estimated by using the weighted histogram analysis method (WHAM). The binding affinity is then computed as the difference in PMF between the binding and unbinding states.

Peramivir binding affinity with influenza A neuraminidase and research on its mutations using an induced-fit docking approach

Influenza A virus (IAV) has caused epidemic infections worldwide, with many strains resistant to inhibitors of a surface protein, neuraminidase (NA), due to point mutations on its structure. A novel NA inhibitor named peramivir was recently approved, but no exhaustive computational research regarding its binding affinity with wild-type and mutant NA has been conducted. In this study, a thorough investigation of IAV-NA PDB entries of 9 subtypes is described, providing a list of residues constituting the protein-ligand binding sites. The results of induced-fit docking approach point out key residues of wild-type NA participating in hydrogen bonds and/or ionic interactions with peramivir, among which Arg 368 is responsible for a peramivir-NA ionic interaction. Mutations on this residue greatly reduced the binding affinity of peramivir with NA, with 3 mutations R378Q, R378K and R378L (NA6) capable of deteriorating the docking performance of peramivir by over 50%. 200 compounds from 6-scaffolds were docked into these 3 mutant versions, revealing 18 compounds giving the most promising results. Among them, CMC-2012-7-1527-56 (benzoic acid scaffold, IC50 = 32 nM in inhibitory assays with IAV) is deemed the most potential inhibitor of mutant NA resisting both peramivir and zanamivir, and should be further investigated.

Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains

Influenza is an annual seasonal epidemic that has continually drawn public attentions, due to the potential death toll and drug resistance. Neuraminidase, which is essential for the spread of influenza virus, has been regarded as a valid target for the treatment of influenza infection. Although neuraminidase drugs have been developed, they are susceptible to drug-resistant mutations in the sialic-binding site. In this study, we established computational models (site-moiety maps) of H1N1 and H5N1 to determine properties of the 150-cavity, which is adjacent to the drug-binding site. The models reveal that hydrogen-bonding interactions with residues R118, D151, and R156 and van der Waals interactions with residues Q136, D151, and T439 are important for identifying 150-cavitiy inhibitors. Based on the models, we discovered three new inhibitors with IC₅₀ values <10 μM that occupies both the 150-cavity and sialic sites. The experimental results identified inhibitors with similar activities against both wild-type and dual H274Y/I222R mutant neuraminidases and showed little cytotoxic effects. Furthermore, we identified three new inhibitors situated at the sialic-binding site with inhibitory effects for normal neuraminidase, but lowered effects for mutant strains. The results suggest that the new inhibitors can be used as a starting point to combat drug-resistant strains.

[Prediction of selective inhibition of neuraminidase from various influenza virus strains by potential inhibitors]

A universal model of inhibition of neuraminidases from various influenza virus strains by a particular has been developed. It is based on known 3D data for neuraminidases from three influenza virus strains (A/Tokyo/3/67, A/tern/Australia/G70C/75, B/Lee/40) and modeling of 3D structure of neuraminidases from other strains (A/PR/8/34 è A/Aichi/2/68). Using docking and molecular dynamics, we have modeled 235 enzyme-ligand complexes for 89 compounds with known IC50 values. Selection of final variants among three results obtained for each enzyme-ligand pair and calculation of independent variables for generation of linear regression equations was performed using MM-PBSA/MM-GBSA. This resulted in the set of equations individual strains and the equations pooling all the data. Thus using this approach it is possible to predict inhibition for neuraminidase from each the considered strains by a particular inhibitor and to predict the range of its action on neuraminidases from various influenza virus strains.

Zwitterionic structures: from physicochemical properties toward computer-aided drug designs

Zwitterions, used widely in chemical, biological and medicinal fields, show distinct physicochemical properties relative to ordinary ampholytes, which largely decide their bioavailability and biological activities. In the present manuscript, these properties are discussed in order to facilitate our understanding of zwitterionic structures, followed by various examples of zwitterionic drugs and the critical role these properties play. We specifically focus our discussions on neuraminidase inhibitors (NAIs), which are used in the treatment and prevention of influenza, covering their computer-assisted design, transformation to zwitterionic isomers and interaction mechanisms of NAIs with proteins. The discovery and development of NAIs provide useful insights that may assist in the exploration of new zwitterionic drugs.

