Simeprevir

Competitive, Reversible, and Noncovalent Binding Modalities

Interactions with Interferon-alpha and HCV NS5B Inhibitors

This compound exhibits synergistic antiviral effects when combined with interferon-alpha (IFN-α) and HCV NS5B inhibitors in HCV replicon cell models. wikipedia.orgresearchgate.net This synergistic interaction underscores the potential for enhanced viral suppression when these agents are used in combination.

The NS3/4A protease, which this compound targets, is known to interfere with host interferon-signaling pathways. By inhibiting this viral protease, this compound can contribute to the recovery of proper IFN-signaling, thereby augmenting the host's innate immune response against HCV. wikipedia.org

Clinical studies have frequently evaluated this compound in combination regimens that include peginterferon alfa, a modified form of interferon-alpha. The addition of this compound to peginterferon alfa and ribavirin has demonstrated significantly improved sustained virological response (SVR) rates in patients with HCV genotype 1 infection compared to peginterferon alfa and ribavirin alone. For instance, in treatment-naïve patients with HCV genotype 1, studies like QUEST-1 and QUEST-2 reported SVR12 rates of approximately 80-81% with this compound in combination with peginterferon alfa 2a and ribavirin, compared to around 50% in the placebo group receiving peginterferon alfa and ribavirin alone.

HCV NS5B inhibitors, such as sofosbuvir, target the viral RNA-dependent RNA polymerase, another critical enzyme for HCV replication. The combination of this compound (an NS3/4A protease inhibitor) and sofosbuvir (an NS5B polymerase inhibitor) has shown high rates of sustained virological response, even in difficult-to-treat populations like patients with cirrhosis. Research has indicated that this compound in combination with an NS5B inhibitor can lead to synergistic antiviral activity. wikipedia.orgresearchgate.net

Interactions with Ribavirin

This compound demonstrates additive effects when combined with ribavirin in HCV replicon cells. wikipedia.orgresearchgate.net Ribavirin is a broad-spectrum antiviral nucleoside analog that inhibits viral genome synthesis, primarily by inhibiting inosine monophosphate dehydrogenase (IMP), an enzyme involved in GTP biosynthesis.

Ribavirin has been a long-standing component of hepatitis C treatment regimens, often used in combination with peginterferon alfa. mims.com The inclusion of this compound in triple therapy regimens with peginterferon alfa and ribavirin has been a common approach for treating chronic HCV infection, particularly for genotypes 1 and 4. This triple therapy has been shown to significantly improve SVR rates and allow for shorter treatment durations compared to dual therapy with peginterferon and ribavirin alone.

A meta-analysis of randomized controlled trials involving 2,301 patients demonstrated that the triple regimen of this compound, peginterferon, and ribavirin resulted in a higher pooled SVR rate and a lower pooled relapse rate compared to dual therapy.

Table 1: Research Findings on this compound Combination Therapies

Intermolecular Interactions and Hydrogen Bonding Network

Role of K136 in Active Site Closure

Within the active site of the HCV NS3/4A protease, Lysine 136 (K136) plays a crucial role in the enzyme's catalytic mechanism and its interaction with inhibitors like this compound. During the enzymatic process, particularly in the transition state, the negatively charged oxygen (oxyanion) of the carboxylate tetrahedral intermediate is stabilized by hydrogen bonds with the backbone amides of Serine 138 (S138) and Glycine 137 (G137), as well as the side chain of K136. This interaction is vital for the stabilization of the oxyanion hole, a key feature in serine protease catalysis.

This compound has been shown to interact with K136 in crystal structures, including those of HCV genotypes 1b and 4a, highlighting its contribution to the inhibitor's binding pattern guidetopharmacology.org. While acidic side chains of natural substrates commonly form hydrogen bonds with K136, this interaction is less prevalent with inhibitors mims.com. Computational studies further emphasize the crucial, albeit distinct, contributions of K136 and S139 sidechains to the binding of HCV NS3/4A inhibitors. K136's ability to adopt different conformations in various crystal structures suggests a dynamic role in facilitating active site closure and optimal inhibitor binding mims.com.

