Biological Activity Profile Research Articles

Automated Structure–Activity Relationship Mining: Connecting Chemical Structure to Biological Profiles

Understanding the structure–activity relationships (SARs) of small molecules is important for developing probes and novel therapeutic agents in chemical biology and drug discovery. Increasingly, multiplexed small-molecule profiling assays allow simultaneous measurement of many biological response parameters for the same compound (e.g., expression levels for many genes or binding constants against many proteins). Although such methods promise to capture SARs with high granularity, few computational methods are available to support SAR analyses of high-dimensional compound activity profiles. Many of these methods are not generally applicable or reduce the activity space to scalar summary statistics before establishing SARs. In this article, we present a versatile computational method that automatically extracts interpretable SAR rules from high-dimensional profiling data. The rules connect chemical structural features of compounds to patterns in their biological activity profiles. We applied our method to data from novel cell-based gene-expression and imaging assays collected on more than 30,000 small molecules. Based on the rules identified for this data set, we prioritized groups of compounds for further study, including a novel set of putative histone deacetylase inhibitors.

Antinociceptive Activity of Dimethyl 7-aryl-2-(2-rimino)-8-[(3-aryl)quinoxalin-2-yl]-9-oxo-1,6-dioxaspiro[4.4]non-3,7-diene-3,4-dicarboxylates

Multi-component reactions (MCR) are effective methods for producing an enormous number of organic compounds in one step from simple and available starting materials [1]. Reactions using isocyanides, which lead to new types of heterocyclic systems, among which highly active compounds with various biological activity profiles are observed, are some of the leading MCRs [2]. The three-component synthesis based on isocyanides, carbonyl compounds, and acetylenedicarboxylate esters is an excellent example of an MCR on the basis of which a multitude of various heterocyclic compounds was recently produced [3]. Herein we present results from a study of the antinociceptive activity of dimethyl 7-aryl-2-(2-R-imino)-8[(3-aryl)quinoxalin-2-yl]-9-oxo-1,6-dioxaspiro[4.4]non-3,7-diene-3,4dicarboxylates (IIa-f), which were prepared by a three-component synthesis from 5-aryl-4-quinoxalin-2-ylfuran-2,3diones (Ia-c) [4], dimethyl acetylenedicarboxylate, and 1-adamantylisocyanide or o-methylphenylisocyanide according to the following reaction [5]:

Identification of Synthetic Steroids in River Water Downstream from Pharmaceutical Manufacture Discharges Based on a Bioanalytical Approach and Passive Sampling

A bioanalytical approach was used to identify chemical contaminants at river sites located downstream from a pharmaceutical factory, where reproductive alterations in wild fish have been previously observed. By using polar organic compound integrative samplers (POCIS) at upstream and downstream sites, biological activity profiles based on in vitro bioassays revealed the occurrence of xenobiotic and steroid-like activities, including very high glucocorticoid, antimineralocorticoid, progestogenic and pregnane X receptor (PXR)-like activities (μg standard-EQ/g of sorbent range), and weak estrogenic activity (ng E2-EQ/g of sorbent range). Chemical analyses detected up to 60 out of 118 targeted steroid and pharmaceutical compounds in the extracts. In vitro profiling of occurring individual chemicals revealed the ability of several ones to act as agonist and/or antagonist of different steroids receptors. Mass balance calculation identified dexamethasone, spironolactone, and 6-alpha-methylprednisolone as major contributors to corticosteroid activities and levonorgestrel as the main contributor to progestogenic activities. Finally, RP-HPLC based fractionation of POCIS extracts and testing activity of fractions confirmed identified compounds and further revealed the presence of other unknown active chemicals. This study is one of the first to report environmental contamination by such chemicals; their possible contribution to in situ effects on fish at the same site is suggested.

Tuning the biological activity profile of antibacterial polymers via subunit substitution pattern.

