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1.
Hepatol Commun ; 8(5)2024 May 01.
Article in English | MEDLINE | ID: mdl-38696369

ABSTRACT

BACKGROUND: Human genetic studies have identified several mitochondrial amidoxime-reducing component 1 (MTARC1) variants as protective against metabolic dysfunction-associated steatotic liver disease. The MTARC1 variants are associated with decreased plasma lipids and liver enzymes and reduced liver-related mortality. However, the role of mARC1 in fatty liver disease is still unclear. METHODS: Given that mARC1 is mainly expressed in hepatocytes, we developed an N-acetylgalactosamine-conjugated mouse Mtarc1 siRNA, applying it in multiple in vivo models to investigate the role of mARC1 using multiomic techniques. RESULTS: In ob/ob mice, knockdown of Mtarc1 in mouse hepatocytes resulted in decreased serum liver enzymes, LDL-cholesterol, and liver triglycerides. Reduction of mARC1 also reduced liver weight, improved lipid profiles, and attenuated liver pathological changes in 2 diet-induced metabolic dysfunction-associated steatohepatitis mouse models. A comprehensive analysis of mARC1-deficient liver from a metabolic dysfunction-associated steatohepatitis mouse model by metabolomics, proteomics, and lipidomics showed that Mtarc1 knockdown partially restored metabolites and lipids altered by diet. CONCLUSIONS: Taken together, reducing mARC1 expression in hepatocytes protects against metabolic dysfunction-associated steatohepatitis in multiple murine models, suggesting a potential therapeutic approach for this chronic liver disease.


Subject(s)
Disease Models, Animal , Gene Knockdown Techniques , Hepatocytes , Animals , Mice , Hepatocytes/metabolism , Liver/metabolism , Male , RNA, Small Interfering/genetics , Mitochondrial Proteins/genetics , Mitochondrial Proteins/metabolism , Non-alcoholic Fatty Liver Disease/genetics , Non-alcoholic Fatty Liver Disease/metabolism , Non-alcoholic Fatty Liver Disease/prevention & control , Mice, Inbred C57BL
2.
J Chromatogr A ; 1661: 462679, 2022 Jan 04.
Article in English | MEDLINE | ID: mdl-34871941

ABSTRACT

N-acetylgalactosamine (GalNAc)-modified small interfering ribonucleic acids (siRNA) have shown promising outcomes for targeted siRNA delivery resulting in gene silencing in vivo; however, their structural complexity requires development of new purification methods to address high purity and recovery requirements. The current study evaluates complementary purification approaches using a mixed-mode Scherzo SS-C18 and anion-exchange (AEX) TSK-gel SuperQ-5PW for a range of single-stranded triantennary GalNAc-oligonucleotides. Initially, the semi-preparative mixed-mode support (10 × 250 mm, 3 µm) was compared against the preparative AEX analogue (21.5 × 300 mm, 13 µm), with the former affording double the recovery and higher purity of 95% over its AEX counterpart displaying 91% for a selected siRNA conjugate. An assortment of GalNAc-modified oligonucleotides was later purified using the mixed-mode resin revealing good recoveries (∼30-60%) and high purities of 90-94% ranging from straightforward to more challenging purifications. High sample loading in the 20 mg range was achieved, which was comparable with the larger preparative TSKgel SuperQ-5PW support. The Scherzo-SS-C18 resin also afforded some degree of resolution between diastereomers containing phosphorothioate functionalities. The TSKgel SuperQ-5PW support was later investigated to provide orthogonal separation selectivity to the Scherzo-SS-C18 column enabling purification of a selected, GalNAc-siRNA conjugate. The developed pH (8.5-11) and salt (0.3-0.7 M) gradients method provided enhanced separation selectivity between the free and conjugated siRNA, while minimizing formation of secondary structures and highlighting a complementary approach to deal with challenging purifications of oligonucleotide-GalNAc conjugates. Together, the use of AEX and mixed-mode columns provide much needed orthogonality to deal with complex GalNAc-modified oligonucleotides and potentially other upcoming modalities.


Subject(s)
Acetylgalactosamine , Oligonucleotides , Anions , Chromatography, Ion Exchange
3.
Nucleic Acid Ther ; 31(5): 324-340, 2021 10.
Article in English | MEDLINE | ID: mdl-34297902