Computational assay of Zanamivir binding affinity with original and mutant influenza neuraminidase 9 using molecular docking

Based upon molecular docking, this study aimed to find notable in silico neuraminidase 9 (NA9) point mutations of the avian influenza A H7N9 virus that possess a Zanamivir resistant property and to determine the lead compound capable of inhibiting these NA9 mutations. Seven amino acids (key residues) at the binding site of neuraminidase 9 responsible for Zanamivir-NA9 direct interactions were identified and 72 commonly occurring mutant NA9 versions were created using the Sybyl-X 2.0 software. The docking scores obtained after Zanamivir was bound to all mutant molecules of NA9 revealed 3 notable mutations R292W, R118P, and R292K that could greatly reduce the binding affinity of the medicine. These 3 mutant NA9 versions were then bound to each of 154 different molecules chosen from 5 groups of compounds to determine which molecule(s) might be capable of inhibiting mutant neuraminidase 9, leading to the discovery of the lead compound of potent mutant NA9 inhibitors. This compound, together with other mutations occurring to NA9 identified in the study, would be used as data for further research regarding neuraminidase inhibitors and synthesizing new viable medications used in the fight against the virus.

RANK-ORDERING THE BINDING AFFINITY FOR FKBP12 AND H1N1 NEURAMINIDASE INHIBITORS IN THE COMBINATION OF A PROTEIN MODEL WITH DENSITY FUNCTIONAL THEORY

The quantum mechanical interaction energies between FKBP12 as well as H1N1 neuraminidase and their inhibitors were directly calculated with an efficient density functional theory by mimicking the whole protein with a protein model composed of the amino acids surrounding the ligands. It was found that the calculated quantum mechanical interaction energies correlate well with the experimental binding free energies with the correlation coefficients of 0.88, 0.86, and the standard deviation of 0.93 and 1.00 kcal/mol, respectively. To compare with force field approach, the binding free energies with the correlation coefficient R = 0.80 and 0.47 were estimated by AutoDock 4.0 programs. It was indicated that the quantum interaction energy shows a better performance in rank-ordering the binding affinity between FKBP12 and H1N1 neuraminidase inhibitors than those of AutoDock 4.0 program. In combination protein model with density functional theory, the estimated quantum interaction energy could be a good predictor or scoring function in structure-based computer-aided drug design. Finally, five new FKBP12 inhibitors were designed based on calculated quantum mechanical interaction energy. In particular, the theoretical K i value of one compound is as low as 0.05 nM, nearly 8-fold more active than FK506.

Synthesis and in vivo influenza virus-inhibitory effect of ester prodrug of 4-guanidino-7-O-methyl-Neu5Ac2en

A series of ester prodrugs of 7-O-methyl derivative of Zanamivir (compound 3) was synthesized and their efficacy was evaluated in an influenza infected mice model by intranasal administration. Compound 7c (CS-8958), octanoyl ester prodrug of the C-9 alcohol of compound 3, was found to be much longer-acting than Zanamivir. Furthermore, the in vivo efficacies of compounds 12a, 12b, and 12c, the linear alkyl ester prodrug of the carboxylic acid, were comparable to that exerted by compound 7c.

Pharmacophore modeling, quantitative structure-activity relationship analysis, and shape-complemented in silico screening allow access to novel influenza neuraminidase inhibitors

Neuraminidase (NA) enzyme is one of the valid targets against influenza viruses. With this in mind, the pharmacophoric space of influenza NA was explored using three sets of diverse inhibitors. Subsequently, genetic algorithm and multiple linear regression analysis were employed to select optimal combinations of pharmacophoric models and 2D descriptors capable of yielding self-consistent and predictive quantitative structure-activity relationships (QSARs) against 181 training compounds. The optimal QSAR equations were validated against 43 external test compounds with r(2)(PRESS) values ranging from 0.488 to 0.591. Interestingly, five orthogonal pharmacophores emerged in the optimal QSAR equations suggesting the existence of several distinct ligand/NA binding modes within the NA binding pocket. The resulting pharmacophores were complemented with tight shape constraints and employed as three-dimensional (3D) search queries against the National Cancer Institute (NCI) list of compounds. Several hits exhibited potent inhibitory activities against NA. The highest ranking hit demonstrated an in vitro IC(50) value of 1.8 muM. Docking studies supported the binding modes suggested by our pharmacophore/QSAR analysis.

Fragment-based quantitative structure-activity relationship (FB-QSAR) for fragment-based drug design

In cooperation with the fragment-based design a new drug design method, the so-called "fragment-based quantitative structure-activity relationship" (FB-QSAR) is proposed. The essence of the new method is that the molecular framework in a family of drug candidates are divided into several fragments according to their substitutes being investigated. The bioactivities of molecules are correlated with the physicochemical properties of the molecular fragments through two sets of coefficients in the linear free energy equations. One coefficient set is for the physicochemical properties and the other for the weight factors of the molecular fragments. Meanwhile, an iterative double least square (IDLS) technique is developed to solve the two sets of coefficients in a training data set alternately and iteratively. The IDLS technique is a feedback procedure with machine learning ability. The standard Two-dimensional quantitative structure-activity relationship (2D-QSAR) is a special case, in the FB-QSAR, when the whole molecule is treated as one entity. The FB-QSAR approach can remarkably enhance the predictive power and provide more structural insights into rational drug design. As an example, the FB-QSAR is applied to build a predictive model of neuraminidase inhibitors for drug development against H5N1 influenza virus.

QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR

The recent wide spreading of the H5N1 avian influenza virus (AIV) in Asia, Europe and Africa and its ability to cause fatal infections in human has raised serious concerns about a pending global flu pandemic. Neuraminidase (NA) inhibitors are currently the only option for treatment or prophylaxis in humans infected with this strain. However, drugs currently on the market often meet with rapidly emerging resistant mutants and only have limited application as inadequate supply of synthetic material. To dig out helpful information for designing potent inhibitors with novel structures against the NA, we used automated docking, CoMFA, CoMSIA, and HQSAR methods to investigate the quantitative structure-activity relationship for 126 NA inhibitors (NIs) with great structural diversities and wide range of bioactivities against influenza A virus. Based on the binding conformations discovered via molecular docking into the crystal structure of NA, CoMFA and CoMSIA models were successfully built with the cross-validated q (2) of 0.813 and 0.771, respectively. HQSAR was also carried out as a complementary study in that HQSAR technique does not require 3D information of these compounds and could provide a detailed molecular fragment contribution to the inhibitory activity. These models also show clearly how steric, electrostatic, hydrophobicity, and individual fragments affect the potency of NA inhibitors. In addition, CoMFA and CoMSIA field distributions are found to be in well agreement with the structural characteristics of the corresponding binding sites. Therefore, the final 3D-QSAR models and the information of the inhibitor-enzyme interaction should be useful in developing novel potent NA inhibitors.

Antiviral drugs for influenza: Tamiflu® past, present and future

Two antiviral drugs that are currently available for the treatment of influenza are effective against all strains of the virus, if used correctly. These are the neuraminidase inhibitors, zanamivir (Relenza®) and oseltamivir (Tamiflu®). These drugs are the result of basic research performed over a 60-year period by many people around the world. They were deliberately synthesized from a knowledge of the x-ray crystal structure of influenza virus neuraminidase. This article provides a brief historical account of some of the scientific events that lead to their creation.

Neuraminidase pharmacophore model derived from diverse classes of inhibitors

A three-dimensional pharmacophore model was developed based on 22 currently available inhibitors, which were carefully selected with great diversity in both molecular structure and bioactivity, for discovering new potent neuraminidase (NA) inhibitors to fight against avian influenza virus. The best hypothesis (Hypo1), consisting of five features, namely, one positive ionizable group, one negative ionizable group, one hydrophobic point, and two hydrogen-bond donors, has a correlation coefficient of 0.902, a root mean square deviation of 1.392, and a cost difference of 72.88, suggesting that a highly predictive pharmacophore model was successfully obtained. The application of the model shows great success in predicting the activities of 88 known NA inhibitors in our test set with a correlation coefficient of 0.818 with a cross-validation of 98% confidence level. Accordingly, our model should be reliable in identifying structurally diverse compounds with desired biological activity.

A QSAR study on influenza neuraminidase inhibitors

Influenza is a major respiratory infection associated with significant morbidity in the general population and mortality in elderly and high-risk patients. It is an RNA virus that contains two major surface glycoproteins, neuraminidase and hemagglutinin. These proteins are essential for infection. Neuraminidase has been found to be a potential target to control influenza virus. In this paper, we have developed 17 quantitative structure-activity relationships (QSAR) for different sets of compounds to understand chemical-biological interactions governing their activities toward influenza neuraminidase.

Sialidase as a target for inhibitors of influenza virus replication

Structure-based drug design has led to the identification of potent and selective inhibitors of influenza virus sialidase, which have antiviral activity in vitro and in experimental animal models of influenza infection. Clinical studies with one such sialidase inhibitor, zanamivir, have shown this compound to be a safe and effective therapy for influenza infections in man. Passage of influenza viruses in the presence of zanamivir in vitro has been shown to result in the selection of viruses with reduced sensitivity to this drug. To date, however, there have been no reports of the isolation of zanamivir-resistant viruses during clinical studies of this compound. Further application of structure-based drug design is yielding novel classes of potent inhibitors of influenza virus sialidase.