Binary nylon-3 copolymers containing cationic and hydrophobic subunits can mimic the biological properties of host-defense peptides, but relationships between composition and activity are not yet well understood for these materials. Hydrophobic subunits in previously studied examples have been limited mostly to cycloalkane-derived structures, with cyclohexyl proving to be particularly promising. The present study evaluates alternative hydrophobic subunits that are isomeric or nearly isomeric with the cyclohexyl example; each has four sp3 carbons in the side chains. The results show that varying the substitution pattern of the hydrophobic subunit leads to relatively small changes in antibacterial activity but causes significant changes in hemolytic activity. We hypothesize that these differences in biological activity profile arise, at least in part, from variations among the conformational propensities of the hydrophobic subunits. The α,α,β,β-tetramethyl unit is optimal among the subunits we have examined, providing copolymers with potent antibacterial activity and excellent prokaryote vs eukaryote selectivity. Bacteria do not readily develop resistance to the new antibacterial nylon-3 copolymers. These findings suggest that variation in subunit conformational properties could be generally valuable in the development of synthetic polymers for biological applications.

Fentanyl-related compounds and derivatives: current status and future prospects for pharmaceutical applications.

Fentanyl and its analogs have been mainstays for the treatment of severe to moderate pain for many years. In this review, we outline the structural and corresponding synthetic strategies that have been used to understand the structure-biological activity relationship in fentanyl-related compounds and derivatives and their biological activity profiles. We discuss how changes in the scaffold structure can change biological and pharmacological activities. Finally, recent efforts to design and synthesize novel multivalent ligands that act as mu and delta opioid receptors and NK-1 receptors are discussed.

Synthesis and evaluation of antiproliferative activity of a novel series of hydroxychavicol analogs

We have recently demonstrated that hydroxychavicol is a major constituent and the most active biophenolic of Piper betel leaves with significant antiproliferative activity in the micro molar range. Herein we present the design, synthesis and evaluation of fifteen novel hydroxychavicol analogs with varying antiproliferative activities in cancer cell lines from two representative tissue types, namely, the prostate and cervix that show very encouraging results compared to the parent compounds. Our long range goal is to develop a structure–activity guided relationship to gain mechanistic insights into novel molecular targets of this class of bioactive molecules for rational drug development. Cytotoxicity-guided experimentation on these novel analogs yielded the following structural factors as the key activity regulators: 1) unlike the hydroxyl substituent at position-4, the position-3 hydroxyl is vital for enhanced activity 2) acetoxyl groups are dispensable for activity as corroborated earlier by others 3) allylic double bonds at 2′C–3′C serve to positively influence antiproliferative activity 4) long saturated side chains at 1′-position negatively regulate antiproliferative activity and 5) maneuvering position-4 with a benzyl group positively impacted the biological activity profile. Most amphiphilic compounds showed moderate to good therapeutic potential as expected on the basis of medicinal chemistry principles. Intriguingly, the most active compound with ten-fold higher activity than the parent molecule was realized by sheer serendipity to employ a silica gel based rearrangement that was further explored using nuclear magnetic resonance spectroscopy and density functional theory calculations. This is the first report to describe strategies for optimal synthesis of a novel series of 15 analogs based upon hydroxychavicol, a simple phytochemical of immense anticancer potential.

Nano-QSAR modeling for predicting biological activity of diverse nanomaterials

Case study-1 (diverse metal core NPs); case study-2 (similar metal core NPs); case study-3 (metal oxide NPs); case study-4 (surface modified multi-walled CNTs); case study-5 (fullerene derivatives).