ABSTRACT

Human genome wide association studies confirm the association of the rs738409 single nucleotide polymorphism (SNP) in the gene encoding protein patatin like phospholipase domain containing 3 (PNPLA3) with nonalcoholic fatty liver disease (NAFLD); the presence of the resulting mutant PNPLA3 I148M protein is a driver of nonalcoholic steatohepatitis (NASH). While Pnpla3-deficient mice do not display an adverse phenotype, the safety of knocking down endogenous wild type PNPLA3 in humans remains unknown. To expand the scope of a potential targeted NAFLD therapeutic to both homozygous and heterozygous PNPLA3 rs738409 populations, we sought to identify a minor allele-specific small interfering RNA (siRNA). Limiting our search to SNP-spanning triggers, a series of chemically modified siRNA were tested in vitro for activity and selectivity toward PNPLA3 rs738409 mRNA. Conjugation of the siRNA to a triantennary N-acetylgalactosamine (GalNAc) ligand enabled in vivo screening using adeno-associated virus to overexpress human PNPLA3I148M versus human PNPLA3I148I in mouse livers. Structure-activity relationship optimization yielded potent and minor allele-specific compounds that achieved high levels of mRNA and protein knockdown of human PNPLA3I148M but not PNPLA3I148I. Testing of the minor allele-specific siRNA in PNPLA3I148M-expressing mice fed a NASH-inducing diet prevented PNPLA3I148M-driven disease phenotypes, thus demonstrating the potential of a precision medicine approach to treating NAFLD.


Subject(s)
Non-alcoholic Fatty Liver Disease , Alleles , Animals , Genome-Wide Association Study , Lipase/genetics , Liver , Membrane Proteins/genetics , Mice , Non-alcoholic Fatty Liver Disease/genetics , Non-alcoholic Fatty Liver Disease/therapy , Phospholipases A2, Calcium-Independent , RNA, Small Interfering/genetics
4.
J Chromatogr A ; 1634: 461633, 2020 Dec 20.
Article in English | MEDLINE | ID: mdl-33189959

ABSTRACT

The current study investigates a method for purification of the G-quadruplex secondary structure, naturally formed by a guanine-rich 21-mer oligonucleotide strand using a monolithic convective interaction media-quaternary amine (CIM-QA) column under ion-exchange conditions. The monolithic support was initially evaluated on a preparative scale against a highly efficient TSKgel SuperQ-5PW ion-exchange support designed for oligonucleotide purification. The CIM analogue demonstrated clear advantages over the particle-based support on the basis of rapid separation times, while also affording high purity of the G-quadruplex. Various parameters were investigated including the type of mobile phase anion, cation, pH and injection load to induce and control quadruplex formation, as well as enhance chromatographic separation and final purity. Potassium afforded the most prominent quadruplex formation, yet sodium allowed for the highest resolution and purity to be achieved with a 30 mg injection on an 8 ml CIM-QA monolithic column. This method was applied to purify in excess of 300 mg of the quadruplex, with excellent retention time precision of under 1% RSD. Native mass spectrometry was utilized to confirm the identity of the intact G-quadruplex under non-denaturing conditions, while ion-pairing reversed-phase methods confirmed the presence of the single-stranded oligonucleotide in high purity (92%) under denaturing conditions. The key advantage of the purification method enables isolation of the G-quadruplex in its native state on a milli-gram scale, allowing structural characterization to further our knowledge of its role and function. The G-quadruplex can also be subsequently denaturated at elevated temperature causing single strand formation if additional reactions are to be pursued, such as annealing to form a duplex, and evaluation in in vitro or in vivo studies.


Subject(s)
Chemistry Techniques, Analytical/methods , Chromatography, Ion Exchange , G-Quadruplexes , Mass Spectrometry , Oligonucleotides/analysis
5.
ACS Chem Biol ; 14(4): 806-818, 2019 04 19.
Article in English | MEDLINE | ID: mdl-30875193

ABSTRACT

Drug discovery research on new pain targets with human genetic validation, including the voltage-gated sodium channel NaV1.7, is being pursued to address the unmet medical need with respect to chronic pain and the rising opioid epidemic. As part of early research efforts on this front, we have previously developed NaV1.7 inhibitory peptide-antibody conjugates with tarantula venom-derived GpTx-1 toxin peptides with an extended half-life (80 h) in rodents but only moderate in vitro activity (hNaV1.7 IC50 = 250 nM) and without in vivo activity. We identified the more potent peptide JzTx-V from our natural peptide collection and improved its selectivity against other sodium channel isoforms through positional analogueing. Here we report utilization of the JzTx-V scaffold in a peptide-antibody conjugate and architectural variations in the linker, peptide loading, and antibody attachment site. We found conjugates with 100-fold improved in vitro potency relative to those of complementary GpTx-1 analogues, but pharmacokinetic and bioimaging analyses of these JzTx-V conjugates revealed a shorter than expected plasma half-life in vivo with accumulation in the liver. In an attempt to increase circulatory serum levels, we sought the reduction of the net +6 charge of the JzTx-V scaffold while retaining a desirable NaV in vitro activity profile. The conjugate of a JzTx-V peptide analogue with a +2 formal charge maintained NaV1.7 potency with 18-fold improved plasma exposure in rodents. Balancing the loss of peptide and conjugate potency associated with the reduction of net charge necessary for improved target exposure resulted in a compound with moderate activity in a NaV1.7-dependent pharmacodynamic model but requires further optimization to identify a conjugate that can fully engage NaV1.7 in vivo.