Influence of Macrocyclic Core on Affinity and Selectivity

The macrocyclic core is a defining feature of this compound, distinguishing it from first-generation linear peptidomimetic inhibitors wikidata.org. This macrocyclic portion significantly enhances the affinity and selectivity characteristics of the compound, enabling rapid association with and slow dissociation from the protein target through noncovalent binding wikidata.org. Macrocyclic structures generally offer functional diversity and stereochemical complexity in a semi-rigid, preorganized conformation, allowing them to bind with higher affinity and selectivity to challenging drug targets compared to more traditional small molecules.

This compound is a 14-membered P1-P3 macrocyclic inhibitor, developed through the strategic replacement of a hydroxyproline moiety with a cyclopentane surrogate within the peptidic framework. Studies involving the incorporation of a P1-P3 macrocyclization strategy and the examination of various ring sizes demonstrated that a 14-membered ring size was optimal for activity. This optimality underscores the critical interplay between the macrocycle and other substituents, such as those in the P3/P4 region. In certain cases, macrocyclic analogs have demonstrated significantly greater potency as NS3 protease inhibitors compared to their non-macrocyclic counterparts, with some macrocyclic derivatives being seven times more potent.

Role of Cyclopropylsulfonamide Moiety

The cyclopropylsulfonamide moiety is an integral part of the this compound structure, as indicated by its chemical name, which includes "N-(cyclopropylsulfonyl)". In the context of HCV NS3/4A protease inhibitors, acyl sulfonamide groups, which are structurally related to cyclopropylsulfonamide, have been shown to significantly improve potency. For instance, in related macrocyclic inhibitors, the replacement of a carboxylic acid group at P1 with an acylsulfonamide bioisostere led to over 100-fold improvement in potency in both enzyme and replicon assays. This highlights the critical contribution of the sulfonamide functionality to the inhibitory activity, likely through favorable interactions within the enzyme's active site.

Significance of Phenanthridine Ring

It is important to note that this compound's chemical structure contains a quinoline ring, specifically a "4-quinolinyl" group, rather than a phenanthridine ring. While phenanthridine moieties are present in some other HCV NS3/4A protease inhibitors, such as paritaprevir mims.com, the significance of a phenanthridine ring cannot be discussed in relation to this compound as it is not a component of its chemical structure.

Stereochemical Requirements in the P3/P4 Region

Stereochemistry in the P3/P4 region of this compound derivatives is crucial for their inhibitory activity. SAR studies revealed that the (S) stereochemical configuration at the stereocenters in the P3/P4 region is essential for potent inhibition. Analogs containing (R)-amino acids at either stereocenter in this region showed significantly reduced potency.

Furthermore, the presence of hydrogen bond donors in the P3/P4 region is vital for maintaining potency. For example, methylation of the cyclohexyl glycine amine amide in this region resulted in a complete loss of inhibitory activity. In contrast, methylation of the terminal amide had no significant effect on potency. Additionally, inhibitors with truncated P3/P4 chains exhibited reduced potency, emphasizing the importance of this region for optimal binding and activity.

Comparative Analysis of Cyclopentane versus Cyclopentene Analogs

During the optimization of this compound, a comparative analysis of cyclopentane and cyclopentene-containing analogs was undertaken. Generally, cyclopentene analogs demonstrated greater potency compared to their cyclopentane counterparts. For instance, a simple norvaline P1 analog with a cyclopentene core (analog 36) was a 100 nM inhibitor against genotype 1a (gt1a) NS3/4A protease, whereas the corresponding cyclopentane analog (analog 29) showed significantly lower potency with a Kᵢ of 2.3 μM.

Despite the observed higher potency of cyclopentene analogs, the decision was made to focus on cyclopentane analogs due to synthetic challenges associated with cyclopentene compounds, including the potential for irreversible covalent attachment via a Michael acceptor in the core.

Table 1: Comparative Potency of Cyclopentane vs. Cyclopentene Analogs against HCV NS3/4A Protease (gt1a)

Table 2: Influence of P3/P4 Stereochemistry and Modifications on NS3 1a Inhibition

Molecular Docking Simulations of this compound and Analogs

This compound, a macrocyclic, non-covalent, and reversible inhibitor, primarily targets the Hepatitis C Virus (HCV) nonstructural protein 3/4A (NS3/4A) serine protease, binding to its active site and thereby inhibiting viral replication mims.commims.comresearchgate.netdrugbank.com. Molecular docking simulations have been crucial in characterizing these interactions and predicting its binding affinity.

