Recombinant Rana pipiens Amphinase-4

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Description

Definition and Origin

Recombinant Amphinase-4 belongs to the pancreatic ribonuclease A superfamily, characterized by its ribonucleolytic activity and selective cytotoxicity toward cancer cells. It is produced via recombinant DNA technology to enable scalable production and minimize batch-to-batch variability compared to natural isolates. Amphinase-4 is one of four polymorphic variants (Amph1–4) identified in R. pipiens oocytes, distinguished by amino acid substitutions at 19 polymorphic positions .

Enzymatic Activity

Amphinase-4 exhibits weak ribonucleolytic activity compared to RNase A but retains substrate selectivity:

  • Catalytic efficiency (kcat/KMk_{cat}/K_M): ~4 orders of magnitude lower than RNase A for RNA substrates .

  • Substrate preference: Limited discrimination between RNA substrates (e.g., rUA, rCA, rUG), unlike Onconase, which favors uracil-guanine sequences .

  • RI evasion: Does not bind mammalian ribonuclease inhibitor (RI), enabling intracellular RNA degradation .

Table 2: Enzymatic Properties vs. Related RNases

Enzymekcat/KMk_{cat}/K_M (rUG)Cytotoxicity (IC₅₀)RI Binding
RNase A1.0 × 10⁷NoneYes
Onconase1.2 × 10⁵0.1–1 µMNo
Amphinase-13.8 × 10³0.5–2 µMNo
Amphinase-4*~1–3 × 10³UndeterminedNo

*Estimated from Amph1–3 data in .

Antitumor Mechanisms

  • RNA degradation: Targets tRNA and microRNA precursors, disrupting protein synthesis and inducing apoptosis .

  • Cytostatic effects: Reduces cellular metabolic activity, prolonging mRNA half-life in co-transfection models .

  • Immunogenicity: Recombinant forms show reduced antigenicity compared to natural isolates .

Preclinical Research Findings

  • Cancer cell lines: Natural Amphinase variants (incl. Amph3) inhibited 60 cancer cell lines in NCI screenings, with IC₅₀ values comparable to Onconase .

  • Antiviral activity: Amph2 demonstrated efficacy against HIV-1 and bio-threat viruses in NIAID/NIH trials .

  • Safety: Recombinant Amph2 showed no detectable cytotoxicity in murine models at therapeutic doses .

Therapeutic Potential

  • Oncology: Potential for conjugation with monoclonal antibodies (e.g., EGFR-targeted therapies) .

  • mRNA therapeutics: Co-expression with mRNA vaccines enhances transgene expression by 3–6× via cytostatic stabilization .

  • Veterinary applications: Improved scalability and safety profiles support use in livestock and companion animals .

Challenges and Future Directions

  • Optimization: Engineering Amph4 for higher catalytic activity while retaining RI evasion.

  • Clinical translation: Limited data on Amph4-specific pharmacokinetics and toxicology .

  • Combination therapies: Synergy with checkpoint inhibitors or chemotherapeutics warrants exploration.

Product Specs

Form
Lyophilized powder. We will ship the in-stock format preferentially. If you have special format requirements, please note them when ordering, and we will fulfill your request.
Lead Time
Delivery times vary based on purchasing method and location. Please consult your local distributor for specific delivery times. All proteins are shipped with standard blue ice packs. For dry ice shipping, please contact us in advance; additional fees apply.
Notes
Avoid repeated freeze-thaw cycles. Working aliquots can be stored at 4°C for up to one week.
Reconstitution
Briefly centrifuge the vial before opening to collect contents. Reconstitute protein in sterile deionized water to a concentration of 0.1-1.0 mg/mL. Adding 5-50% glycerol (final concentration) is recommended for long-term storage at -20°C/-80°C. Our default final glycerol concentration is 50% for your reference.
Shelf Life
Shelf life depends on storage conditions, buffer components, storage temperature, and protein stability. Generally, the liquid form is stable for 6 months at -20°C/-80°C, while the lyophilized form is stable for 12 months at -20°C/-80°C.
Storage Condition
Store at -20°C/-80°C upon receipt. Aliquot for multiple uses. Avoid repeated freeze-thaw cycles.
Tag Info
The tag type will be determined during the manufacturing process. If you require a specific tag, please inform us, and we will prioritize its development.
Synonyms
; Amphinase-4; EC 3.1.27.-
Buffer Before Lyophilization
Tris/PBS-based buffer, 6% Trehalose.
Datasheet
Please contact us to get it.
Expression Region
1-114
Protein Length
full length protein
Purity
>85% (SDS-PAGE)
Species
Lithobates pipiens (Northern leopard frog) (Rana pipiens)
Target Protein Sequence
KPKEDKEWVK FKAKHITSQS VADFNCNKTM NDPDFTPDGQ CKPVNTFIHS NTGPVKDICR RASGRVNKSS TQQFPLTTCN KPIRCKYSQS NTTNFICITC RDNYPVHFVK IGKC
Uniprot No.

