Peptidomimetics derived from natural products

Molecular Scaffold Hopping via Holistic Molecular Representation

Molecular descriptors encode a variety of molecular representations for computer-assisted drug discovery. Here, we focus on the Weighted Holistic Atom Localization and Entity Shape (WHALES) descriptors, which were originally designed for scaffold hopping from natural products to synthetic molecules. WHALES descriptors capture molecular shape and partial charges simultaneously. We introduce the key aspects of the WHALES concept and provide a step-by-step guide on how to use these descriptors for virtual compound screening and scaffold hopping. The results presented can be reproduced by using the code freely available from URL: github.com/ETHmodlab/scaffold_hopping_whales .

Brønsted acid-promoted thiazole synthesis under metal-free conditions using sulfur powder as the sulfur source

A Brønsted acid-promoted sulfuration/annulation reaction for the one-pot synthesis of bis-substituted thiazoles from benzylamines, acetophenones, and sulfur powder has been developed. One C–N bond and multi C–S bonds were selectively formed in one pot. The choice of the Brønsted acid was the key to the high efficiency of this transformation under metal-free conditions.

A Brønsted acid-promoted protocol for the synthesis of 2,4-disubstituted thiazoles from benzylamines, acetophenones, and sulfur powder under metal-free conditions is described.

Perspectives for clinical use of engineered human host defense antimicrobial peptides

Infectious diseases caused by bacteria, viruses or fungi are among the leading causes of death worldwide. The emergence of drug-resistance mechanisms, especially among bacteria, threatens the efficacy of all current antimicrobial agents, some of them already ineffective. As a result, there is an urgent need for new antimicrobial drugs. Host defense antimicrobial peptides (HDPs) are natural occurring and well-conserved peptides of innate immunity, broadly active against Gram-negative and Gram-positive bacteria, viruses and fungi. They also are able to exert immunomodulatory and adjuvant functions by acting as chemotactic for immune cells, and inducing cytokines and chemokines secretion. Moreover, they show low propensity to elicit microbial adaptation, probably because of their non-specific mechanism of action, and are able to neutralize exotoxins and endotoxins. HDPs have the potential to be a great source of novel antimicrobial agents. The goal of this review is to provide an overview of the advances made in the development of human defensins as well as the cathelicidin LL-37 and their derivatives as antimicrobial agents against bacteria, viruses and fungi for clinical use.

Examination of a Structural Model of Peptidomimicry by Cyclic Acyldepsipeptide Antibiotics in Their Interaction with the ClpP Peptidase

The cyclic acyldepsipeptide (ADEP) antibiotics act by binding the ClpP peptidase and dysregulating its activity. Their exocyclic N-acylphenylalanine is thought to structurally mimic the ClpP-binding, (I/L)GF tripeptide loop of the peptidase's accessory ATPases. We found that ADEP analogues with exocyclic N-acyl tripeptides or dipeptides resembling the (I/L)GF motif were weak ClpP activators and had no bioactivity. In contrast, ADEP analogues possessing difluorophenylalanine N-capped with methyl-branched acyl groups-like the side chains of residues in the (I/L)GF motifs-were superior to the parent ADEP with respect to both ClpP activation and bioactivity. We contend that the ADEP's N-acylphenylalanine moiety is not simply a stand-in for the ATPases' (I/L)GF motif; it likely has physicochemical properties that are better suited for ClpP binding. Further, our finding that the methyl-branching on the acyl group of the ADEPs improves activity opens new avenues for optimization.

Triazolo-β-aza-ε-amino acid and its aromatic analogue as novel scaffolds for β-turn peptidomimetics

Triazolo-β-aza-ε-amino acid and its aromatic analogue (AlTAA/ArTAA) in the peptide backbone mark a novel class of conformationally constrained molecular scaffolds to induce β-turn conformations. This was demonstrated in a Leu-enkephalin analogue and in other designed peptides.

