Structural diversity of bicyclic amino acids

Summary. Over the years biomedical research has been constantly oriented towards the development of new therapeutics based on bioactive peptides and their analogues. In particular, the generation of compounds having structures and functions similar to bioactive peptides, named “peptidomimetics”, raised much interest among organic and medicinal chemists due to the possibility by using such compounds to improve both potency and stability of peptidic lead compounds. In the context of this research area, unnatural amino acids are of great interest in drug discovery, and their use as new building blocks for the development of peptidomimetics with high diversity level and possessing high-ordered structures is of special interest. In particular, medicinal chemistry has taken advantage of the use of amino acid homologues and of cyclic and polycyclic templates to introduce elements of diversity for the generation of new molecules as drug candidates. Bicyclic amino acids have been developed as reverse turn mimetics and dipeptide isosteres, and the constraint imposed by their structures has been reported as a tool for controlling the conformational preferences of modified peptides. Moreover, synthetic efforts have been driven to the generation of diverse structures based on the modulation of ring size and scaffold decoration by suitable functional groups. Herein is reported an overview of different classes of bicyclic amino acids, taking into account the strategies to achieve structurally diverse templates, and some implications in medicinal chemistry are also disclosed. Authors’ address: Antonio Guarna, Dipartimento di Chimica Organica “Ugo Schiff” and Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Bioattivi (HeteroBioLab), Università degli Studi di Firenze, Polo Scientifico e Tecnologico, Via della Lastruccia 13, I-50019 Sesto Fiorentino, Firenze, Italy     

Recent encounters with atropisomerism in drug discovery

Atropisomerism is stereochemistry arising from restricted bond rotation that creates a chiral axis. Atropisomers are subject to time-dependent inversion of chirality via bond rotation, a property which in drug molecules introduces complexity and challenges for drug discovery and development processes. Greater recognition of the occurrence of atropisomerism and improved characterization techniques have helped medicinal chemists successfully advance atropisomeric drug molecules. This review provides recent examples of atropisomerism encountered in medicinal chemistry efforts and the strategies used to address the accompanying challenges.     

Inside the Mind of a Medicinal Chemist: The Role of Human Bias in Compound Prioritization during Drug Discovery

Medicinal chemists’ “intuition” is critical for success in modern drug discovery. Early in the discovery process, chemists select a subset of compounds for further research, often from many viable candidates. These decisions determine the success of a discovery campaign, and ultimately what kind of drugs are developed and marketed to the public. Surprisingly little is known about the cognitive aspects of chemists’ decision-making when they prioritize compounds. We investigate 1) how and to what extent chemists simplify the problem of identifying promising compounds, 2) whether chemists agree with each other about the criteria used for such decisions, and 3) how accurately chemists report the criteria they use for these decisions. Chemists were surveyed and asked to select chemical fragments that they would be willing to develop into a lead compound from a set of ∼4,000 available fragments. Based on each chemist’s selections, computational classifiers were built to model each chemist’s selection strategy. Results suggest that chemists greatly simplified the problem, typically using only 1–2 of many possible parameters when making their selections. Although chemists tended to use the same parameters to select compounds, differing value preferences for these parameters led to an overall lack of consensus in compound selections. Moreover, what little agreement there was among the chemists was largely in what fragments were undesirable. Furthermore, chemists were often unaware of the parameters (such as compound size) which were statistically significant in their selections, and overestimated the number of parameters they employed. A critical evaluation of the problem space faced by medicinal chemists and cognitive models of categorization were especially useful in understanding the low consensus between chemists.     

Mutagenicity in a Molecule: Identification of Core Structural Features of Mutagenicity Using a Scaffold Analysis

With advances in the development and application of Ames mutagenicity in silico prediction tools, the International Conference on Harmonisation (ICH) has amended its M7 guideline to reflect the use of such prediction models for the detection of mutagenic activity in early drug safety evaluation processes. Since current Ames mutagenicity prediction tools only focus on functional group alerts or side chain modifications of an analog series, these tools are unable to identify mutagenicity derived from core structures or specific scaffolds of a compound. In this study, a large collection of 6512 compounds are used to perform scaffold tree analysis. By relating different scaffolds on constructed scaffold trees with Ames mutagenicity, four major and one minor novel mutagenic groups of scaffold are identified. The recognized mutagenic groups of scaffold can serve as a guide for medicinal chemists to prevent the development of potentially mutagenic therapeutic agents in early drug design or development phases, by modifying the core structures of mutagenic compounds to form non-mutagenic compounds. In addition, five series of substructures are provided as recommendations, for direct modification of potentially mutagenic scaffolds to decrease associated mutagenic activities.     