Target Background

Function
Endonuclease. Hydrolyzes highly polymerized RNA, poly(U), poly(C), and the dinucleotides CpA and UpA. Also hydrolyzes rCA, rUA, and rUG. Exhibits cytotoxic activity against cultured human submaxillary gland carcinoma cells.
Protein Families
Pancreatic ribonuclease family
Subcellular Location
Secreted.

Q&A

What is Amphinase-4 and how does it differ from other Amphinase variants?

Amphinase-4 (Amph-4) is one of four variants of a cytotoxic ribonuclease isolated from the oocytes of the Northern Leopard frog (Rana pipiens). The four Amphinase variants (Amph-1-4) share 86.8-99.1% sequence identity among themselves . Each variant is 114 amino acid residues in length and is N-glycosylated at two positions . Amphinase-4 belongs to the ribonuclease A superfamily and shares 38.2-40.0% sequence identity with Onconase, another cytotoxic ribonuclease from the same frog species .

All Amphinase variants demonstrate cytostatic and cytotoxic activity against human cancer cell lines, with effectiveness and cell cycle specificity generally similar across the variants . The enzymatic and cytotoxic activities of all variants follow comparable patterns, but subtle sequence differences may contribute to minor variations in substrate specificity and catalytic efficiency.

What is the biological role of Amphinase-4 in Rana pipiens oocytes?

The cytostatic properties of these ribonucleases likely contribute to reducing metabolic activity and cellular innate immune reactivity, potentially creating conditions favorable for early embryonic development . The retention of ribonucleolytic activity combined with the ability to evade ribonuclease inhibitors suggests that controlled RNA degradation within the oocyte or protection against pathogens may be important functions of these enzymes in their natural context.

What are the key structural features of Amphinase-4 that contribute to its unique properties?

Amphinase-4, like other Amphinase variants, possesses several distinctive structural features that contribute to its unique biochemical properties:

  • Size and N-terminal structure: At 114 amino acid residues, Amphinase-4 is the largest among amphibian ribonucleases . Unlike Onconase, which has an N-terminal pyroglutamate, Amphinase-4 has a six-residue extension at the N-terminus .

  • Glycosylation: Amphinase-4 is N-glycosylated at two positions, although the glycan component has little to no influence on single-stranded RNA cleavage, ribonuclease inhibitor evasion, or cytotoxicity .

  • Disulfide bonding: It maintains the characteristic pattern of cysteine residues found in frog ribonucleases, including the C-terminal disulfide bond that distinguishes amphibian ribonucleases from mammalian counterparts .

  • Active site configuration: Structural features that contribute to Amphinase-4's low ribonucleolytic activity include the fixture of Lys14 in an obstructive position, the ejection of Lys42, and a lack of constraints on the conformations of Lys42 and His107 . Additionally, an unusual α2-β1 loop may play a catalytic role that differs from other ribonucleases .

  • Rudimentary B₂ subsite: The B₂ subsite (where the nucleotide base binds) is described as "rudimentary," which affects substrate binding and specificity .

These structural features collectively enable Amphinase-4 to evade human ribonuclease inhibitor protein while maintaining sufficient ribonucleolytic activity for its cytotoxic effects.

How does the crystal structure of Amphinase compare to other ribonucleases, and what implications does this have for enzyme function?