Synthesis of α-amino acid derivatives and peptides via enantioselective addition of masked acyl cyanides to imines

A general, asymmetric synthesis of amino acid derivatives is reported. Masked acyl cyanide (MAC) reagents are shown to be effective umpolung synthons for enantioselective additions to N-Boc-aldimines. The reactions are catalyzed by a modified cinchona alkaloid, which can function as a bifunctional, hydrogen bonding catalyst, and afford adducts in excellent yields (90–98%) and high enantioselectivities (up to 97.5:2.5 er). Unmasking the addition products gives acyl cyanide intermediates that are intercepted by a variety of nucleophiles to afford α-amino acid derivatives. Notably, the methodology provides an alternative method for peptide bond formation.

Structure-based design of potent and selective Leishmania N-myristoyltransferase inhibitors

Inhibitors of LeishmaniaN-myristoyltransferase (NMT), a potential target for the treatment of leishmaniasis, obtained from a high-throughput screen, were resynthesized to validate activity. Crystal structures bound to Leishmania major NMT were obtained, and the active diastereoisomer of one of the inhibitors was identified. On the basis of structural insights, enzyme inhibition was increased 40-fold through hybridization of two distinct binding modes, resulting in novel, highly potent Leishmania donovani NMT inhibitors with good selectivity over the human enzyme.

Diverse modes of binding in structures of Leishmania major N-myristoyltransferase with selective inhibitors

The leishmaniases are a spectrum of global diseases of poverty associated with immune dysfunction and are the cause of high morbidity. Despite the long history of these diseases, no effective vaccine is available and the currently used drugs are variously compromised by moderate efficacy, complex side effects and the emergence of resistance. It is therefore widely accepted that new therapies are needed. N-Myristoyltransferase (NMT) has been validated pre-clinically as a target for the treatment of fungal and parasitic infections. In a previously reported high-throughput screening program, a number of hit compounds with activity against NMT from Leishmania donovani have been identified. Here, high-resolution crystal structures of representative compounds from four hit series in ternary complexes with myristoyl-CoA and NMT from the closely related L. major are reported. The structures reveal that the inhibitors associate with the peptide-binding groove at a site adjacent to the bound myristoyl-CoA and the catalytic α-carboxylate of Leu421. Each inhibitor makes extensive apolar contacts as well as a small number of polar contacts with the protein. Remarkably, the compounds exploit different features of the peptide-binding groove and collectively occupy a substantial volume of this pocket, suggesting that there is potential for the design of chimaeric inhibitors with significantly enhanced binding. Despite the high conservation of the active sites of the parasite and human NMTs, the inhibitors act selectively over the host enzyme. The role of conformational flexibility in the side chain of Tyr217 in conferring selectivity is discussed.

Parallel solid-phase synthesis of diaryltriazoles

A series of substituted diaryltriazoles was prepared by a solid-phase-synthesis protocol using a modified Wang resin. The copper(I)- or ruthenium(II)-catalyzed 1,3-cycloaddition on the polymer bead allowed a rapid synthesis of the target compounds in a parallel fashion with in many cases good to excellent yields. Substituted diaryltriazoles resemble a molecular structure similar to established terphenyl-alpha-helix peptide mimics and have therefore the potential to act as selective inhibitors for protein-protein interactions.

Backbone alignment modeling of the structure-activity relationships of opioid ligands

Opioid studies are an important area of modern medicinal chemistry research. In this study we have provided innovative considerations to some long-standing problems in opioid studies, specifically the opioid pharmacophore and the potential binding modes of opioid ligands. Based on a new peptide backbone-alignment concept that we have developed along with this study, we discuss a wide variety of opioid ligands with respect to their structure-activity relationships.