Studies on HCV NS3/4A protease have shown that this compound maintains a consistent binding pattern across different genotypes, such as 1b and 4a. In genotype 1b, this compound interacts with residues including H57, K136, G137, S139, and R155. For genotype 4a, interactions are observed with Q41, H57, K136, G137, and S139. Notably, this compound's ability to bind to the catalytic triad residues H57 and S139 contributes to its activity across these genotypes longdom.org.

Beyond HCV, this compound has been investigated through molecular docking for its potential inhibitory activity against other viral proteases, particularly the SARS-CoV-2 main protease (Mpro) and papain-like protease (PLpro) tandfonline.comujpronline.comujpronline.comnih.govchemrxiv.orgnih.govbiorxiv.orgnih.govacs.orgresearchgate.net. Docking simulations have consistently predicted favorable binding affinities for this compound with SARS-CoV-2 Mpro. Reported binding scores and free energies vary across studies depending on the specific docking algorithm and protein structure used:

The interaction of this compound with SARS-CoV-2 Mpro active site is often characterized by hydrogen bonds and hydrophobic contacts. For instance, hydrogen bonds have been observed with Cys 44 and Gly 143 tandfonline.com. During molecular dynamics simulations, three hydrogen bonds with Gly 143, Ser 144, and Cys 145 of Mpro were consistently maintained tandfonline.com. Other studies reported hydrogen bonds with Asn 119, His 163, and Thr 26, alongside sigma and pi interactions with His 41, Cys 145, and Met 49 nih.gov.

Comparative docking studies have also involved this compound's degradation products against SARS-CoV-2 Mpro, revealing that acidic degradant 2 exhibited superior binding affinity compared to this compound itself and a natural ligand ujpronline.comujpronline.com. Other NS3/4A protease inhibitors like Paritaprevir and Vaniprevir have been compared with this compound in their efficacy against different HCV genotypes, with this compound generally retaining activity across genotypes longdom.orgnih.gov.

Electric Field Calculations for Structure-Function Relationships

Electric field calculations represent a sophisticated computational approach used to establish explicit links between molecular structure and function, particularly in understanding protein-ligand interactions and enzyme catalysis arxiv.org. By projecting electric fields onto specific bonds or atoms within a molecular system, researchers can identify the components that contribute to stabilizing intermolecular interactions, both covalent and non-covalent, within an active site arxiv.org. This method can significantly narrow the exploration space in drug discovery by pinpointing key residues that exert functional consequences on a bound ligand arxiv.org.

While electric field calculations are a valuable tool in computational biophysics for analyzing electrostatics-driven events and understanding how biomolecules create suitable electrostatic environments for biological purposes, specific detailed research findings applying electric field calculations directly to this compound's interaction with HCV NS3/4A protease or other target proteins were not found in the provided search results researchgate.netnih.gov. However, the general methodology suggests that such calculations could provide deeper insights into the precise electrostatic contributions of this compound's chemical moieties to its binding affinity and inhibitory mechanism.

Analysis of Active Site Flexibility

The flexibility of the active site of target proteins plays a crucial role in drug binding and efficacy, and this aspect is often investigated using molecular dynamics (MD) simulations. For this compound, MD simulations have provided insights into its interaction with both HCV NS3/4A protease and SARS-CoV-2 Mpro.

For HCV NS3/4A protease, the flexibility of the active site is known to influence the susceptibility to drug resistance mutations. Inhibitors, including this compound, that feature a P1-P3 macrocycle are more prone to resistance mutations at residue S138, which is located near the active site nih.gov. This highlights the importance of understanding active site flexibility in the development of robust antiviral agents with higher barriers to drug resistance.

Amino Acid Substitutions at NS3 Positions S122, R155, and D168

Genotype-Specific Resistance Profiles (e.g., R155K in 1a, D168E/V in 1b)

Distribution Studies in Non-Human Models (e.g., Liver:Blood Ratio in Rat)

Preclinical studies in animal models have demonstrated that simeprevir undergoes extensive distribution, particularly to the gut and liver tissues. drugbank.comfda.govwikidoc.org In rats, a liver:blood ratio of 29:1 was observed, indicating significant accumulation within the liver. drugbank.comfda.govwikidoc.orgnih.gov While human distribution into compartments other than plasma has not been fully evaluated, preclinical findings in humans showed high tissue/plasma AUC ratios, with the small intestine exhibiting a ratio of 128 and the liver a ratio of 39. nih.gov this compound is largely confined to the plasma rather than the cellular components of the blood, as indicated by a blood:plasma ratio of approximately 0.66. fda.gov