Subject(s)
Immunoconjugates , NAV1.7 Voltage-Gated Sodium Channel/metabolism , Peptides/chemistry , Spider Venoms/chemistry , Voltage-Gated Sodium Channel Blockers , Animals , Antibodies/chemistry , Drug Discovery , Humans , Immunoconjugates/chemistry , Immunoconjugates/pharmacokinetics , Male , Mice , Molecular Targeted Therapy , NAV1.7 Voltage-Gated Sodium Channel/immunology , Peptides/pharmacokinetics , Spider Venoms/pharmacokinetics , Voltage-Gated Sodium Channel Blockers/chemistry , Voltage-Gated Sodium Channel Blockers/pharmacokinetics
6.
J Med Chem ; 61(21): 9500-9512, 2018 11 08.
Article in English | MEDLINE | ID: mdl-30346167

ABSTRACT

Inhibitors of the voltage-gated sodium channel NaV1.7 are being investigated as pain therapeutics due to compelling human genetics. We previously identified NaV1.7-inhibitory peptides GpTx-1 and JzTx-V from tarantula venom screens. Potency and selectivity were modulated through attribute-based positional scans of native residues via chemical synthesis. Herein, we report JzTx-V lead optimization to identify a pharmacodynamically active peptide variant. Molecular docking of peptide ensembles from NMR into a homology model-derived NaV1.7 structure supported prioritization of key residues clustered on a hydrophobic face of the disulfide-rich folded peptide for derivatization. Replacing Trp24 with 5-Br-Trp24 identified lead peptides with activity in electrophysiology assays in engineered and neuronal cells. 5-Br-Trp24 containing peptide AM-6120 was characterized in X-ray crystallography and pharmacokinetic studies and blocked histamine-induced pruritis in mice after subcutaneous administration, demonstrating systemic NaV1.7-dependent pharmacodynamics. Our data suggests a need for high target coverage based on plasma exposure for impacting in vivo end points with selectivity-optimized peptidic NaV1.7 inhibitors.


Subject(s)
Drug Discovery , Histamine/adverse effects , NAV1.7 Voltage-Gated Sodium Channel/metabolism , Peptides/chemistry , Peptides/pharmacology , Pruritus/drug therapy , Spider Venoms/chemistry , Animals , HEK293 Cells , Humans , Mice , Molecular Docking Simulation , NAV1.7 Voltage-Gated Sodium Channel/chemistry , Peptides/pharmacokinetics , Peptides/therapeutic use , Protein Conformation , Protein Folding , Pruritus/chemically induced , Structure-Activity Relationship , Tissue Distribution , Voltage-Gated Sodium Channel Blockers/chemistry , Voltage-Gated Sodium Channel Blockers/pharmacokinetics , Voltage-Gated Sodium Channel Blockers/pharmacology , Voltage-Gated Sodium Channel Blockers/therapeutic use
7.
PLoS One ; 13(5): e0196791, 2018.
Article in English | MEDLINE | ID: mdl-29723257

ABSTRACT

Identification of voltage-gated sodium channel NaV1.7 inhibitors for chronic pain therapeutic development is an area of vigorous pursuit. In an effort to identify more potent leads compared to our previously reported GpTx-1 peptide series, electrophysiology screening of fractionated tarantula venom discovered the NaV1.7 inhibitory peptide JzTx-V from the Chinese earth tiger tarantula Chilobrachys jingzhao. The parent peptide displayed nominal selectivity over the skeletal muscle NaV1.4 channel. Attribute-based positional scan analoging identified a key Ile28Glu mutation that improved NaV1.4 selectivity over 100-fold, and further optimization yielded the potent and selective peptide leads AM-8145 and AM-0422. NMR analyses revealed that the Ile28Glu substitution changed peptide conformation, pointing to a structural rationale for the selectivity gains. AM-8145 and AM-0422 as well as GpTx-1 and HwTx-IV competed for ProTx-II binding in HEK293 cells expressing human NaV1.7, suggesting that these NaV1.7 inhibitory peptides interact with a similar binding site. AM-8145 potently blocked native tetrodotoxin-sensitive (TTX-S) channels in mouse dorsal root ganglia (DRG) neurons, exhibited 30- to 120-fold selectivity over other human TTX-S channels and exhibited over 1,000-fold selectivity over other human tetrodotoxin-resistant (TTX-R) channels. Leveraging NaV1.7-NaV1.5 chimeras containing various voltage-sensor and pore regions, AM-8145 mapped to the second voltage-sensor domain of NaV1.7. AM-0422, but not the inactive peptide analog AM-8374, dose-dependently blocked capsaicin-induced DRG neuron action potential firing using a multi-electrode array readout and mechanically-induced C-fiber spiking in a saphenous skin-nerve preparation. Collectively, AM-8145 and AM-0422 represent potent, new engineered NaV1.7 inhibitory peptides derived from the JzTx-V scaffold with improved NaV selectivity and biological activity in blocking action potential firing in both DRG neurons and C-fibers.