Design, synthesis, and PASS-assisted evaluation of novel 2-substituted benzimidazole derivatives as potent anthelmintics

A series of novel 2-substituted benzimidazole analogs has been designed and synthesized by connecting the benzimidazole nucleus with variedly substituted chalcone moieties through an amino linker. The designed analogs were predicted for their biological activity profile through the computer software PASS. The compounds were predicted to have potent anthelmintic activity. These were synthesized and the activity of each compound was evaluated experimentally at the concentrations of 0.1, 0.2, and 0.5 % in terms of mortality time and paralysis time for the helminthes. The experimentally observed activity was found to comply with the PASS predicted activity. All compounds showed dose-dependent activities. The compounds with an electron releasing group at the para position on phenyl ring in the chalcone moiety (8 and 9) were the most active in comparison to those bearing electron withdrawing groups. The corresponding ortho analogs (4 and 5) also revealed good paralytic and lethal activities. The higher activities of 8 and 9 may be attributed to the favorable electronic interactions of the electron releasing groups present at para position of the phenyl ring. Comparative analysis of the Lipinski’s parameters and the activities of the compounds revealed all the compounds to comply with the Lipinski’s rule of five. Further an optimum hydrophilicity and total polar surface area in the range of 65–80 of the molecule are required for the potent activity, but Molar refractance is not found to have any significant role in determining the anthelmintic activity.

Methods for the synthesis of xanthine-derived polycyclic fused systems

Abstract Xanthines are a widely known group of alkaloids, commonly used as bronchodilators and psycho and cardiac stimulants. Most of their actions are principally connected with either antagonism of adenosine receptors or phosphodiesterase inhibition; nevertheless, other profiles of their biological activity – antiviral, antitumor or anticancer – are also known. Here, we present a review of the main synthetic methods to obtain xanthine-derived heterocyclic fused systems. The five-, six- or seven-membered heterocyclic ring is attached to the purine-2,6-dione core with one or two bridgehead (ring junction) nitrogen atoms. The biological activity profile of the individual heterocyclic systems is mentioned.

General Theory for Multiple Input-Output Perturbations in Complex Molecular Systems. 1. Linear QSPR Electronegativity Models in Physical, Organic, and Medicinal Chemistry

In general perturbation methods starts with a known exact solution of a problem and add "small" variation terms in order to approach to a solution for a related problem without known exact solution. Perturbation theory has been widely used in almost all areas of science. Bhor's quantum model, Heisenberg's matrix mechanincs, Feyman diagrams, and Poincare's chaos model or "butterfly effect" in complex systems are examples of perturbation theories. On the other hand, the study of Quantitative Structure-Property Relationships (QSPR) in molecular complex systems is an ideal area for the application of perturbation theory. There are several problems with exact experimental solutions (new chemical reactions, physicochemical properties, drug activity and distribution, metabolic networks, etc.) in public databases like CHEMBL. However, in all these cases, we have an even larger list of related problems without known solutions. We need to know the change in all these properties after a perturbation of initial boundary conditions. It means, when we test large sets of similar, but different, compounds and/or chemical reactions under the slightly different conditions (temperature, time, solvents, enzymes, assays, protein targets, tissues, partition systems, organisms, etc.). However, to the best of our knowledge, there is no QSPR general-purpose perturbation theory to solve this problem. In this work, firstly we review general aspects and applications of both perturbation theory and QSPR models. Secondly, we formulate a general-purpose perturbation theory for multiple-boundary QSPR problems. Last, we develop three new QSPR-Perturbation theory models. The first model classify correctly >100,000 pairs of intra-molecular carbolithiations with 75-95% of Accuracy (Ac), Sensitivity (Sn), and Specificity (Sp). The model predicts probabilities of variations in the yield and enantiomeric excess of reactions due to at least one perturbation in boundary conditions (solvent, temperature, temperature of addition, or time of reaction). The model also account for changes in chemical structure (connectivity structure and/or chirality paterns in substrate, product, electrophile agent, organolithium, and ligand of the asymmetric catalyst). The second model classifies more than 150,000 cases with 85-100% of Ac, Sn, and Sp. The data contains experimental shifts in up to 18 different pharmacological parameters determined in >3000 assays of ADMET (Absorption, Distribution, Metabolism, Elimination, and Toxicity) properties and/or interactions between 31723 drugs and 100 targets (metabolizing enzymes, drug transporters, or organisms). The third model classifies more than 260,000 cases of perturbations in the self-aggregation of drugs and surfactants to form micelles with Ac, Sn, and Sp of 94-95%. The model predicts changes in 8 physicochemical and/or thermodynamics output parameters (critic micelle concentration, aggregation number, degree of ionization, surface area, enthalpy, free energy, entropy, heat capacity) of self-aggregation due to perturbations. The perturbations refers to changes in initial temperature, solvent, salt, salt concentration, solvent, and/or structure of the anion or cation of more than 150 different drugs and surfactants. QSPR-Perturbation Theory models may be useful for multi-objective optimization of organic synthesis, physicochemical properties, biological activity, metabolism, and distribution profiles towards the design of new drugs, surfactants, asymmetric ligands for catalysts, and other materials.