The crystal structure of Amphinase-2 (which shares high sequence identity with Amphinase-4) has been determined at 1.8 Å resolution for the natural form and 1.9 Å for the recombinant form . While specific structural data for Amphinase-4 is not detailed in the current literature, several important comparative observations can be made:

  • Core fold conservation: Like other members of the ribonuclease A superfamily, Amphinase maintains the characteristic structural fold of RNase A while exhibiting unique modifications .

  • N-terminal differences: The extended N-terminus in Amphinase differs markedly from Onconase's pyroglutamate residue, which is an integral part of Onconase's active site . Crystallographic analysis indicates the N-terminus in Amphinase is unlikely to play a catalytic role .

  • Active site configuration: The positioning of catalytic residues differs significantly from RNase A. In Amphinase, Lys14 is fixed in an obstructive position with accompanying ejection of Lys42, and there's a lack of constraints on the conformations of Lys42 and His107 . This atypical arrangement contributes to its reduced catalytic efficiency compared to RNase A.

  • Substrate binding regions: The B₂ subsite in Amphinase is rudimentary , which explains its limited substrate discrimination compared to Onconase and RNase A .

These structural differences have important functional implications:

  • The aberrant active site geometry explains the 10⁴-fold lower catalytic efficiency compared to RNase A .

  • The structural features that prevent effective binding of the human ribonuclease inhibitor allow Amphinase to retain activity within cellular environments.

  • The limited substrate discrimination suggests broader RNA targeting capabilities compared to more substrate-specific ribonucleases.

What expression systems are most effective for producing active recombinant Amphinase-4?

While the literature doesn't provide explicit details on expression systems specifically optimized for Amphinase-4, successful production of recombinant Amphinase-2 has been reported, resulting in a protein whose crystal structure was determined at 1.9 Å resolution . Based on this and considerations of Amphinase-4's structural features, the following methodological approach would be recommended:

When designing expression systems for Amphinase-4, researchers should consider whether glycosylation is required for their specific application, as this will significantly influence the choice of expression system and downstream purification processes.

What quality control measures are essential for ensuring the consistency and reproducibility of experiments using recombinant Amphinase-4?

To ensure experimental reproducibility with recombinant Amphinase-4, the following quality control measures should be implemented:

  • Purity and homogeneity assessment:

    • SDS-PAGE analysis under reducing and non-reducing conditions to verify size, purity, and disulfide bond formation

    • Mass spectrometry to confirm molecular weight and detect potential post-translational modifications

    • Size exclusion chromatography to assess aggregation state and homogeneity

  • Structural verification:

    • Circular dichroism spectroscopy to confirm proper protein folding

    • Glycosylation analysis if using eukaryotic expression systems

    • N-terminal sequencing to verify correct processing of the N-terminal extension

  • Functional characterization:

    • Ribonucleolytic activity using fluorogenic substrates such as 6-FAM-dArC(dA)₂-6-TAMRA (rCA), 6-FAM-dArU(dA)₂-6-TAMRA (rUA), and 6-FAM-dArUdGdA-6-TAMRA (rUG)

    • Inhibition assays with human ribonuclease inhibitor to confirm RI evasion

    • Cytotoxicity testing against reference cell lines such as HL-60, Jurkat, or U-937 leukemia cells

    • Comparison with enzymatically inactive controls (e.g., through alkylation of the active site histidine)

  • Batch consistency verification:

    • Establishing acceptance criteria for each quality attribute

    • Comparison to reference standards

    • Lot-to-lot testing to ensure consistent biological activity

  • Stability profiling:

    • Accelerated and real-time stability studies under various storage conditions

    • Activity retention monitoring over time

    • Freeze-thaw stability assessment

The enzymatically inactive form of Amphinase-4 (e.g., through active site histidine alkylation) serves as an essential negative control, as demonstrated with Amph-2 where this modification reduced ribonuclease activity by over 98% and eliminated cytotoxic effects .

How can the ribonucleolytic activity of Amphinase-4 be accurately measured in experimental settings?

