ABSTRACT
Bicycles are constrained bicyclic peptides formed through reaction of three cysteine residues within a linear sequence with a trivalent, symmetrical small molecule scaffold. Bicycles with high binding affinities to therapeutically important targets can be discovered using screening technologies such as phage display. Increasing the chemical diversity of Bicycles should improve the probability of finding hits to new targets and can be achieved by expanding the toolbox of Bicycle forming chemistries. Gold(III) S-arylation has recently been described as a method for the efficient bioconjugation of cysteine residues under conditions compatible with phage display. Herein, we explore the scope and generality of this methodology for Bicycle construction through the synthesis and evaluation of four novel tris-Gold complexes. These new scaffolds were systematically reacted with a variety of peptide sequences, varying in amino acid loop lengths. All four scaffolds proved to be capable and selective reactive partners for each peptide sequence and afforded the desired Bicycle products in 13-48% isolated yield. This work exemplifies Gold-mediated arylation as a general approach for construction of novel, highly constrained Bicycles.
Subject(s)
Cysteine , Gold , Amino Acid Sequence , Bicycling , Cysteine/chemistry , Gold/chemistry , Peptide Library , Peptides/chemistryABSTRACT
Growing antibiotic resistance is rapidly threatening the efficacy of treatments for Gram-negative infections. Bicycle molecules, constrained bicyclic peptides from diverse libraries generated by bacteriophage display that bind with high affinity to a chosen target are a potential new class of antibiotics. The generally impermeable bacterial outer membrane currently limits the access of peptides to bacteria. The conjugation of membrane active peptides offers an avenue for outer membrane penetration. Here, we investigate which physicochemical properties of a specific membrane active peptide (MAP), derived from ixosin-B, could be tweaked to enhance the penetration of conjugates by generating multiple MAP-Bicycle conjugate variants. We demonstrate that charge and hydrophobicity are important factors, which enhance penetration and, therefore, antimicrobial potency. Interestingly, we show that induction of secondary structure, but not a change in amphipathicity, is vital for effective penetration of the Gram-negative outer membrane. These results offer insights into the ways vectors could be designed to deliver Bicycle molecules (and other cargos) through biological membranes.
Subject(s)
Anti-Bacterial Agents , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry , Hydrophobic and Hydrophilic Interactions , Microbial Sensitivity Tests , Bacterial Outer Membrane/drug effects , Gram-Negative Bacteria/drug effects , Peptides, Cyclic/pharmacology , Peptides, Cyclic/chemistryABSTRACT
Angiotensin-converting enzyme 2 (ACE2) is a metalloprotease that cleaves angiotensin II, a peptide substrate involved in the regulation of hypertension. Here, we identified a series of constrained bicyclic peptides, Bicycle, inhibitors of human ACE2 by panning highly diverse bacteriophage display libraries. These were used to generate X-ray crystal structures which were used to inform the design of additional Bicycles with increased affinity and inhibition of ACE2 enzymatic activity. This novel structural class of ACE2 inhibitors is among the most potent ACE2 inhibitors yet described in vitro, representing a valuable tool to further probe ACE2 function and for potential therapeutic utility.
Subject(s)
Angiotensin-Converting Enzyme 2 , Carboxypeptidases , Humans , Carboxypeptidases/chemistry , Peptidyl-Dipeptidase A , Bicycling , Peptides/pharmacology , Angiotensin II , Peptide FragmentsABSTRACT
COVID-19 has stimulated the rapid development of new antibody and small molecule therapeutics to inhibit SARS-CoV-2 infection. Here we describe a third antiviral modality that combines the drug-like advantages of both. Bicycles are entropically constrained peptides stabilized by a central chemical scaffold into a bi-cyclic structure. Rapid screening of diverse bacteriophage libraries against SARS-CoV-2 Spike yielded unique Bicycle binders across the entire protein. Exploiting Bicycles' inherent chemical combinability, we converted early micromolar hits into nanomolar viral inhibitors through simple multimerization. We also show how combining Bicycles against different epitopes into a single biparatopic agent allows Spike from diverse variants of concern (VoC) to be targeted (Alpha, Beta, Delta and Omicron). Finally, we demonstrate in both male hACE2-transgenic mice and Syrian golden hamsters that both multimerized and biparatopic Bicycles reduce viraemia and prevent host inflammation. These results introduce Bicycles as a potential antiviral modality to tackle new and rapidly evolving viruses.