Parallel synthesis of glycomimetic libraries: targeting a C-type lectin

We have developed methods for the parallel synthesis of two libraries of non-carbohydrate-based analogues of mannose on a solid support. The natural product shikimic acid was used as a key building block. The ability of the compounds to block the binding of the C-type lectin MBP-A to a mannosylated surface was assessed in a high-throughput assay. Ten library members with inhibitory activities equivalent to that of alpha-methyl mannopyranoside were identified. [reaction: see text]

Synthesis and anti-influenza evaluation of polyvalent sialidase inhibitors bearing 4-guanidino-Neu5Ac2en derivatives

We synthesized polyvalent sialidase inhibitors bearing 4-guanidino-Neu5Ac2en analogues on the polyglutamic acid back bone, via a spacer of alkyl ether at the C-7 position. These multivalent conjugates 9 and 10 showed enhancement of antiviral activity against infuenza A virus and more potent efficacy in vivo relative to a monomeric sialidase inhibitor.

Synthesis and anti-influenza virus activity of 4-guanidino-7-substituted Neu5Ac2en derivatives

Substitution of 7-OH by small hydrophobic groups on zanamivir resulted in the retaining of low nanomolar inhibitory activities against not only influenza A virus sialidase but also influenza A virus in cell culture. These compounds were prepared by treatment of the corresponding 7-substituted sialic acids derived from 4-modified N-acetyl-D-mannosamine (ManNAc) using enzyme-catalyzed aldol condensation.

A new series of C3-aza carbocyclic influenza neuraminidase inhibitors: synthesis and inhibitory activity

The synthesis and influenza neuraminidase inhibitory activity of a new series of C3-aza carbocyclic neuraminidase inhibitors are described. Analogues 3c and 3j, bearing a 3-pentyl group, exhibit influenza A inhibitory activities comparable to that of 1.

Characterization of human influenza virus variants selected in vitro in the presence of the neuraminidase inhibitor GS 4071

An oral prodrug of GS 4071, a potent and selective inhibitor of influenza neuraminidases, is currently under clinical development for the treatment and prophylaxis of influenza virus infections in humans. To investigate the potential development of resistance during the clinical use of this compound, variants of the human influenza A/Victoria/3/75 (H3N2) virus with reduced susceptibility to the neuraminidase inhibitor GS 4071 were selected in vitro by passaging the virus in MDCK cells in the presence of inhibitor. After eight passages, variants containing two amino acid substitutions in the hemagglutinin (A28T in HA1 and R124M in HA2) but no changes in the neuraminidase were isolated. These variants exhibited a 10-fold reduction in susceptibility to GS 4071 and zanamivir (GG167) in an in vitro plaque reduction assay. After 12 passages, a second variant containing these hemagglutinin mutations and a Lys substitution for the conserved Arg292 of the neuraminidase was isolated. The mutant neuraminidase enzyme exhibited high-level (30,000-fold) resistance to GS 4071, but only moderate (30-fold) resistance to zanamivir and 4-amino-Neu5Ac2en, the amino analog of zanamivir. The mutant enzyme had weaker affinity for the fluorogenic substrate 2'-(4-methylumbelliferyl)-alpha-D-N-acetylneuraminic acid and lower enzymatic activity compared to the wild-type enzyme. The viral variant containing the mutant neuraminidase did not replicate as well as the wild-type virus in culture and was 10,000-fold less infectious than the wild-type virus in a mouse model. These results suggest that although the R292K neuraminidase mutation confers high-level resistance to GS 4071 in vitro, its effect on viral virulence is likely to render this mutation of limited clinical significance.

Structure-activity relationship studies of novel carbocyclic influenza neuraminidase inhibitors

A series of influenza neuraminidase inhibitors with the cyclohexene scaffold containing lipophilic side chains have been synthesized and evaluated for influenza A and B neuraminidase inhibitory activity. The size and geometry of side chains have been modified systematically in order to investigate structure-activity relationships of this class of compounds. The X-ray crystal structures of several analogues complexed with neuraminidase revealed that the lipophilic side chains bound to the hydrophobic pocket consisted of Glu276, Ala246, Arg224, and Ile222 of the enzyme active site. The structure-activity relationship studies of this series have also demonstrated remarkably different inhibitory potency between influenza A and B neuraminidase. This indicated that the lipophilic side chains had quite different hydrophobic interactions with influenza A and B neuraminidase despite their complete homology in the active site. Influenza B neuraminidase appeared to be much more sensitive toward the increased steric bulkiness of inhibitors compared to influenza A neuraminidase. From the extensive structure-activity relationship investigation reported in this article, GS 4071 emerged as one of the most potent influenza neuraminidase inhibitors against both influenza A and B strains.