Subject(s)
Analgesics/isolation & purification , NAV1.7 Voltage-Gated Sodium Channel/drug effects , Peptides/chemistry , Sodium Channel Blockers/isolation & purification , Spider Venoms/chemistry , Action Potentials/drug effects , Amino Acid Substitution , Analgesics/pharmacology , Animals , Capsaicin/pharmacology , Cell Line , Drug Evaluation, Preclinical , Ganglia, Spinal/drug effects , Humans , Male , Mice, Inbred C57BL , Mutagenesis, Site-Directed , Nerve Fibers, Unmyelinated/drug effects , Nuclear Magnetic Resonance, Biomolecular , Patch-Clamp Techniques , Physical Stimulation , Protein Engineering , Recombinant Proteins/drug effects , Sodium Channel Blockers/pharmacology , Structure-Activity Relationship , Tetrodotoxin/pharmacology
8.
ACS Chem Biol ; 12(9): 2427-2435, 2017 09 15.
Article in English | MEDLINE | ID: mdl-28800217

ABSTRACT

The voltage-gated sodium channel NaV1.7 is a genetically validated pain target under investigation for the development of analgesics. A therapeutic with a less frequent dosing regimen would be of value for treating chronic pain; however functional NaV1.7 targeting antibodies are not known. In this report, we describe NaV1.7 inhibitory peptide-antibody conjugates as an alternate construct for potential prolonged channel blockade through chemical derivatization of engineered antibodies. We previously identified NaV1.7 inhibitory peptide GpTx-1 from tarantula venom and optimized its potency and selectivity. Tethering GpTx-1 peptides to antibodies bifunctionally couples FcRn-based antibody recycling attributes to the NaV1.7 targeting function of the peptide warhead. Herein, we conjugated a GpTx-1 peptide to specific engineered cysteines in a carrier anti-2,4-dinitrophenol monoclonal antibody using polyethylene glycol linkers. The reactivity of 13 potential cysteine conjugation sites in the antibody scaffold was tuned using a model alkylating agent. Subsequent reactions with the peptide identified cysteine locations with the highest conversion to desired conjugates, which blocked NaV1.7 currents in whole cell electrophysiology. Variations in attachment site, linker, and peptide loading established design parameters for potency optimization. Antibody conjugation led to in vivo half-life extension by 130-fold relative to a nonconjugated GpTx-1 peptide and differential biodistribution to nerve fibers in wild-type but not NaV1.7 knockout mice. This study describes the optimization and application of antibody derivatization technology to functionally inhibit NaV1.7 in engineered and neuronal cells.


Subject(s)
Immunoconjugates/pharmacology , NAV1.7 Voltage-Gated Sodium Channel/metabolism , Peptides/pharmacology , Voltage-Gated Sodium Channel Blockers/pharmacology , Animals , HEK293 Cells , Humans , Immunoconjugates/chemistry , Immunoconjugates/pharmacokinetics , Male , Mice , Models, Molecular , Peptides/chemistry , Peptides/pharmacokinetics , Tissue Distribution , Voltage-Gated Sodium Channel Blockers/chemistry , Voltage-Gated Sodium Channel Blockers/pharmacokinetics
9.
J Med Chem ; 59(6): 2704-17, 2016 Mar 24.
Article in English | MEDLINE | ID: mdl-26890998

ABSTRACT

There is interest in the identification and optimization of new molecular entities selectively targeting ion channels of therapeutic relevance. Peptide toxins represent a rich source of pharmacology for ion channels, and we recently reported GpTx-1 analogs that inhibit NaV1.7, a voltage-gated sodium ion channel that is a compelling target for improved treatment of pain. Here we utilize multi-attribute positional scan (MAPS) analoging, combining high-throughput synthesis and electrophysiology, to interrogate the interaction of GpTx-1 with NaV1.7 and related NaV subtypes. After one round of MAPS analoging, we found novel substitutions at multiple residue positions not previously identified, specifically glutamic acid at positions 10 or 11 or lysine at position 18, that produce peptides with single digit nanomolar potency on NaV1.7 and 500-fold selectivity against off-target sodium channels. Docking studies with a NaV1.7 homology model and peptide NMR structure generated a model consistent with the key potency and selectivity modifications mapped in this work.