Localized Heuristic Inverse Quantitative Structure Activity Relationship with Bulk Descriptors Using Numerical Gradients

State-of-the-art quantitative structure-activity relationship (QSAR) models are often based on nonlinear machine learning algorithms, which are difficult to interpret. From a pharmaceutical perspective, QSARs are used to enhance the chemical design process. Ultimately, they should not only provide a prediction but also contribute to a mechanistic understanding and guide modifications to the chemical structure, promoting compounds with desirable biological activity profiles. Global ranking of descriptor importance and inverse QSAR have been used for these purposes. This paper introduces localized heuristic inverse QSAR, which provides an assessment of the relative ability of the descriptors to influence the biological response in an area localized around the predicted compound. The method is based on numerical gradients with parameters optimized using data sets sampled from analytical functions. The heuristic character of the method reduces the computational requirements and makes it applicable not only to fragment based methods but also to QSARs based on bulk descriptors. The application of the method is illustrated on congeneric QSAR data sets, and it is shown that the predicted influential descriptors can be used to guide structural modifications that affect the biological response in the desired direction. The method is implemented into the AZOrange Open Source QSAR package. The current implementation of localized heuristic inverse QSAR is a step toward a generally applicable method for elucidating the structure activity relationship specifically for a congeneric region of chemical space when using QSARs based on bulk properties. Consequently, this method could contribute to accelerating the chemical design process in pharmaceutical projects, as well as provide information that could enhance the mechanistic understanding for individual scaffolds.

FRI0021 Alx-0061, an anti-IL-6r nanobody® for therapeutic use in rheumatoid arthritis, demonstrates in vitro a differential biological activity profile as compared to tocilizumab

BackgroundInterleukin-6 (IL-6) is a pleiotropic cytokine inducing a wide range of biological activities via its receptor, which can either be soluble (sIL-6R) or membrane-bound (mIL-6R). Blocking of IL-6R results in...

Design of Peptide and Peptidomimetic Ligands with Novel Pharmacological Activity Profiles

Peptide hormones and neurotransmitters are of central importance in most aspects of intercellular communication and are involved in virtually all degenerative diseases. In this review, we discuss physicochemical approaches to the design of novel peptide and peptidomimetic agonists, antagonists, inverse agonists, and related compounds that have unique biological activity profiles, reduced toxic side effects, and, if desired, the ability to cross the blood-brain barrier. Designing ligands for specific biological and medical needs is emphasized, as is the close collaboration of chemists and biologists to maximize the chances for success. Special emphasis is placed on the use of conformational (ϕ-ψ space) and topographical (χ space) considerations in design.

Phytochemical Profile and Qualification of Biological Activity of an Isolated Fraction of Bellis perennis

This study describes the isolation and identification of apigenin-7-O-ghicopyranoside, a flavonoid isolated from the flowers of Bellis perennis L., Asteraceae, an species with a broad spectrum of biological activities. The in vitro antioxidant activity and the inhibition of the enzyme acetylcholinesterase were evaluated. The flavonoid showed strong in vitro antioxidant potential, because of the capacity of removal of hydroxyl radicals and nitric oxide, and also prevented the formation of thiobarbituric acid-reactive substances. These parameters were inhibited at the highest concentration of ApG at rates of 77.7%, 72% and 73.4%, respectively, in addition to inhibiting acetylcholinesterase, suggesting potential use in the treatment of neurodegenerative diseases.