Subject(s)
COVID-19 , SARS-CoV-2 , Male , Animals , Cricetinae , Mice , Antiviral Agents/pharmacology , Peptides/pharmacology , Antibodies , Mesocricetus , Mice, Transgenic , Spike Glycoprotein, Coronavirus/geneticsABSTRACT
Antimicrobial peptides (AMPs) are short oligopeptides that can penetrate the bacterial inner and outer membranes. Together with cell-penetrating peptides (CPPs), they are called membrane active peptides; peptides which can translocate across biological membranes. Over the last fifty years, attempts have been made to understand the molecular features that drive the interactions of membranes with membrane active peptides. This review examines the features of a membrane these peptides exploit for translocation, as well as the physicochemical characteristics of membrane active peptides which are important for translocation. Moreover, it presents examples of how these features have been used in recent years to create conjugates consisting of a membrane active peptide, called a "vector", attached to either a current or novel antibiotic, called a "cargo" or "payload". In addition, the review discusses what properties may contribute to an ideal peptide vector able to deliver cargoes across the bacterial outer membrane as the rising issue of antimicrobial resistance demands new strategies to be employed to combat this global public health threat.
ABSTRACT
Bicycle toxin conjugates (BTCs) are a promising new class of molecules for targeted delivery of toxin payloads into tumors. Herein we describe the discovery of BT8009, a Nectin-4 targeting BTC currently under clinical evaluation. Nectin-4 is overexpressed in multiple tumor types and is a clinically validated target for selective delivery of cytotoxic payloads. A Nectin-4 targeting bicyclic peptide was identified by phage display, which showed highly selective binding for Nectin-4 but suffered from low plasma stability and poor physicochemical properties. Multiparameter chemical optimization involving introduction of non-natural amino acids resulted in a lead Bicycle that demonstrated high affinity for Nectin-4, good stability in biological matrices, and a much-improved physicochemical profile. The optimized Bicycle was conjugated to the cytotoxin Monomethyl auristatin E via a cleavable linker to give the targeted drug conjugate BT8009, which demonstrates potent anticancer activity in in vivo rodent models.
Subject(s)
Antineoplastic Agents , Immunoconjugates , Immunotoxins , Neoplasms , Humans , Nectins , Bicycling , Neoplasms/drug therapy , Neoplasms/pathology , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Antineoplastic Agents/chemistry , Cell Adhesion Molecules , Cell Line, TumorABSTRACT
Multiple tumor types overexpress Nectin-4 and the antibody-drug conjugate (ADC), enfortumab vedotin (EV) shows striking efficacy in clinical trials for metastatic urothelial cancer, which expresses high levels of Nectin-4, validating Nectin-4 as a clinical target for toxin delivery in this indication. Despite excellent data in urothelial cancer, little efficacy data are reported for EV in other Nectin-4 expressing tumors and EV therapy can produce significant toxicities in many patients, frequently leading to discontinuation of treatment. Thus, additional approaches to this target with the potential to extend utility and reduce toxicity are warranted. We describe the preclinical development of BT8009, a "Bicycle Toxin Conjugate" (BTC) consisting of a Nectin-4-binding bicyclic peptide, a cleavable linker system and the cell penetrant toxin mono-methylauristatin E (MMAE). BT8009 shows significant antitumor activity in preclinical tumor models, across a variety of cancer indications and is well tolerated in preclinical safety studies. In several models, it shows superior or equivalent antitumor activity to an EV analog. As a small hydrophilic peptide-based drug BT8009 rapidly diffuses from the systemic circulation, through tissues to penetrate the tumor and target tumor cells. It is renally eliminated from the circulation, with a half-life of 1-2 hours in rat and non-human primate. These physical and PK characteristics differentiate BT8009 from ADCs and may provide benefit in terms of tumor penetration and reduced systemic exposure. BT8009 is currently in a Phase 1/2 multicenter clinical trial across the US, Canada, and Europe, enrolling patients with advanced solid tumors associated with Nectin-4 expression.