Subject(s)
NAV1.7 Voltage-Gated Sodium Channel/drug effects , Peptides/pharmacology , Sodium Channel Blockers/chemistry , Sodium Channel Blockers/pharmacology , Spider Venoms/pharmacology , Amino Acid Sequence , HEK293 Cells , High-Throughput Screening Assays , Humans , Magnetic Resonance Spectroscopy , Models, Molecular , Molecular Docking Simulation , Molecular Sequence Data , Substrate Specificity
10.
J Med Chem ; 58(17): 6784-802, 2015 Sep 10.
Article in English | MEDLINE | ID: mdl-26288216

ABSTRACT

To realize the medicinal potential of peptide toxins, naturally occurring disulfide-rich peptides, as ion channel antagonists, more efficient pharmaceutical optimization technologies must be developed. Here, we show that the therapeutic properties of multiple cysteine toxin peptides can be rapidly and substantially improved by combining direct chemical strategies with high-throughput electrophysiology. We applied whole-molecule, brute-force, structure-activity analoging to ShK, a peptide toxin from the sea anemone Stichodactyla helianthus that inhibits the voltage-gated potassium ion channel Kv1.3, to effectively discover critical structural changes for 15× selectivity against the closely related neuronal ion channel Kv1.1. Subsequent site-specific polymer conjugation resulted in an exquisitely selective Kv1.3 antagonist (>1000× over Kv1.1) with picomolar functional activity in whole blood and a pharmacokinetic profile suitable for weekly administration in primates. The pharmacological potential of the optimized toxin peptide was demonstrated by potent and sustained inhibition of cytokine secretion from T cells, a therapeutic target for autoimmune diseases, in cynomolgus monkeys.


Subject(s)
Cnidarian Venoms/chemistry , Kv1.3 Potassium Channel/antagonists & inhibitors , Peptides/chemistry , Polyethylene Glycols/chemistry , Animals , CHO Cells , Cnidarian Venoms/pharmacokinetics , Cnidarian Venoms/pharmacology , Cricetulus , Crystallography, X-Ray , Dogs , HEK293 Cells , Humans , Interferon-gamma/blood , Interferon-gamma/metabolism , Interleukin-17/blood , Interleukin-17/metabolism , Interleukin-2/blood , Interleukin-2/metabolism , Kv1.1 Potassium Channel/antagonists & inhibitors , Macaca fascicularis , Male , Mice , Molecular Docking Simulation , Patch-Clamp Techniques , Peptides/pharmacokinetics , Peptides/pharmacology , Rats, Sprague-Dawley , Species Specificity , Stereoisomerism , Structure-Activity Relationship , T-Lymphocytes/drug effects , T-Lymphocytes/metabolism
11.
Bioorg Med Chem Lett ; 25(21): 4866-4871, 2015 Nov 01.
Article in English | MEDLINE | ID: mdl-26112439

ABSTRACT

Many efforts are underway to develop selective inhibitors of the voltage-gated sodium channel NaV1.7 as new analgesics. Thus far, however, in vitro selectivity has proved difficult for small molecules, and peptides generally lack appropriate pharmacokinetic properties. We previously identified the NaV1.7 inhibitory peptide GpTx-1 from tarantula venom and optimized its potency and selectivity via structure-guided analoging. To further understand GpTx-1 binding to NaV1.7, we have mapped the binding site to transmembrane segments 1-4 of the second pseudosubunit internal repeat (commonly referred to as Site 4) using NaV1.5/NaV1.7 chimeric protein constructs. We also report that select GpTx-1 amino acid residues apparently not contacting NaV1.7 can be derivatized with a hydrophilic polymer without adversely affecting peptide potency. Homodimerization of GpTx-1 with a bifunctional polyethylene glycol (PEG) linker resulted in a compound with increased potency and a significantly reduced off-rate, demonstrating the ability to modulate the function and properties of GpTx-1 by linking to additional molecules.


Subject(s)
NAV1.7 Voltage-Gated Sodium Channel/metabolism , Peptides/chemistry , Peptides/pharmacology , Protein Engineering , Voltage-Gated Sodium Channel Blockers/pharmacology , Dimerization , Dose-Response Relationship, Drug , Humans , Molecular Conformation , Protein Binding , Protein Structure, Tertiary , Structure-Activity Relationship , Voltage-Gated Sodium Channel Blockers/chemistry
12.
J Med Chem ; 58(5): 2299-314, 2015 Mar 12.
Article in English | MEDLINE | ID: mdl-25658507

ABSTRACT

NaV1.7 is a voltage-gated sodium ion channel implicated by human genetic evidence as a therapeutic target for the treatment of pain. Screening fractionated venom from the tarantula Grammostola porteri led to the identification of a 34-residue peptide, termed GpTx-1, with potent activity on NaV1.7 (IC50 = 10 nM) and promising selectivity against key NaV subtypes (20× and 1000× over NaV1.4 and NaV1.5, respectively). NMR structural analysis of the chemically synthesized three disulfide peptide was consistent with an inhibitory cystine knot motif. Alanine scanning of GpTx-1 revealed that residues Trp(29), Lys(31), and Phe(34) near the C-terminus are critical for potent NaV1.7 antagonist activity. Substitution of Ala for Phe at position 5 conferred 300-fold selectivity against NaV1.4. A structure-guided campaign afforded additive improvements in potency and NaV subtype selectivity, culminating in the design of [Ala5,Phe6,Leu26,Arg28]GpTx-1 with a NaV1.7 IC50 value of 1.6 nM and >1000× selectivity against NaV1.4 and NaV1.5.