Bothropstoxin-I reduces evoked acetylcholine release from rat motor nerve terminals: Radiochemical and real-time video-microscopy studies

Understanding the biological activity profile of the snake venom components is fundamental for improving the treatment of snakebite envenomings and may also contribute for the development of new potential therapeutic agents. In this work, we tested the effects of BthTX-I, a Lys49 PLA2 homologue from the Bothrops jararacussu snake venom. While this toxin induces conspicuous myonecrosis by a catalytically independent mechanism, a series of in vitro studies support the hypothesis that BthTX-I might also exert a neuromuscular blocking activity due to its ability to alter the integrity of muscle cell membranes. To gain insight into the mechanisms of this inhibitory neuromuscular effect, for the first time, the influence of BthTX-I on nerve-evoked ACh release was directly quantified by radiochemical and real-time video-microscopy methods. Our results show that the neuromuscular blockade produced by in vitro exposure to BthTX-I (1 μM) results from the summation of both pre- and postsynaptic effects. Modifications affecting the presynaptic apparatus were revealed by the significant reduction of nerve-evoked [3H]-ACh release; real-time measurements of transmitter exocytosis using the FM4-64 fluorescent dye fully supported radiochemical data. The postsynaptic effect of BthTX-I was characterized by typical histological alterations in the architecture of skeletal muscle fibers, increase in the outflow of the intracellular lactate dehydrogenase enzyme and progressive depolarization of the muscle resting membrane potential. In conclusion, these findings suggest that the neuromuscular blockade produced by BthTX-I results from transient depolarization of skeletal muscle fibers, consequent to its general membrane-destabilizing effect, and subsequent decrease of evoked ACh release from motor nerve terminals.

A Facile Synthesis of Arylazonicotinates for Dyeing Polyester Fabrics under Microwave Irradiation and Their Biological Activity Profiles

A as textile dyes and the fastness properties of the dyed samples were measured. Most of the dyed fabrics tested displayed very good washing and perspiration fastness and series of 2-hydroxy- and 2-amino-6-substituted-5-arylazonicotinate monoazo compounds 7a–e and 9a–c were prepared via condensation of 3-oxo-3-substituted-2-arylhydrazonals 2a–e with active methylene nitriles 3a–d using microwave irradiation as an energy source. These substances were then tested moderate light fastness. Finally, the biological activity of the synthesized compounds against Gram positive bacteria, Gram negative bacteria and yeast were evaluated.

Fluorescently labeled macrolides as a tool for monitoring cellular and tissue distribution of azithromycin

Exceptional therapeutic effects of macrolides in treating various infections and inflammatory conditions can be significantly contributed to their unique pharmacokinetic properties. Macrolides accumulate in cells and tissues, with concentrations usually 10 to more than 100 times higher of those measured in plasma. Intracellular distribution of macrolides has so far been examined using extensive subcellular fractionation techniques, radiolabeled compounds and conventional pharmacokinetic methods. In this study we evaluated four fluorescently labeled macrolides on their applicability to monitor azithromycin distribution in vitro and in vivo. 9-Deoxo-9a-{3-[(7-nitro-2,1,3-benzoxadiazol-4-yl)amino]propyl}-9a-aza-9a-homoerythromycin A (9a-NBD-azithromycin) was selected as a compound with most similar cellular pharmacokinetics to azithromycin. 9a-NBD-azithromycin demonstrated antimicrobial properties comparable to azithromycin, displayed the same biological activity profile in LPS-stimulated J774A.1 murine macrophage cells and, even though it accumulated in cells almost 50% more than azithromycin, it showed same rate of retention. Identical to azithromycin, 9a-NBD-azithromycin was localized in lysosomes of J774A.1 cells.Two hours after 9a-NBD-azithromycin was administered intraperitonally to mice, a strong fluorescent signal was located in kidneys and liver and slightly weaker in the spleen. In kidneys, the signal was concentrated in tubuli, and glomeruli were negative. Patchy florescence in hepatocytes supports lysosomal cellular localization. Weaker staining of white pulp compared to red pulp of spleen is in agreement with lower accumulation of azithromycin in lymphocytes compared to other cell types present.We conclude that 9a-NBD-azithromycin can be used as a fluorescent analog of azithromycin to visualize its distribution in in vitro systems, and is also suitable for in vivo studies.