Effects of structure on inhibitory activity in a series of mechanism-based inhibitors of human neutrophil elastase

A structurally-diverse series of carboxylate derivatives based on the 1,2,5-thiadiazolidin-one 1,1 dioxide scaffold were synthesized and used to probe the S' subsites of human neutrophil elastase (HNE) and neutrophil proteinase 3 (Pr 3). Several compounds are potent inhibitors of HNE but devoid of inhibitory activity toward Pr 3, suggesting that the S' subsites of HNE exhibit significant plasticity and can, unlike Pr 3, tolerate various large hydrophobic groups. The results provide a promising framework for the design of highly selective inhibitors of the two enzymes.

Therapeutic potential of HDPs as immunomodulatory agents

One of the most significant advances in medical history is the discovery and development of antibiotics, which in the middle of last century was flourishing and appeared to be the ultimate solution to the treatment of life-threatening human bacterial diseases. However, lately there has been a huge decline in the rate of discovery of new antimicrobial intervention strategies in parallel with an increasing incidence of multidrug-resistant pathogens; if these circumstances do not change we will continue to approach the end of the antibiotic era. Facing this dark future, scientists are considering new strategies for intervention tailored around the appropriate (selective) stimulation of the host's immune system, and particularly rapid acting innate immunity, as an alternative to direct targeting of microbial pathogens. One recent player in such an immunomodulatory strategy is the naturally occurring host defence peptides (HDP) and their synthetic innate defence regulator (IDR) analogues. In this chapter, we will discuss the potential therapeutic use of HDPs and IDRs as immunomodulatory agents.

Phosphorylated hydroxyethylamines as novel inhibitors of the bacterial cell wall biosynthesis enzymes MurC to MurF

Enzymes involved in the biosynthesis of bacterial peptidoglycan represent important targets for development of new antibacterial drugs. Among them, Mur ligases (MurC to MurF) catalyze the formation of the final cytoplasmic precursor UDP-N-acetylmuramyl-pentapeptide from UDP-N-acetylmuramic acid. We present the design, synthesis and biological evaluation of a series of phosphorylated hydroxyethylamines as new type of small-molecule inhibitors of Mur ligases. We show that the phosphate group attached to the hydroxyl moiety of the hydroxyethylamine core is essential for good inhibitory activity. The IC(50) values of these inhibitors were in the micromolar range, which makes them a promising starting point for the development of multiple inhibitors of Mur ligases as potential antibacterial agents. In addition, 1-(4-methoxyphenylsulfonamido)-3-morpholinopropan-2-yl dihydrogen phosphate 7a was discovered as one of the best inhibitors of MurE described so far.

Positional scanning for peptide secondary structure by systematic solid-phase synthesis of amino lactam peptides

Incorporation of amino lactams into biologically active peptides has been commonly used to restrict conformational mobility, enhance selectivity, and increase potency. A solid-phase method using a Fmoc-protection strategy has been developed for the systematic synthesis of peptides containing configurationally defined alpha- and beta-amino gamma-lactams. N-Alkylation of N-silyl peptides with five- and six-member cyclic sulfamidates 9 and 8 minimized bis-alkylation and provided N-alkyl peptides, which underwent lactam annulation under microwave heating. Employing this solid-phase protocol on the growth hormone secretagogue GHRP-6, as well as on the allosteric modulator of the IL-1 receptor 101.10, has furnished 16 lactam derivatives and validated the effectiveness of this approach on peptides bearing aliphatic, aromatic, branched, charged, and heteroatomic side chains. The binding affinity IC(50) values of the GHRP-6 lactam analogues on both the GHS-R1a and CD36 receptors are reported as well as inhibition of thymocyte proliferation measurements for the 101.10 lactam analogues. In these cases, lactam analogues were prepared exhibiting similar or improved properties compared with the parent peptide. Considering the potential for amino lactams to induce peptide turn conformations, the effective method described herein for their supported construction on growing peptides, and for the systematical amino lactam scan of peptides, has proven useful for the rapid identification of the secondary structure necessary for peptide biological activity.