Accurate measurement of Amphinase-4's ribonucleolytic activity requires sensitive methods due to its relatively weak catalytic efficiency. Based on established approaches for Amphinase variants, the following methodological procedures are recommended:

  • Fluorogenic substrate assays:

    • Utilize fluorescent resonance energy transfer (FRET) substrates such as 6-FAM-dArC(dA)₂-6-TAMRA (rCA), 6-FAM-dArU(dA)₂-6-TAMRA (rUA), and 6-FAM-dArUdGdA-6-TAMRA (rUG)

    • Monitor fluorescence increase as a function of time to determine initial velocity

    • Calculate kinetic parameters (kcat, KM, kcat/KM) through appropriate models such as Michaelis-Menten kinetics

    • Expect kcat/KM values approximately 10⁴-fold lower than RNase A and 10²-fold lower than Onconase

  • Substrate preference determination:

    • Compare relative activities against different substrates (rCA, rUA, rUG)

    • Unlike Onconase, which shows strong preference for uracil at B₁ and guanine at B₂ positions, expect limited substrate discrimination by Amphinase-4

  • Ribonuclease inhibitor resistance assay:

    • Measure activity in the presence of increasing concentrations of human ribonuclease inhibitor (RI)

    • Verify maintained activity even at high RI concentrations, confirming the characteristic RI evasion of Amphinase-4

  • Activity-cytotoxicity correlation:

    • Compare cytotoxic effects of active Amphinase-4 with an enzymatically inactive form (e.g., through histidine alkylation)

    • Verify that the cytotoxic activity requires intact ribonucleolytic function

When interpreting ribonucleolytic activity data for Amphinase-4, researchers should account for its significantly lower catalytic efficiency compared to RNase A, which may necessitate longer reaction times or higher enzyme concentrations to observe measurable activity.

What are the cellular mechanisms by which Amphinase-4 exerts its cytotoxic effects on cancer cells?

Amphinase-4 exerts its cytotoxic effects through a multi-step process involving cellular entry, ribonucleolytic activity, and activation of apoptotic pathways. The current understanding of these mechanisms includes:

  • Cellular entry and evasion of inhibition:

    • Amphinase-4, being highly cationic, likely binds to negatively charged components on cancer cell surfaces with higher affinity than to normal cells

    • After internalization, it evades the cytosolic ribonuclease inhibitor (RI) , allowing it to maintain enzymatic activity within the cell

  • RNA degradation:

    • While specific RNA targets for Amphinase-4 are not explicitly identified in the literature, evidence from related ribonucleases suggests tRNA and microRNA precursors may be critical targets

    • RNA degradation leads to disruption of protein synthesis and potentially other RNA-dependent cellular processes

  • Cell cycle arrest:

    • Amphinase-4 treatment results in a distinct accumulation of cells in G₁ phase of the cell cycle

    • This cytostatic effect precedes the induction of apoptosis

  • Apoptosis induction through multiple pathways:

    • DNA fragmentation, evidenced by the presence of "sub-G₁" cells and TUNEL-positivity

    • Activation of caspase cascades

    • Concurrent activation of serine proteases

    • Activation of transglutaminase, which contributes to apoptotic body formation

  • Dependence on ribonucleolytic activity:

    • The cytotoxic effects require intact ribonucleolytic activity; enzymatically inactive Amphinase-2 (with active site histidine alkylated) showed over 98% reduction in ribonuclease activity and essentially no induction of apoptosis

The cytostatic effects of Amphinase-4 begin at concentrations of 0.5-10.0 μg/ml (38-770 nM) , with apoptotic effects becoming more pronounced at higher concentrations or with longer exposure times. At equimolar concentrations, Amphinase variants show somewhat more pronounced cytotoxic effects than Onconase .

How does Amphinase-4 compare structurally and functionally to Onconase and other therapeutic ribonucleases?