Subject(s)
Carcinoma, Transitional Cell , Immunoconjugates , Immunotoxins , Rats , Animals , Nectins , Bicycling , Immunoconjugates/pharmacology , Immunoconjugates/therapeutic use , Cell Adhesion Molecules/metabolism , Carcinoma, Transitional Cell/drug therapyABSTRACT
Heteroalicyclic carboxamidines were synthesised and evaluated as inhibitors of nitric oxide synthases. (2R)-2-Pyrrolidinecarboxamidine, in particular, was shown to be a highly potent in vitro (IC(50)=0.12 µM) and selective iNOS inhibitor (>100-fold vs both eNOS and nNOS), with probable binding to the key anchoring glutamate residue and co-ordination to the haem iron.
Subject(s)
Amidines/chemical synthesis , Amidines/pharmacology , Enzyme Activation/drug effects , Enzyme Inhibitors/pharmacology , Heme/antagonists & inhibitors , Heterocyclic Compounds/chemical synthesis , Nitric Oxide Synthase Type II/antagonists & inhibitors , Proline/analogs & derivatives , Amidines/chemistry , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/chemistry , Heterocyclic Compounds/chemistry , Heterocyclic Compounds/pharmacology , Humans , Inhibitory Concentration 50 , Models, Molecular , Molecular Structure , Proline/chemical synthesis , Proline/chemistry , Proline/pharmacologyABSTRACT
A series of analogues of the pyrazole lead 1 were synthesized in which the heterocyclic core was replaced with an imidazole. A number of potent antagonists were identified and structure-activity relationships (SAR) were investigated both with respect to activity at the P2X(7) receptor and in vitro metabolic stability. Compound 10 was identified as a potent P2X(7) antagonist with reduced in vitro metabolism and high solubility.
Subject(s)
Anti-Inflammatory Agents, Non-Steroidal/chemical synthesis , Imidazoles/chemistry , Purinergic P2 Receptor Antagonists , Animals , Anti-Inflammatory Agents, Non-Steroidal/chemistry , Anti-Inflammatory Agents, Non-Steroidal/pharmacology , Humans , Imidazoles/chemical synthesis , Imidazoles/pharmacology , Pyrazoles/chemistry , Rats , Receptors, Purinergic P2/metabolism , Receptors, Purinergic P2X7 , Structure-Activity RelationshipABSTRACT
A series of 3-amino-6-aryl-pyridazines have been identified as CB(2) agonists with high efficacy and selectivity against the CB(1) receptor. Details of the investigation of structure-activity relationships (SAR) are disclosed, which led to the identification of pyridazine analogue 35, a compound with high potency in an in vivo model of inflammatory pain.
Subject(s)
Anti-Inflammatory Agents/chemical synthesis , Isoquinolines/chemical synthesis , Pyridazines/chemical synthesis , Receptor, Cannabinoid, CB2/agonists , Animals , Anti-Inflammatory Agents/chemistry , Anti-Inflammatory Agents/pharmacokinetics , Isoquinolines/chemistry , Isoquinolines/pharmacokinetics , Pain/drug therapy , Pyridazines/chemistry , Pyridazines/pharmacokinetics , Rats , Receptor, Cannabinoid, CB2/metabolism , Structure-Activity RelationshipABSTRACT
Structure-activity relationships (SAR) of analogues of lead compound 1 were investigated and compound 16 was selected for further study in animal models of pain. Compound 16 was shown to be a potent antihyperalgesic agent in both the rat acute complete Freund's adjuvant (CFA) model of inflammatory pain [Iadarola, M. J.; Douglass, J.; Civelli, O.; Naranjo, J. R. rain Res.1988, 455, 205] and the knee joint model of chronic inflammatory pain [Wilson, A. W.; Medhurst, S. J.; Dixon, C. I.; Bontoft, N. C.; Winyard, L. A.; Brackenborough, K. T.; De Alba, J.; Clarke, C. J.; Gunthorpe, M. J.; Hicks, G. A.; Bountra, C.; McQueen, D. S.; Chessell, I. P. Eur. J. Pain2006, 10, 537].
Subject(s)
Acetamides/chemistry , Purinergic P2X Receptor Antagonists , Pyrazoles/chemistry , Acetamides/chemical synthesis , Acetamides/therapeutic use , Administration, Oral , Animals , Disease Models, Animal , Humans , Pain/drug therapy , Pyrazoles/chemical synthesis , Rats , Receptors, Purinergic P2X7/metabolism , Structure-Activity RelationshipABSTRACT
High-throughput screening identified compound 1 as a potent P2X(7) receptor antagonist suitable for lead optimisation. Structure-activity relationships (SAR) of a series of (1H-pyrazol-4-yl)acetamides were investigated and compound 32 was identified as a potent P2X(7) antagonist with enhanced potency and favourable physicochemical and pharmacokinetic properties.