Design of selective neuronal nitric oxide synthase inhibitors for the prevention and treatment of neurodegenerative diseases

Nitric oxide (NO), which is produced from L-arginine by the nitric oxide synthase (NOS) family of enzymes, is an important second-messenger molecule that regulates several physiological functions. In endothelial cells, it relaxes smooth muscle, which decreases blood pressure. Macrophage cells produce NO as an immune defense system to destroy pathogens and microorganisms. In neuronal cells, NO controls the release of neurotransmitters and is involved in synaptogenesis, synaptic plasticity, memory function, and neuroendocrine secretion. NO is a free radical that is commonly thought to contribute to oxidative damage and molecule and tissue destruction, and thus it is somewhat surprising that it has so many significant beneficial physiological effects. However, the cell is generally protected from NO's toxic effects, except under certain pathological conditions in which excessive NO is produced. In that case, tissue damage and oxidative stress can result, leading to a wide variety of diseases, including rheumatoid arthritis, Alzheimer's disease, and Parkinson's disease, among others. In this Account, we describe research aimed at identifying small molecules that can selectively inhibit only the neuronal isozyme of NOS, nNOS. By targeting only nNOS, we attained the beneficial effects of lowering excess NO in the brain without the detrimental effects of inhibition of the two isozymes found elsewhere in the body (eNOS and iNOS). Initially, in pursuit of this goal, we sought to identify differences in the second sphere of amino acids in the active site of the isozymes. From this study, the first class of dual nNOS-selective inhibitors was identified. The moieties important for selectivity in the best lead compound were determined by structure modification. Enhancement provided highly potent, nNOS-selective dipeptide amides and peptidomimetics, which were active in a rabbit model for fetal neurodegeneration. Crystal structures of these compounds bound to NOS isozymes showed a one-amino-acid difference between nNOS and eNOS in the second sphere of amino acids; this was the difference that we were searching for from the beginning of this project. With the aid of these crystal structures, we developed a new fragment-based de novo design method called "fragment hopping", which allowed the design of a new class of nonpeptide nNOS-selective inhibitors. These compounds were modified to give low nanomolar, highly dual-selective nNOS inhibitors, which we recently showed are active in a rabbit model for the prevention of neurobehavioral symptoms of cerebral palsy. These compounds could also have general application in other neurodegenerative diseases for which excess NO is responsible.

Degradation of paclitaxel and related compounds in aqueous solutions I: epimerization

Paclitaxel and other taxanes have complex structures including the presence of numerous hydrolytically sensitive ester groups and a chiral center that readily undergoes epimerization thus making their kinetics complex. The present study attempts to understand the mechanism of epimerization at the 7-position of paclitaxel, 7-epi-taxol, 10-deacetyltaxol, 7-epi-10-deacetyltaxol, baccatin III and 10-deacetylbaccatin III. Kinetics were studied as function of temperature, pH and buffer concentration and analyzed using a stability indicating assay and LC/MS to identify degradation products. Epimerization was base catalyzed with no evidence of acid catalysis noted. The observed equilibrium constant for epimerization, K, indicated a thermodynamically more favorable S-epimer and a small free energy change between the two epimers. For all of the compounds in this study, removal of the C10 acetyl group increases the epimerization rate in basic aqueous solutions. The observed base-catalyzed epimerization in near neutral to higher pH range suggests a possible rapid deprotonation/protonation of the C7 -OH, followed by a structural rearrangement through a retroaldol/aldol mechanism to form the epimer. Moreover, the rate-limiting step of structure rearrangement most likely occurs with the formation of an enolate intermediate.

Diastereoselective Synthesis of α-Methyl and α-Hydroxy-β-Amino Acids via 4-Substituted-1,3-Oxazinan-6-ones

1,3-oxazinan-6-ones have been utilized in a series of enolate reactions to produce 5-hydroxy and 5-alkyl-4-substituted-1,3-oxazinan-6-ones with excellent trans diastereoselectivity. Highlighting the versatility of the oxazinanone, a number of transformations were performed to produce a variety of protected N-H and N-methyl alpha-hydroxy- and alpha-methyl-beta-amino acids.