Subject(s)
NAV1.7 Voltage-Gated Sodium Channel/chemistry , Peptide Fragments/pharmacology , Spider Venoms/pharmacology , Voltage-Gated Sodium Channel Blockers/pharmacology , Animals , Electrophysiology , Female , High-Throughput Screening Assays , Humans , Magnetic Resonance Spectroscopy , Male , Mice , Mice, Inbred C57BL , NAV1.7 Voltage-Gated Sodium Channel/blood , Peptide Fragments/chemistry , Protein Conformation , Rats , Spectrometry, Mass, Electrospray Ionization , Spider Venoms/chemistry , Spiders , Structure-Activity Relationship , Voltage-Gated Sodium Channel Blockers/chemistry
13.
Anal Chem ; 84(1): 262-6, 2012 Jan 03.
Article in English | MEDLINE | ID: mdl-22126836

ABSTRACT

The determination of the disulfide bond connectivity in a peptide or protein represents a significant challenge. It is notoriously difficult to use NMR spectroscopy to assign disulfide connectivities because NMR spectra lack direct evidence for disulfide bonds. These bonds are typically inferred from three-dimensional structure calculations, which can result in ambiguous disulfide assignment. Here, we present a new NMR based methodology, in which the disulfide connectivity is obtained by applying Bayesian rules of inference to the local topology of cysteine residues. We illustrate how this approach successfully predicts the disulfide connectivity in proteins for which crystal structures are available in the protein data bank (PDB). We also demonstrate how this methodology is used with experimental NMR data for peptides with complex disulfide topologies, including hepcidin, Kalata-B1, and µ-Conotoxin KIIIA. In the case of µ-Conotoxin KIIIA, the PADLOC connectivity (1-15,2-9,4-16) differs from previously published results; additional evidence is presented demonstrating unequivocally that this newly proposed connectivity is correct.


Subject(s)
Disulfides/chemistry , Nuclear Magnetic Resonance, Biomolecular/methods , Peptides/chemistry , Proteins/chemistry , Bayes Theorem , Chromatography, High Pressure Liquid , Models, Chemical
14.
Methods Mol Biol ; 716: 73-88, 2011.
Article in English | MEDLINE | ID: mdl-21318901

ABSTRACT

Since the advent of solid-phase peptide synthesis (SPPS) in the late 1950s, numerous advancements in the underlying chemistry (i.e., orthogonal protection strategy, coupling reagents, and solid support matrices) have greatly improved the efficiency of the technique. More recently, application of microwave radiation to SPPS has been found to reduce reaction time and/or increase the initial purity of synthetic peptide products. In this protocol, conditions are described to accomplish rapid peptide coupling and 9-fluorenylmethoxycarbonyl (Fmoc) removal reactions under temperature-controlled conditions in either a manual or automated synthesis format using a microwave reactor. These microwave-assisted peptide synthesis procedures have been used to rapidly prepare a "difficult" peptide sequence from the acyl carrier protein, ACP(65-74), in less than 3 h and the reduced, linear precursor to human hepcidin, in high initial purity.


Subject(s)
Combinatorial Chemistry Techniques/methods , Microwaves , Peptides/chemical synthesis , Acyl Carrier Protein/chemical synthesis , Acyl Carrier Protein/chemistry , Amino Acid Sequence , Antimicrobial Cationic Peptides/chemical synthesis , Antimicrobial Cationic Peptides/chemistry , Combinatorial Chemistry Techniques/economics , Combinatorial Chemistry Techniques/instrumentation , Fluorenes , Hepcidins , Humans , Molecular Sequence Data , Peptides/chemistry
15.
J Comb Chem ; 12(5): 676-86, 2010 Sep 13.
Article in English | MEDLINE | ID: mdl-20666436