Cyclic Peptides Containing Biaryl and Biaryl Ether Linkages

This review describes the isolation, activities and synthetic approaches of the naturally occurring cyclic peptides containing biaryl and/or biaryl ether linkages. These compounds range from monocyclic, to bicyclic, to the polycyclic glycopeptide antibiotics, and most of them exhibit significant biological properties such as cytotoxic or antimicrobial activities. Interestingly, vancomycin is used clinically as the antibiotic of last resort for the treatment of methicillin-resistant Staphylococcus aureus. The medicinal significance and the structural complexity of these macrocycles have challenged chemists towards the total synthesis of these compounds and in designing synthetic analogues. Non-natural macrocycles reported from 1999 to 2004 are also covered.     

Design,synthesis, in-silico studies and biological screening of quinazolinone analogues as potential antibacterial agents against MRSA

Type or The emergence of resistance to antibiotic has developed a complicated situation in the treatment of bacterial infections. Considering the antimicrobial resistance phenomenon as one of the greatest challenge of medicinal chemists for search of better anti-bacterial agents, which have potential narrow spectrum activity with low development of resistance potential and low toxicity to host. Cross-linking of peptidoglycan is a key step catalyze by Penicillin binding protein (PBP) to maintain integrity of cell wall in bacterial cell. However, these Penicillin binding protein (PBP) has developed resistance in methicillin-resistant Staphylococcus aureus (MRSA) due to acquisition of additional PBP2a. Various Quinazolinone analogues are reported in literature as potential anti-bacterial agents against MRSA. In present study new quinazolinone analogues has been designed, guided by molecular docking, In-silico and MM-GBSA study. Newly designed molecules have been synthesized by medicinal chemistry route and their characterization was done by using IR, NMR, & HR-MS techniques. Biological evaluation of synthesized compounds has been done on wild type Gram-negative (Escherichia coli), Gram-positive (Staphylococcus aureus) and resistant MRSA bacterial strains using Streptomycin, Kanamycin and Linezolid as standard drugs respectively. The in vitro evaluation results have shown that compound 5f is active with MIC value 15.625 μg/mL against S. aureus and with MIC value 31.25 μg/mL against MRSA.     

Predictive models for estimating cytotoxicity on the basis of chemical structures

Cytotoxicity is a critical property in determining the fate of a small molecule in the drug discovery pipeline. Cytotoxic compounds are identified and triaged in both target-based and cell-based phenotypic approaches due to their off-target toxicity or on-target and on-mechanism toxicity for oncology and neurodegenerative targets. It is critical that chemical-induced cytotoxicity be reliably predicted before drug candidates advance to the late stage of development, or more ideally, before compounds are synthesized. In this study, we assessed the cell-based cytotoxicity of nearly 10,000 compounds in NCATS annotated libraries against four ‘normal’ cell lines (HEK 293, NIH 3T3, CRL-7250 and HaCat) using CellTiter-Glo (CTG) technology and constructed highly predictive models to estimate cytotoxicity from chemical structures. There are 5,241 non-redundant compounds having unambiguous activities in the four different cell lines, among which 11.8% compounds exhibited cytotoxicity in two or more cell lines and are thus labelled cytotoxic. The support vector classification (SVC) models trained with 80% randomly selected molecules achieved the area under the receiver operating characteristic curve (AUC-ROC) of 0.88 on average for the remaining 20% compounds in the test sets in 10 repeating experiments. Application of under-sampling rebalancing method further improved the averaged AUC-ROC to 0.90. Analysis of structural features shared by cytotoxic compounds may offer medicinal chemists heuristic design ideas to eliminate undesirable cytotoxicity. The profiling of cytotoxicity of drug-like molecules with annotated primary mechanism of action (MOA) will inform on the roles played by different targets or pathways in cellular viability. The predictive models for cytotoxicity (accessible at https://tripod.nih.gov/web_adme/cytotox.html) provide the scientific community a fast yet reliable way to prioritize molecules with little or no cytotoxicity for downstream development.     