Amphinase-4 exhibits several distinctive structural and functional characteristics when compared to Onconase and other therapeutic ribonucleases:

Structural Comparisons:

FeatureAmphinase-4OnconaseRNase A (mammalian)
Size114 amino acids (largest amphibian RNase) 104 amino acids (smallest RNase A superfamily member) 124 amino acids
N-terminusSix-residue extension Pyroglutamate residue essential for activity No pyroglutamate
GlycosylationN-glycosylated at two positions Non-glycosylatedNon-glycosylated
Disulfide bondsContains characteristic C-terminal disulfide of frog RNases Contains characteristic C-terminal disulfide Lacks the C-terminal disulfide
Active siteLys14 in obstructive position, ejected Lys42 Optimized for uracil and guanine recognition Well-defined B₁ and B₂ subsites

Functional Comparisons:

PropertyAmphinase-4OnconaseRNase A (mammalian)
Catalytic efficiency~10⁴-fold lower than RNase A, ~10²-fold lower than Onconase ~10²-fold lower than RNase A Highest activity
Substrate specificityLittle discrimination between substrates Strong preference for uracil at B₁ and guanine at B₂ Preference for pyrimidines at B₁
RI sensitivityResistant to RI Resistant to RI Highly sensitive to RI
CytotoxicityEffective at 0.5-10.0 μg/ml; more potent than Onconase at equimolar concentrations Less potent than Amphinase at equimolar concentrations Limited due to RI inhibition
Clinical statusPre-clinical development Advanced clinical trials for malignant mesothelioma Various derivatives in development

What advantages might Amphinase-4 offer over Onconase for cancer research and potential therapeutic applications?

Amphinase-4 presents several potential advantages over Onconase for cancer research and therapeutic development:

  • Enhanced cytotoxic potency:

    • At equimolar concentrations, Amphinase variants demonstrate more pronounced cytotoxic effects than Onconase

    • Similar apoptotic effects were observed with Amphinase at 1 μg/ml compared to Onconase at 5 μg/ml , suggesting higher potency that could allow for lower therapeutic doses

  • Broader substrate specificity:

    • Unlike Onconase, which shows strong preference for specific RNA sequences, Amphinase variants demonstrate little discrimination between different RNA substrates

    • This broader specificity might allow Amphinase-4 to target a wider range of RNA species within cancer cells, potentially affecting multiple cellular pathways simultaneously

  • Structural opportunities for engineering:

    • The six-residue N-terminal extension provides a potential site for targeted modifications or conjugation strategies

    • The presence of N-glycosylation sites offers opportunities for glycoengineering to optimize pharmacokinetic properties

    • The unique active site configuration presents targets for structure-guided mutations to enhance activity while maintaining RI evasion

  • Potential for reduced immunogenicity:

    • While not explicitly demonstrated for Amphinase-4, the experience with recombinant Ranpirnase suggests that recombinant versions lacking certain modifications can exhibit reduced antigenicity while retaining key activities

    • This could potentially translate to improved tolerability in therapeutic applications

  • Cell cycle effects:

    • The G₁ phase arrest induced by Amphinase-4 might be particularly valuable for combination with therapeutics targeting other cell cycle phases

    • This cytostatic effect could also be leveraged in applications where temporary reduction in cellular metabolism is desired, such as in enhancing transgene expression

These advantages suggest that Amphinase-4 could represent a valuable addition to the arsenal of cytotoxic ribonucleases for cancer research and potential therapeutic development, offering complementary properties to the more extensively studied Onconase.

How can Amphinase-4 be utilized for targeting specific RNA species in cancer research?

Leveraging Amphinase-4 for targeting specific RNA species requires strategic approaches that capitalize on its inherent properties while overcoming limitations. The following methodological strategies can be employed:

  • Conjugation with targeting moieties:

    • Utilize the N-terminal six-residue extension or surface-exposed residues for conjugation with RNA-binding proteins or domains that recognize specific RNA structures

    • Develop aptamer-Amphinase-4 conjugates that can bind to specific RNA sequences before delivering the ribonucleolytic activity

    • Create antibody-Amphinase-4 fusion proteins to target cell surface proteins overexpressed on specific cancer types, enhancing selective delivery

  • Structure-guided engineering:

    • Modify the rudimentary B₂ subsite to enhance recognition of specific nucleotide sequences

    • Introduce mutations in the substrate binding region that increase affinity for particular RNA structural motifs, such as those found in oncogenic microRNAs

    • Optimize the unusual α2-β1 loop to enhance interaction with target RNAs

  • Leveraging the cytostatic effect:

    • Use Amphinase-4's ability to induce a cytostatic state to stabilize specific mRNAs or modulate the activity of RNA-binding proteins

    • Combine with other RNA-targeted therapies such as antisense oligonucleotides or siRNAs to enhance their efficacy through reduced cellular metabolism

  • Experimental validation approaches:

    • Implement RNA-seq or targeted RNA analysis to identify which RNA species are preferentially degraded by Amphinase-4 in different cell types

    • Use RNA immunoprecipitation followed by sequencing (RIP-seq) with tagged Amphinase-4 to identify directly bound RNA targets

    • Develop reporter systems with specific RNA structural elements to rapidly screen engineered Amphinase-4 variants for enhanced targeting specificity

The effectiveness of these approaches would be assessed through comparative cytotoxicity studies, specific RNA quantification, and functional assays relevant to the targeted RNA species. While Amphinase-4 naturally shows limited substrate discrimination , these engineering approaches could potentially enhance its specificity for research applications requiring targeted RNA degradation.

What synergistic effects have been observed when combining Amphinase variants with other cancer therapeutics?

While the literature does not provide specific data on synergistic effects of Amphinase-4 with other cancer therapeutics, valuable insights can be derived from information about related ribonucleases and the mechanisms of Amphinase action. Onconase, which shares many properties with Amphinase variants, "was shown to be strongly synergistic when combined with numerous other antitumor modalities" .

Based on the mechanisms of action of Amphinase variants, several potential synergistic approaches can be identified:

To properly investigate these potential synergistic effects, researchers should design combination studies using standard methodologies such as:

  • Combination index (CI) determination using the Chou-Talalay method

  • Isobologram analysis to distinguish between additive and synergistic effects

  • Sequential vs. simultaneous treatment comparisons to identify optimal scheduling

  • In vivo combination studies in appropriate animal models to verify synergistic effects observed in vitro

What are the most effective methods for studying the cellular uptake and intracellular trafficking of Amphinase-4?

Investigating the cellular uptake and intracellular trafficking of Amphinase-4 requires sophisticated techniques that preserve protein functionality while enabling sensitive detection. The following methodological approaches are recommended:

  • Fluorescent labeling strategies:

    • Site-specific labeling using maleimide chemistry on surface-exposed cysteine residues introduced through mutagenesis

    • N-terminal labeling leveraging the unique six-residue extension that is not critical for catalytic activity

    • Genetic fusion with fluorescent proteins (ensuring the fusion does not disrupt ribonucleolytic activity or RI evasion)

  • Live-cell imaging techniques:

    • Confocal microscopy with Z-stack acquisition to track the three-dimensional localization within cells

    • Time-lapse imaging to monitor the kinetics of uptake and intracellular movement

    • Fluorescence recovery after photobleaching (FRAP) to assess mobility within cellular compartments

  • Co-localization studies:

    • Simultaneous labeling of cellular compartments (endosomes, lysosomes, Golgi, ER, nucleus) to determine trafficking pathways

    • Immunofluorescence to detect interaction with specific cellular components

    • Super-resolution microscopy (STORM, PALM) for nanoscale resolution of localization patterns

  • Biochemical fractionation approaches:

    • Subcellular fractionation followed by Western blotting or enzyme activity assays to quantify distribution

    • Density gradient centrifugation to separate vesicular compartments containing Amphinase-4

    • Immunoprecipitation to identify protein interactions during trafficking

  • Mechanistic investigations:

    • Pharmacological inhibitors of different endocytic pathways (clathrin-mediated, caveolin-mediated, macropinocytosis)

    • siRNA knockdown of key trafficking proteins to determine dependence on specific pathways

    • Temperature-dependent studies (4°C vs. 37°C) to distinguish between active uptake and passive diffusion

  • Functional correlation:

    • Correlating internalization efficiency with cytotoxic potency across different cell lines

    • Assessing the impact of manipulating cellular uptake on downstream RNA degradation and apoptosis induction

    • Comparing uptake mechanisms with Onconase to identify unique aspects of Amphinase-4 trafficking

These methodological approaches would provide comprehensive insights into how Amphinase-4 enters cells and reaches its intracellular targets, which is crucial for understanding its mechanism of action and for designing strategies to enhance its therapeutic potential.