Subject(s)
Acetamides/chemistry , Anti-Infective Agents/chemical synthesis , Purinergic P2 Receptor Antagonists , Pyrazoles/chemical synthesis , Acetamides/chemical synthesis , Acetamides/pharmacokinetics , Administration, Oral , Animals , Anti-Infective Agents/chemistry , Anti-Infective Agents/pharmacokinetics , High-Throughput Screening Assays , Humans , Injections, Intravenous , Pyrazoles/chemistry , Pyrazoles/pharmacokinetics , Rats , Receptors, Purinergic P2/metabolism , Receptors, Purinergic P2X7 , Structure-Activity RelationshipABSTRACT
A backup molecule to compound 2 was sought by targeting the most likely metabolically vulnerable site in this molecule. Compound 18 was subsequently identified as a potent P2X(7) antagonist with very low in vivo clearance and high oral bioavailability in all species examined. Some evidence to support the role of P2X(7) in the etiology of pain is also presented.
Subject(s)
Imidazolines/pharmacology , Purinergic Antagonists/pharmacology , Receptors, Purinergic P2X7/drug effects , Administration, Oral , Animals , Biological Availability , Half-Life , Haplorhini , Imidazolines/administration & dosage , Imidazolines/chemistry , Imidazolines/pharmacokinetics , Purinergic Antagonists/administration & dosage , Purinergic Antagonists/chemistry , Purinergic Antagonists/pharmacokinetics , RatsABSTRACT
A computational lead-hopping exercise identified compound 4 as a structurally distinct P2X(7) receptor antagonist. Structure-activity relationships (SAR) of a series of pyroglutamic acid amide analogues of 4 were investigated and compound 31 was identified as a potent P2X(7) antagonist with excellent in vivo activity in animal models of pain, and a profile suitable for progression to clinical studies.
Subject(s)
Amides/pharmacology , Purinergic P2 Receptor Antagonists/pharmacology , Pyrrolidonecarboxylic Acid/chemistry , Receptors, Purinergic P2X7/drug effects , Amides/chemistry , Drug Discovery , Models, Molecular , Purinergic P2 Receptor Antagonists/chemistry , Structure-Activity RelationshipABSTRACT
The treatment of infection by Gram-negative bacteria is increasingly challenging as resistance to existing antibiotics spreads. Constrained peptides, selected for high target specificity and affinity via library display technologies, are an emerging therapeutic modality in many disease areas and may be a fertile source of new antibiotics. Currently, the utility of constrained peptides and other large molecules as antibiotics is limited by the outer membrane (OM) barrier of Gram-negative bacteria. However, the addition of certain moieties to large molecules can confer the ability to cross the OM; these moieties function as intramolecular trans-OM "vectors". Here, we present a method to systematically assess the carrying capacity of candidate trans-OM vectors using a real-time luminescence assay ("SLALOM", Split Luciferase Assay for Live monitoring of Outer Membrane transit), reporting on periplasmic entry. We demonstrate the usefulness of our tools by constructing a 3800 Da chimeric compound composed of a constrained bicyclic peptide (Bicycle) with a periplasmic target, linked to an intramolecular peptide vector; the resulting chimera is a broad-spectrum inhibitor of pathogenic Gram-negative bacterial growth.
Subject(s)
Gram-Negative Bacteria , Periplasm , Anti-Bacterial Agents/pharmacology , ChimeraABSTRACT
2-Amino-5-aryl-pyridines, exemplified by compound 1, had been identified as a synthetically tractable series of CB(2) agonists from a high-throughput screen of the GlaxoSmithKline compound collection. Described herein are the results of an investigation of the structure-activity relationships (SAR) which led to the identification a number of potent and selective agonists.