Structure elucidation of glycoprotein glycans and of polysaccharides by NMR spectroscopy

The applicability of 1H-NMR spectroscopy for the determination of the primary and tertiary structure of carbohydrate-containing molecules is demonstrated. For classes of known compounds the characterization can be based on chemical shifts observed in 1D NMR spectra with or without the aid of a computer database. For more complex structure determinations 2D NMR techniques are required. Here the application of 2D NMR is demonstrated for the primary structure determination of two bacterial exopolysaccharides, for the spatial structure determination of a disaccharide and a glycoprotein hormone.     

NMR metabolomics of berry quality in sea buckthorn (Hippophae L.)

Sea buckthorn (Hippophae L.) is a woody perennial shrub or small tree whose berries are rich in bioactive compounds with powerful nutritional and medicinal properties. Untargeted ¹H nuclear magnetic resonance (NMR) spectroscopy and principal component analysis (PCA) were used to characterize the metabolic profile of berry quality. There was strong separation in the NMR signal intensity of bioactive compounds between pulp and seeds, such as amino acids [gamma-aminobutyric acid (GABA), aspartate, glutamate, theanine, and proline], organic acids (citrate, succinate, malate, acetate, quinate, and heriguard), and carbohydrates (sucrose, fructose, glucose, and melibiose). Sea buckthorn cultivars could be clearly separated into two groups using principal component analysis (PCA) based on NMR spectroscopy of bioactive compounds in the pulp and seeds. Several metabolic compounds such as sugar, organic acids, and amino acids could serve as biomarkers for prediction of berry quality and for classification of germplasm collections. This dataset provides potential information concerning the mechanisms of berry quality formation and contributes to increasing the breeding efficiency of sea buckthorn quality improvement.     

In vitro estrogenic activity of Achillea millefolium L.

Isolation and biological characterization of pure compounds was used to identify and characterize estrogenic activity and estrogen receptors (ER) preference in chemical components of Achillea millefolium. This medicinal plant is used in folk medicine as an emmenagogue. In vitro assay, based on recombinant MCF-7 cells, showed estrogenic activity in a crude extract of the aerial parts of A. millefolium. After fractionation of the crude extract with increasing polar solvents, estrogenic activity was found in the methanol/water fraction. Nine compounds were isolated and characterized by HR-MS spectra and 1D- and 2D-NMR techniques. In particular, dihydrodehydrodiconiferyl alcohol 9-O-beta-D-glucopyranoside - a glycosyl-neolignan - was isolated for the first time from the genus Achillea in addition to six flavone derivatives, apigenin, apigenin-7-O-beta-D-glucopyranoside, luteolin, luteolin-7-O-beta-D-glucopyranoside, luteolin-4'-O-beta-D-glucopyranoside, rutin, and two caffeic acid derivatives, 3,5-dicaffeoylquinic acid and chlorogenic acid. Apigenin and luteolin, the most important estrogenic compounds among those tested, were studied for their ability to activate alpha or beta estrogen receptors (ERalpha, ERbeta) using transiently transfected cells. Our results suggest that isolation and biological characterization of estrogenic compounds in traditionally used medicinal plants could be a first step in better assessing further (e.g. in vivo) tests of nutraceutical and pharmacological strategies based on phytoestrogens.     

CYP264B1 from Sorangium cellulosum So ce56: a fascinating norisoprenoid and sesquiterpene hydroxylase

Many terpenes and terpenoid compounds are known as bioactive substances with desirable fragrance and medicinal activities. Modification of such compounds to yield new derivatives with desired properties is particularly attractive. Cytochrome P450 monooxygenases are potential enzymes for these reactions due to their capability of performing different reactions on a variety of substrates. We report here the characterization of CYP264B1 from Sorangium cellulosum So ce56 as a novel sesquiterpene hydroxylase. CYP264B1 was able to convert various sesquiterpenes including nootkatone and norisoprenoids (α-ionone and β-ionone). Nootkatone, an important grapefruit aromatic sesquiterpenoid, was hydroxylated mainly at position C-13. The product has been shown to have the highest antiproliferative activity compared with other nootkatone derivatives. In addition, CYP264B1 was found to hydroxylate α- and β-ionone, important aroma compounds of floral scents, regioselectively at position C-3. The products, 3-hydroxy-β-ionone and 13-hydroxy-nootkatone, were confirmed by (1)H and (13)C NMR. The kinetics of the product formation was analyzed by high-performance liquid chromatography, and the K ( m ) and k (cat) values were calculated. The results of docking α-/β-ionone and nootkatone into a homology model of CYP264B1 revealed insights into the structural basis of these selective hydroxylations.     