What experimental design considerations are important when evaluating the efficacy of Amphinase-4 against drug-resistant cancer cell lines?

Evaluating Amphinase-4's efficacy against drug-resistant cancer cell lines requires careful experimental design to ensure valid, reproducible results that properly address the underlying resistance mechanisms. The following methodological considerations are critical:

  • Cell line selection and characterization:

    • Include paired sensitive and resistant cell lines with well-characterized resistance mechanisms

    • Verify the resistance phenotype before each experiment through resistance marker expression or standard drug sensitivity testing

    • Document the passage number and maintain consistent culture conditions to prevent phenotypic drift

  • Resistance mechanism assessment:

    • Categorize cell lines based on resistance mechanisms (e.g., efflux pump overexpression, anti-apoptotic pathway upregulation, altered metabolism)

    • Measure expression levels of relevant resistance factors (e.g., P-glycoprotein, MRP1, BCRP for drug efflux; BCL-2, MCL-1 for apoptotic resistance)

    • Determine cross-resistance profiles to conventional therapeutics

  • Cytotoxicity evaluation:

    • Employ multiple complementary assays (e.g., MTT/MTS, ATP-based viability, clonogenic survival) to overcome assay-specific artifacts

    • Establish full dose-response curves rather than single-point measurements

    • Calculate IC50, IC90 values, and resistance indices (ratio of IC50 in resistant vs. sensitive cells)

  • Cell death mechanism analysis:

    • Determine whether Amphinase-4 induces apoptosis through caspase activation, serine protease activation, and transglutaminase activation in resistant cells

    • Evaluate cell cycle effects to confirm G₁ arrest occurs in resistant cell models

    • Assess whether resistance mechanisms affect Amphinase-4's ability to induce its characteristic apoptotic pathway

  • Intracellular activity verification:

    • Measure cellular uptake to ensure resistance is not due to reduced internalization

    • Confirm ribonucleolytic activity within resistant cells through RNA degradation assays

    • Verify that RNA targets of Amphinase-4 are still accessible in resistant cells

  • Combination strategies:

    • Test Amphinase-4 in combination with resistance-modulating agents (e.g., efflux pump inhibitors)

    • Evaluate synergy with drugs that target complementary pathways

    • Determine whether Amphinase-4 can resensitize resistant cells to conventional therapeutics

  • Controls and benchmarking:

    • Include Onconase as a benchmark, given its similar mechanism but lower potency at equimolar concentrations

    • Use enzymatically inactive Amphinase-4 (e.g., with alkylated active site histidine) as a negative control

    • Include conventional therapeutics to which the cells are resistant as reference compounds

  • In vivo validation:

    • Confirm promising in vitro findings in xenograft models established from resistant cell lines

    • Monitor not only tumor growth inhibition but also changes in resistance marker expression

By adhering to these methodological considerations, researchers can generate robust data on Amphinase-4's efficacy against drug-resistant cancer cell lines and gain insights into its potential for addressing clinical resistance.

What are the most promising approaches for engineering Amphinase-4 variants with enhanced therapeutic properties?

Engineering Amphinase-4 for enhanced therapeutic properties represents an exciting frontier in ribonuclease research. Based on its structural and functional characteristics, several promising engineering approaches can be pursued:

  • Active site optimization:

    • Address the suboptimal positioning of Lys14 (fixed in an obstructive position) and Lys42 (ejected from optimal position)

    • Introduce mutations that stabilize His107 in a more favorable conformation for catalysis

    • Enhance the rudimentary B₂ subsite to improve substrate binding while maintaining broad specificity

  • N-terminal modifications:

    • Leverage the unique six-residue N-terminal extension for site-specific conjugation strategies

    • Explore truncations or substitutions in this region to optimize stability and cellular uptake

    • Potentially introduce pyroglutamate or other modifications that might enhance catalytic activity

  • Stability engineering:

    • Introduce additional disulfide bonds to enhance thermal stability

    • Optimize surface charge distribution to improve solubility and reduce aggregation