ABSTRACT

Intracellular levels of the hypoxia-inducible transcription factor (HIF) are regulated under normoxic conditions by prolyl hydroxylases (PHD1, 2, and 3). Treatment of cells with PHD inhibitors stabilizes HIF-1α, eliciting an artificial hypoxic response that includes the transcription of genes involved in erythropoiesis, angiogenesis, and glycolysis. The different in vivo roles of the three PHD isoforms are not yet known, making a PHD-selective inhibitor useful as a biological tool. Although several chemical series of PHD inhibitors have been described, significant isoform selectivity has not been reported. Here we report the synthesis and activity of dipeptidyl analogues derived from a potent but non-selective quinolone scaffold. The compounds were prepared by Pd-catalyzed reductive carbonylation of the 6-iodoquinolone derivative to form the aldehyde directly, which was then attached to a solid support via reductive amination. Amino acids were coupled, and the resulting dipeptidyl-quinolone derivatives were screened, revealing retention of PHD inhibitory activity but an altered PHD1, 2, and 3 selectivity profile. The compounds were found to be ∼10-fold more potent against PHD1 and PHD3 than against PHD2, whereas the specific parent compound had shown no appreciable selectivity among the different PHD isoforms.


Subject(s)
Dipeptides/pharmacology , Enzyme Inhibitors/pharmacology , Isoenzymes/antagonists & inhibitors , Procollagen-Proline Dioxygenase/antagonists & inhibitors , Quinolones/pharmacology , Combinatorial Chemistry Techniques , Dipeptides/chemical synthesis , Dipeptides/chemistry , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/chemistry , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Isoenzymes/chemistry , Isoenzymes/metabolism , Molecular Structure , Procollagen-Proline Dioxygenase/chemistry , Procollagen-Proline Dioxygenase/metabolism , Quinolones/chemical synthesis , Quinolones/chemistry , Stereoisomerism , Structure-Activity Relationship
16.
J Comb Chem ; 10(2): 204-15, 2008.
Article in English | MEDLINE | ID: mdl-18275161

ABSTRACT

We describe the use of parallel and split-and-mix library synthesis strategies for exploration of structure-activity relationships among peptidic foldamer ligands for the BH3-recognition cleft of the anti-apoptotic protein Bcl-xL. This effort began with a chimeric (alpha/beta+alpha)-peptide oligomer (composed of an alpha/beta-peptide segment and an alpha-peptide segment) that we previously identified to bind tightly to the target cleft on Bcl-xL. The side chains that interact with Bcl-xL were varied in a 1000-member one-bead-one-compound library. Fluorescence polarization (FP) screening identified four new analogues with binding affinities similar to that of the lead compound but no analogues with enhanced affinity. These results suggested that significant improvements in affinity were unlikely in this series. We then used library synthesis to examine backbone variations in the C-terminal alpha-peptide segment of the lead compound. These studies provided an opportunity for direct comparison of parallel and split-and-mix synthesis formats for foldamer libraries with respect to synthetic variability and assay sensitivity. We found that compounds from both the parallel and one-bead-one-compound libraries could be reliably screened in a competition FP assay without purification of library members. Our findings should facilitate the use of combinatorial library synthesis for exploration of foldamers as inhibitors of protein-protein interactions.


Subject(s)
Proteins/chemistry , Binding Sites , Chromatography, High Pressure Liquid , Combinatorial Chemistry Techniques , Ligands , Proteins/metabolism , Spectrophotometry, Ultraviolet , Structure-Activity Relationship
17.
Chembiochem ; 8(8): 903-16, 2007 May 25.
Article in English | MEDLINE | ID: mdl-17503422

ABSTRACT

Protein-protein interactions play crucial roles in cell-signaling events and are often implicated in human disease. Molecules that bind tightly to functional protein-surface sites and show high stability to degradative enzymes could be valuable pharmacological tools for dissection of cell-signaling networks and might ultimately lead to therapeutic agents. We recently described oligomers containing both alpha- and beta-amino acid residues that bind tightly to the BH3 recognition site of the anti-apoptotic protein Bcl-x(L). The oligomers with highest affinity had a nine-residue N-terminal segment with a 1:1 alpha:beta residue repeat and a six-residue C-terminal segment containing exclusively proteinogenic alpha-residues. The N-terminal portions of such (alpha/beta+alpha)-peptides are highly resistant to proteolysis, but the C-terminal alpha-segments are susceptible. This study emerged from efforts to modify the alpha-segment in an (alpha/beta+alpha)-peptide in a way that would diminish proteolytic degradation but retain high affinity for Bcl-x(L). Some of the oligomers reported here could prove useful in certain biological applications, particularly those for which extended incubation in a biological milieu is required.