Subject(s)
Pyridines/chemical synthesis , Pyridines/pharmacology , Receptor, Cannabinoid, CB2/agonists , Drug Design , Molecular Structure , Pyridines/chemistry , Stereoisomerism , Structure-Activity RelationshipABSTRACT
Many years of work have been invested in the identification of potent and selective COX-2 inhibitors for the treatment of chronic inflammatory pain. One issue faced by workers is the balance between the lipophilicity required for potent enzyme inhibition and the physical properties necessary for drug absorption and distribution in vivo. Frequently approaches to reduce lipophilicity through introduction of polar functionality is hampered by highly challenging chemistry to prepare key molecules. We have complemented traditional synthetic chemistry with a biotransformations approach which efficiently provided access to an array of key target molecules.
Subject(s)
Cyclooxygenase 2 Inhibitors/chemical synthesis , Biotransformation , Chemistry, Pharmaceutical/methods , Cyclooxygenase 2/chemistry , Cyclooxygenase 2 Inhibitors/pharmacology , Drug Design , Humans , Inflammation/drug therapy , Inhibitory Concentration 50 , Models, Chemical , Molecular Structure , Structure-Activity RelationshipABSTRACT
A novel series of [4-[4-(methylsulfonyl)phenyl]-6-(trifluoromethyl)-2-pyrimidine-based cyclooxygenase-2 (COX-2) inhibitors, which have a different arrangement of substituents compared to the more common 1,2-diarylheterocycle based molecules, have been discovered. For example, 2-(butyloxy)-4-[4-(methylsulfonyl)phenyl]-6-(trifluoromethyl)pyrimidine (47), a member of the 2-pyrimidinyl ether series, has been shown to be a potent and selective inhibitor with a favourable pharmacokinetic profile, high brain penetration and good efficacy in rat models of hypersensitivity.
Subject(s)
Amines/chemical synthesis , Cyclooxygenase 2 Inhibitors/chemical synthesis , Ethers/chemical synthesis , Pyrimidines/chemical synthesis , Sulfones/chemical synthesis , Amines/pharmacology , Animals , Brain/drug effects , Brain/metabolism , Chemistry, Pharmaceutical/methods , Cyclooxygenase 2/chemistry , Cyclooxygenase 2 Inhibitors/pharmacology , Disease Models, Animal , Drug Design , Ethers/pharmacology , Humans , Inflammation , Inhibitory Concentration 50 , Mice , Molecular Structure , Neurodegenerative Diseases/drug therapy , Pyrimidines/pharmacology , Rats , Sulfones/pharmacologyABSTRACT
Identifying novel small-molecule P2X1 and P2X4 ligands with sub-type specificity and high-affinity remains a pharmacological challenge. Here we use computational methods, electrophysiology and fluorescent microplate assays to screen for ligand candidates acting at these receptors. Modelling and docking identified 80 compounds for testing at P2X4 receptors, and 20 of these showed >50% inhibition in fluorescence-based assays, making them appealing for further SAR studies. Confirmation of activity by two-electrode voltage clamp, followed by their elaboration resulted in only minor improvements in potency, with the highest IC50 being 295⯵M. Testing on P2X1 receptors, resulted in a series of biguanide compounds that yielded a maximum IC50 of 100⯵M, but no consistent SAR could be found. Potencies of established antagonists gave expected results, although the measured potencies varied between techniques and no antagonism could be found for compounds such as paroxetine, carbamazepine, 9(10H)-acridanone, acridinol and phenoxazine-type heterocycles. This study highlights the challenge of identifying P2X4 and P2X1 ligands and suggests that a combination of complimentary approaches is needed if we are to be confident of ligand activities at these receptors.
Subject(s)
Drug Discovery/methods , Ligands , Purinergic Antagonists/pharmacology , Receptors, Purinergic P2X1/drug effects , Receptors, Purinergic P2X4/drug effects , Animals , Biguanides/pharmacology , Cells, Cultured , Computer Simulation , Humans , Molecular Docking Simulation , Oocytes/physiology , Patch-Clamp Techniques , Purinergic Agonists/pharmacology , Structure-Activity Relationship , Xenopus laevisABSTRACT
This article is focusing on further optimization of previously described hydroxy ethylamine (HEA) BACE-1 inhibitors obtained from a focused library with the support of X-ray crystallography. Optimization of the non-prime side of our inhibitors and introduction of a 6-membered sultam substituent binding to Asn-294 as well as a fluorine in the C-2 position led to derivatives with nanomolar potency in cell-based assays.