    • Modify glycosylation sites or patterns to enhance serum half-life while maintaining activity

  • Targeted delivery systems:

    • Develop fusion proteins with cancer-targeting peptides or antibody fragments

    • Create conditionally active variants that are activated in the tumor microenvironment

    • Design stimuli-responsive formulations that release active Amphinase-4 preferentially in cancer cells

  • Immune modulation:

    • Engineer variants with reduced immunogenicity by modifying potential epitope regions

    • Create fusion proteins with immunomodulatory domains to enhance anti-tumor immune responses

    • Develop Amphinase-4 variants that selectively target immunosuppressive RNA species in the tumor microenvironment

  • Synergy optimization:

    • Design variants specifically optimized to complement other therapeutic modalities

    • Engineer bifunctional molecules combining Amphinase-4 with other anti-cancer agents

    • Modify properties to enhance penetration into solid tumors when used in combination therapies

Each engineering approach should be systematically evaluated through:

  • Structure-activity relationship studies

  • Comprehensive in vitro characterization of ribonucleolytic activity and cytotoxicity

  • Assessment of pharmacokinetic properties and immunogenicity

  • In vivo efficacy and safety evaluation in appropriate animal models

The recent success with recombinant Ranpirnase in enhancing transgene expression suggests that engineered Amphinase-4 variants might find applications beyond direct cancer therapy, potentially extending to RNA-based therapeutic delivery or enhancement.

What role might Amphinase-4 play in developing novel approaches to overcome treatment resistance in cancer therapy?

Amphinase-4 holds significant potential for addressing treatment resistance in cancer therapy due to its unique mechanism of action and molecular properties. Several promising research directions can be explored:

  • Targeting resistance-associated RNA species:

    • Investigate Amphinase-4's ability to degrade mRNAs encoding drug efflux pumps or anti-apoptotic proteins

    • Develop engineered variants with enhanced specificity for microRNAs involved in resistance pathways

    • Study whether Amphinase-4 can degrade long non-coding RNAs that contribute to therapy resistance

  • Exploiting alternative cell death pathways:

    • Since Amphinase-4 activates multiple apoptotic mechanisms including caspases, serine proteases, and transglutaminase , it may overcome apoptotic defects in resistant cells

    • Investigate whether Amphinase-4 can induce alternative cell death modes (e.g., necroptosis, pyroptosis) in apoptosis-resistant cells

    • Characterize the efficacy of Amphinase-4 against cancer stem cells or dormant cancer cells that often resist conventional therapies

  • Preventing resistance development:

    • Explore whether combining Amphinase-4 with conventional therapies from the outset can delay or prevent resistance development

    • Investigate potential effects on epigenetic mechanisms that contribute to acquired resistance

    • Study whether the G₁ arrest induced by Amphinase-4 affects the evolution of resistant clones

  • Addressing microenvironmental resistance factors:

    • Evaluate Amphinase-4's activity under hypoxic, acidic, or nutrient-deprived conditions that characterize the tumor microenvironment

    • Determine whether Amphinase-4 can disrupt RNA-dependent communication between cancer cells and stromal cells

    • Investigate effects on angiogenesis and extracellular matrix remodeling that contribute to therapy resistance

  • Immunotherapy resistance:

    • Explore Amphinase-4's impact on RNA species involved in immune evasion mechanisms

    • Study whether Amphinase-4 treatment can convert "cold" tumors to "hot" tumors more responsive to immunotherapy

    • Investigate combination approaches with immune checkpoint inhibitors or adoptive cell therapies

  • Technological applications in resistance research:

    • Develop Amphinase-4-based tools for identifying resistance-associated RNA species

    • Create RNA degradation profiles as biomarkers for predicting treatment response

    • Utilize the cytostatic properties of engineered Amphinase-4 variants to modulate cellular states during therapy

These research directions would benefit from multidisciplinary approaches combining structural biology, RNA biology, cancer biology, and immunology. The unique properties of Amphinase-4, particularly its ability to evade ribonuclease inhibitor while maintaining sufficient catalytic activity for biological effects, position it as a valuable tool in addressing the persistent challenge of treatment resistance in cancer therapy.

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