Enhancing specificity and sensitivity of pharmacophore-based virtual screening by incorporating chemical and shape features--a case study of HIV protease inhibitors

Virtual screening (VS), if applied appropriately, could significantly shorten the hit identification and hit-to-lead processes in drug discovery. Recently, the version of VS that is based upon similarity to a pharmacophore has received increased attention. This is due to two major factors: first, the public availability of the ZINC1 conformational database has provided a large selection pool with high-quality and purchasable small molecules; second, new technology has enabled a more accurate and flexible definition of pharmacophore models coupled with an efficient search speed. The major goal of this study was to achieve improved specificity and sensitivity of pharmacophore-based VS by optimizing the variables used to generate conformations of small molecules and those used to construct pharmacophore models from known inhibitors or from inhibitor-protein complex structures. By using human immunodeficiency virus protease and its inhibitors (PIs) as a case study, the impact of the key variables, including the selection of chemical features, involvement of excluded volumes (EV), the tolerance radius of excluded volumes, energy windows, and the maximum number of conformers in conformation generation, was explored. Protein flexibility was simulated by adjusting the sizes of EV. Our best pharmacophore model, combining both chemical features and excluded volumes, was able to correctly identify 60 out of 75 structurally diverse known PIs, while misclassifying only 5 out of 75 similar compounds that are not inhibitors. To evaluate the specificity of the model, 1193 oral drugs on the market were screened, and 25 original hits were identified, including 5 out of 6 known PI drugs.

Synthesis of Conformationally Constrained Cyclic Peptides Using an Intramolecular Sonogashira Coupling

[Reaction: see text]. Small peptides having a 3-bromobenzyl group at the C-termini and n-alkynoyl group at the N-termini undergo a smooth copper-free intramolecular Sonogashira coupling reaction to afford the corresponding cyclic peptides in moderate yields. Scope and limitations of this macrocyclization is demonstrated with di-, tri-, and tetrapeptides.

Solution phase parallel synthesis and evaluation of MAPK inhibitory activities of close structural analogues of a Ras pathway modulator

A solution phase parallel synthesis approach was undertaken to rapidly explore the structure-activity relationship of an inhibitor of the Ras/Raf protein interaction identified from a small molecule compound library. Evaluation of the MAPK pathway signaling inhibitory activity of the synthesized analogues as well as their antiproliferative activity and ability to inhibit soft agar growth were performed.

Stereoselective synthesis of photoreactive peptidomimetic gamma-secretase inhibitors

The first asymmetric synthesis of novel, potent photoreactive gamma-secretase inhibitors 2 and 3 has been accomplished. Two stereoselective methods for the preparation of lactone 9 are described. Protected benzophenone intermediate 19 is prepared via an aldol-elimination reaction followed by a PtO(2)-catalyzed asymmetric hydrogenation. Two routes leading from 19 to compounds 2 and 3 are evaluated. The application of 3 as an activity-based probe has been demonstrated by localizing gamma-secretase activity in the plasma membrane of intact cells.

Molecular recognition: the fragment approach in lead generation

The successful practice of medicinal chemistry is crucially dependent on the principles of molecular recognition: the first and "fundamental" requirement for a drug is to bind to its target; specificity, or at least selectivity, of binding is also a must. Subsequent optimization steps to develop a lead compound into a drug are a complex mixture of processes that are not yet fully understood or predictable. Fortunately, criteria exist to discard leads that would be intractable for optimization. The concepts of non-lead-likeness and lead-likeness, in respect to drug-likeness and non-drug-likeness, have prompted a rich discussion in the recent medicinal chemistry literature. The fragment approach is an emerging philosophy in the process of lead compound discovery. The basic interactions responsible for binding affinity are defined from the "protein interactions world" and key structural fragments are combined according to the criteria of three-dimensional diversity to find new leads. New techniques in screening are used for the detection of the weaker interactions of fragments with their targets that might be undetectable in classical biological assays.