Phenolic compounds from the Mongolian medicinal plant Scorzonera radiata

Chromatographic separation of a crude extract obtained from aerial parts of the Mongolian medicinal plant Scorzonera radiata yielded fifteen natural compounds, including two new flavonoids and one new quinic acid congener, as well as four flavones and eight quinic acid derivatives, all of which are known natural compounds. The structures of the isolated compounds were elucidated on the basis of NMR (1H, 13C, COSY, HMBC, ROESY, and TOCSY) and mass spectrometric data. The antioxidant activities of the quinic acid derivatives were evaluated by the DPPH assay.     

Beyond Rf tagging

The split-pool diversity orientated synthesis method, which requires some form of encoding to track the synthesis of discrete compounds, has been the lynchpin of most combinatorial synthesis efforts. The use of encoding methods in combinatorial chemistry has matured, and depending on their level of resources, chemists now have a diverse choice of encoding methods available. New methods of encoding have been developed that are inexpensive, simple to incorporate into any laboratory, and utilize analytical equipment such as MS, FTIR and NMR that are readily available to most organic chemists.     

A concise synthesis of 1,4-dihydro-[1,4]diazepine-5,7-dione,a novel 7-TM receptor ligand core structure with melanocortin receptor agonist activity

Finding small non-peptide molecules for G protein-coupled receptors (GPCR) whose endogenous ligands are peptides, is a very important task for medicinal chemists. Over the years, compounds mimicking peptide structures have been discovered, and scaffolds emulating peptide backbones have been designed. In our work on GPCR ligands, including cholecystokinin receptor-1 (CCKR-1) agonists, we have employed benzodiazepines as a core structure. Looking for ways to reduce molecular weight and possibly improve physical properties of GPCR ligands, we embarked on the search for molecules providing similar scaffolds to the benzodiazepine with lower molecular weight. One of our target core structures was 1,4-dihydro-[1,4]diazepine-5,7-dione. There was not, however, a known synthetic route to such molecules. Here we report the discovery of a simple and concise method for synthesis of 2-[6-(1H-indazol-3-ylmethyl)-5,7-dioxo-4-phenyl-4,5,6,7-tetrahydro-[1,4]diazepin-1-yl]-N-isopropyl-N-phenyl-acetamide as an example of a compound containing the tetrahydrodiazepine-5,7-dione core. Compounds from this series were tested in numerous GPCR assays and demonstrated activity at melanocortin 1 and 4 receptors (MC1R and MC4R). Selected compounds from this series were tested in vivo in Peptide YY (PYY)-induced food intake. Compounds dosed by intracerebroventricular and oral routes reduced PYY-induced food intake and this effect was reversed by the cyclic peptide MC4R antagonist SHU9119.     

Deciphering the Antimicrobial Potential of Taxus wallichiana Zucc: Identification and Characterization Using Bioassay-Guided Fractionation

Taxus wallichiana Zucc. is a high valued medicinal plant and has been mainly studied for its anti-cancer properties. However, research on its other important biological activities, such as its antimicrobial potential, still needs attention. The focus of the present study is to investigate the antimicrobial activity of secondary metabolites of T. wallichiana needles against 3 different groups of microorganisms, i. e., bacteria, actinobacteria, and fungi. Bioactive compounds from T. wallichiana needles were separated through column chromatography, and, TLC-bioautography. Mobile phases were optimized using Snyder's selectivity triangle. Antimicrobial spots were fractionated and compounds were identified by gas chromatography-mass spectroscopy (GC/MS) and liquid chromatography-mass spectrometry (LC/MS). Functional groups were characterized using Fourier transform infrared spectrometry (FTIR) and nuclear magnetic resonance (NMR) was used to identify the molecular structures. GC/MS and LC/MS data analysis confirm the presence of fatty acids (arachidic acid, behenic acid, palmitic acid, and stearic acid), vitamins (nicotinamide), and alkaloids (cinchonine, timolol), aminobenzamides (procainamide), carbocyclic sugar (myoinositol), and alkane hydrocarbon (hexadecane), having antimicrobial activity in the needles of T. wallichiana. To the best of our knowledge, this is the first report on the isolation and characterization of antimicrobial compounds from the needles of Taxus wallichiana (Himalayan yew). The data obtained from the present study will be supportive to the new drug discoveries in modern medicine with various combinations of medicinal plant's active constituents that can be used for curing many diseases.     