Table 1: this compound Distribution Ratios in Preclinical Models

Hepatic Uptake Mechanisms: Role of Organic Anion Transporting Polypeptides (OATP1B1/3, OATP2B1)

Hepatic uptake of this compound is primarily mediated by organic anion transporting polypeptides (OATP) 1B1 and OATP1B3. drugbank.comfda.govwikidoc.orgnih.govfda.govnih.gov In vitro data and physiologically-based pharmacokinetic (PBPK) modeling and simulations suggest that this active uptake process is a major mechanism contributing to the distribution of this compound into the liver. fda.govwikidoc.orgfda.gov OATP2B1 has also been identified as a substrate for this compound. fda.gov The saturation of OATP1B1/3-mediated hepatic uptake is a significant factor contributing to the nonlinear pharmacokinetics observed with this compound. fda.govnih.govnih.govresearchgate.net Furthermore, in vitro studies have indicated that this compound can inhibit the uptake transporters OATP1B1, OATP1B3, and OATP2B1. nih.govnih.govfda.govresearchgate.net

Elimination Pathways: Predominance of Biliary Excretion

This compound is predominantly eliminated from the body through biliary excretion. drugbank.comfda.govnih.govnih.govfda.govhivclinic.caeuropa.eudrugs.commims.comwvu.edu Renal clearance plays an insignificant role in its elimination. nih.goveuropa.eu A radioactivity study demonstrated that following a single oral administration of radiolabeled this compound, approximately 91% of the total radioactivity was recovered in the feces, while less than 1% was detected in the urine. drugbank.comnih.govfda.govhivclinic.caeuropa.eudrugs.commims.comwvu.edu

Excretion of Unchanged Drug versus Metabolites

In the feces, the unchanged form of this compound accounted for approximately 31% of the total administered dose. drugbank.comnih.govfda.govhivclinic.caeuropa.eudrugs.commims.comwvu.edu In plasma, unchanged this compound was the primary circulating substance, representing about 85% of the circulating radioactivity 24 hours post-dose. fda.govfda.gov One minor metabolite, M21, was identified in plasma, constituting approximately 8% of the this compound area under the curve (AUC). fda.govhivclinic.ca In feces, M21, in combination with M22, was a major metabolite, accounting for 25.9% of the dose (with an M21/M22 ratio of 60/40). fda.gov These metabolites, M21 and M22, are formed through oxidation on the macrocyclic moiety of this compound. fda.govfda.govhivclinic.caeuropa.eu Several other metabolites were also identified in feces, though none individually comprised more than 6% of the dose. fda.gov No accumulation of metabolites has been observed following multiple-dose administration of this compound. hivclinic.ca

Protein Binding Characteristics in Plasma (>99.9%)

This compound exhibits extensive binding to plasma proteins, with more than 99.9% of the drug bound. drugbank.comfda.govwikidoc.orgnih.govfda.govhivclinic.cadrugs.commims.com The primary plasma protein responsible for this binding is albumin, with alpha 1-acid glycoprotein contributing to a lesser extent. drugbank.comfda.govwikidoc.orgnih.govhivclinic.cadrugs.commims.com This high plasma protein binding is not significantly altered in patients with renal or hepatic impairment. fda.govwikidoc.orgnih.gov

Table 2: this compound Plasma Protein Binding

Nonlinear Pharmacokinetics Attributed to Saturation of Hepatic Uptake and Metabolism

This compound demonstrates nonlinear pharmacokinetics at therapeutic doses. fda.govnih.govnih.govresearchgate.nethivclinic.ca This nonlinearity is primarily attributed to the saturation of both hepatic uptake, mediated by OATP1B1/3, and hepatic metabolism, predominantly by the CYP3A4 enzyme. fda.govnih.govnih.govresearchgate.nethivclinic.ca At higher doses (e.g., above 100 mg once daily in healthy subjects and 75 mg once daily in HCV-infected patients), the maximum plasma concentrations (Cmax) and area under the plasma concentration-time curve (AUC) values increase more than dose-proportionally. nih.govfda.govnih.govresearchgate.net The interplay between hepatic uptake and CYP3A4 metabolism is a key factor in the observed nonlinear pharmacokinetics of this compound. nih.govresearchgate.netdoi.org