Subject(s)
Amino Acids/chemistry , Peptide Fragments/chemistry , Peptide Hydrolases/chemistry , Proto-Oncogene Proteins/chemistry , bcl-X Protein/chemistry , Binding Sites , Binding, Competitive , Molecular Structure , Peptide Library , Protein Folding , Protein Structure, Secondary , Time Factors
18.
Biopolymers ; 88(5): 657-86, 2007.
Article in English | MEDLINE | ID: mdl-17427181

ABSTRACT

The tremendous challenge of inhibiting therapeutically important protein-protein interactions has created the opportunity to extend traditional medicinal chemistry to a new class of targets and to explore nontraditional strategies. Here we review a widely studied system, the interaction between tumor suppressor p53 and its natural antagonist MDM2, for which both traditional and nontraditional approaches have been reported. This system has been a testing ground for novel proteomimetic scaffold-based strategies, i.e., for attempts to mimic the recognition surface displayed by a folded protein with unnatural oligomers. Retroinverso peptides, peptoids, terphenyls, beta-hairpins, p-oligobenzamides, beta-peptides, and miniproteins have all been explored as inhibitors of the p53/MDM2 interaction, and we focus on these oligomer-based efforts. Traditional approaches have been successful as well, and we briefly review small molecule inhibitors along with other strategies for reactivation of the p53 pathway, for comparison with oligomer- based approaches. We close with comments on an emerging dichotomy among protein-protein interaction targets.


Subject(s)
Proto-Oncogene Proteins c-mdm2/chemistry , Proto-Oncogene Proteins c-mdm2/metabolism , Tumor Suppressor Protein p53/chemistry , Tumor Suppressor Protein p53/metabolism , Animals , Humans , Models, Molecular , Molecular Mimicry , Protein Binding , Signal Transduction
19.
Nat Protoc ; 2(3): 624-31, 2007.
Article in English | MEDLINE | ID: mdl-17406623

ABSTRACT

The application of microwave irradiation to solid-phase peptide synthesis increases product purity and reduces reaction time. Parallel synthesis in 96-well polypropylene filter plates with microwave irradiation is an efficient method for the rapid generation of combinatorial peptide libraries in sufficient purity to assay the products directly for biological activity without HPLC purification. In this protocol, the solid-phase support is arrayed into each well of a 96-well plate, reagents are delivered using a multichannel pipette and a microwave reactor is used to complete peptide coupling reactions in 6 min and Fmoc-removal reactions in 4 min under temperature-controlled conditions. The microwave-assisted parallel peptide synthesis protocol has been used to generate a library of difficult hexa-beta-peptides in 61% average initial purity (50% yield) and has been applied to the preparation of longer alpha- and beta-peptides. Using this protocol, a library of 96 different hexapeptides can be synthesized in 24 h (excluding characterization).


Subject(s)
Combinatorial Chemistry Techniques/methods , Microwaves , Peptide Library , Peptides/chemical synthesis , Peptides/radiation effects
20.
J Cell Biol ; 174(7): 1047-58, 2006 Sep 25.
Article in English | MEDLINE | ID: mdl-17000881

ABSTRACT

Establishment of angiogenic circuits that orchestrate blood vessel development and remodeling requires an exquisite balance between the activities of pro- and antiangiogenic factors. However, the logic that permits complex signal integration by vascular endothelium is poorly understood. We demonstrate that a "neuropeptide," neurokinin-B (NK-B), reversibly inhibits endothelial cell vascular network assembly and opposes angiogenesis in the chicken chorioallantoic membrane. Disruption of endogenous NK-B signaling promoted angiogenesis. Mechanistic analyses defined a multicomponent pathway in which NK-B signaling converges upon cellular processes essential for angiogenesis. NK-B-mediated ablation of Ca2+ oscillations and elevation of 3'-5' [corrected] cyclic adenosine monophosphate (cAMP) reduced cellular proliferation, migration, and vascular endothelial growth factor receptor expression and induced the antiangiogenic protein calreticulin. Whereas NK-B initiated certain responses, other activities required additional stimuli that increase cAMP. Although NK-B is a neurotransmitter/ neuromodulator and NK-B overexpression characterizes the pregnancy-associated disorder preeclampsia, NK-B had not been linked to vascular remodeling. These results establish a conserved mechanism in which NK-B instigates multiple activities that collectively oppose vascular remodeling.


Subject(s)
Angiogenesis Inhibitors/physiology , Neurokinin B/physiology , Signal Transduction/physiology , Thromboxane A2/physiology , 1-Methyl-3-isobutylxanthine/pharmacology , Angiogenesis Inhibitors/pharmacology , Animals , Calcium/metabolism , Calcium Signaling/drug effects , Cell Line , Cell Movement/drug effects , Chick Embryo , Chorioallantoic Membrane/blood supply , Chorioallantoic Membrane/drug effects , Down-Regulation/drug effects , Drug Synergism , Endothelial Cells/drug effects , Endothelial Cells/physiology , Mice , Models, Biological , Muscle, Smooth, Vascular/physiology , Neurokinin B/pharmacology , Neurotransmitter Agents/pharmacology , Neurotransmitter Agents/physiology , Receptors, Vascular Endothelial Growth Factor/physiology , Signal Transduction/drug effects , Thromboxane A2/pharmacology , Vascular Endothelial Growth Factor A/physiology
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