Comparative docking studies of labdane-type diterpenes with forskolin at the active site of adenylyl cyclase

Diterpen labd-13(E)-ene-8a,15-diol (1) is a natural product found to possess potential cytotoxic and cytostatic effects against human cancer cell lines. Adenylyl cyclases (ACs) are promising pharmacological targets for treating heart failure, cancer, and psychosis. It has been demonstrated that forskolin is a potent adenylyl cyclase activator. Labdane 1 belongs to same family as forskolin. Its conformational properties are explored using a combination of 1D, 2D NMR spectroscopy, and molecular modeling techniques. The derived low energy conformers are subjected to docking calculations aiming to reveal similarities and differences in the binding mode between 1 and forskolin. Additionally, docking calculations performed on the 1alpha,9alpha-OH and 1alpha-OH derivatives of 1 suggest major contribution of 1alpha position in increasing binding affinity. This information may be of paramount importance to medicinal chemists who are interested in the synthesis of proposed analogs and test the docking results through in vitro experiments.     

Dynamic diversity and small-molecule evolution: a new paradigm for ligand identification.

A longstanding goal of organic, medicinal and bioorganic chemists has been the discovery of efficient methods for designing or identifying biologically active compounds. Recently, several groups have reported using the directed evolution of combinatorial libraries as a new method of identifying compounds capable of binding tightly to a target molecule. Although significant development remains to be done, the initial results suggest that dynamic diversity and associated selection methods will prove to be valuable additions to the drug-discovery process.     

Nor-lignan and sesquiterpenes from Cremanthodium ellisii

A nor-lignan and two sesquiterpenes, along with six known compounds, have been isolated from the medicinal plant Cremanthodium ellisii. Their structures were determined on the basis of spectral evidence, especially 2D NMR (1H-1H COSY, HMQC, HMBC).     

Isolation of two new phenolic compounds from the fruit of Chaenomeles speciosa (Sweet) Nakai

Phytochemical research on the anti-inflammatory activities of Chaenomeles speciosa (Sweet) Nakai (Rosaceae) to investigate the main components of 10% ethanol fraction of the crude extract of C. speciosa fruit in an attempt to find bioactive compounds or new compounds from this medicinal plant. The phytochemical investigation succeeded in isolating two new phenolic compounds, specpolyphenol A (1) and specphenoside A (2), together with three known phenyl glycosides (3–5) from the fraction. The structures of the new compounds were deduced from comprehensive spectroscopic analyses including IR, EI-MS, ¹H NMR, ¹³C NMR, DEPT, COSY, HMBC and HMQC. The structures of the three known compounds 3, 4 and 5 were identified by comparison of their spectral data with those reported in the literature.     

Structure of a novel leech carboxypeptidase inhibitor determined free in solution and in complex with human carboxypeptidase A2

Leech carboxypeptidase inhibitor (LCI) is a novel protein inhibitor present in the medicinal leech Hirudo medicinalis. The structures of LCI free and bound to carboxypeptidase A2 (CPA2)have been determined by NMR and X-ray crystallography, respectively. The LCI structure defines a new protein motif that comprises a five-stranded antiparallel beta-sheet and one short alpha-helix. This structure is preserved in the complex with human CPA2 in the X-ray structure, where the contact regions between the inhibitor and the protease are defined. The C-terminal tail of LCI becomes rigid upon binding the protease as shown in the NMR relaxation studies, and it interacts with the carboxypeptidase in a substrate-like manner. The homology between the C-terminal tails of LCI and the potato carboxypeptidase inhibitor represents a striking example of convergent evolution dictated by the target protease. These new structures are of biotechnological interest since they could elucidate the control mechanism of metallo-carboxypeptidases and could be used as lead compounds for the search of fibrinolytic drugs.