Vasoactive intestinal peptide suppresses ovarian granulosa cell apoptosis in vitro by up-regulating Bcl-2 gene expression

Vasoactive intestinal peptide (VIP) is an endogenous peptide showing a rich profile of biological activities. Within ovaries, VIP directly regulates the ovarian functions, including granulosa cells (GCs) development. In the present study, the effects of VIP on proliferation and apoptosis in goose granulosa cells were demonstrated and its underlying mechanism investigated. A strategy of RNAi-mediated “gene silencing” of Bcl-2 (RV-Bcl-2), over-expression of Bcl-2 (JLV-Bcl-2) synthesis, and exogenous VIP was used to treat goose GCs. The results showed the amounts of Bcl-2 protein were negatively correlated with apoptosis of goose GCs in all experimental groups. Compared with other control groups, apoptosis was decreased in goose GCs following treatment of 100nM VIP, and the amount of Bcl-2 protein was increased (P<0.05) increased. However, VIP failed to exert an effect on cell proliferation (P>0.05). In conclusion, the exogenous VIP plays an important role in inhibiting apoptosis of goose GCs via inducing Bcl-2 gene expression.

New Expression Method and Characterization of Recombinant Human Granulocyte Colony Stimulating Factor in a Stable Protein Formulation

Human recombinant granulocyte colony stimulating factor (rhG-CSF) is widely used in hematology and oncology for the treatment of neutropenia, for the restoration of neutrophil production after bone marrow transplantation, for myelodysplastic syndromes, and aplastic anemia. The E. coli expression system is commonly used for fast recombinant production of rhG-CSF at a large scale. We have applied a novel autoinduction method for the batch expression of rhG-CSF to study whether this new system would increase cell mass and target-protein yield compared to conventional E. coli cell culture and induction with isopropyl β-D-thiogalactopyranoside (IPTG). We could demonstrate 3-fold higher culture densities and a 5-fold higher protein yield compared to IPTG induction without the need to monitor cell growth in a shortened 24 h expression procedure. rhG-CSF expressed in autoinduction media was successfully extracted from E. coli inclusion bodies and refolded by dialysis. After size exclusion chromatography (SEC) purification, rhG-CSF showed similar conformation, biological activity and aggregation profile compared to the commercially available biosimilar TEVAgrastim(®) (TEVA Pharma AG). Expression by autoinduction is suggested as a cost- and time-effective method for rhG-CSF production.

Profiling Environmental Chemicals for Activity in the Antioxidant Response Element Signaling Pathway Using a High Throughput Screening Approach

Background: Oxidative stress has been implicated in the pathogenesis of a variety of diseases ranging from cancer to neurodegeneration, highlighting the need to identify chemicals that can induce this effect. The antioxidant response element (ARE) signaling pathway plays an important role in the amelioration of oxidative stress. Thus, assays that detect the up-regulation of this pathway could be useful for identifying chemicals that induce oxidative stress.Objectives: We used cell-based reporter methods and informatics tools to efficiently screen a large collection of environmental chemicals and identify compounds that induce oxidative stress.Methods: We utilized two cell-based ARE assay reporters, β-lactamase and luciferase, to screen a U.S. National Toxicology Program 1,408-compound library (NTP 1408, which contains 1,340 unique compounds) for their ability to induce oxidative stress in HepG2 cells using quantitative high throughput screening (qHTS).Results: Roughly 3% (34 of 1,340) of the unique compounds demonstrated activity across both cell-based assays. Based on biological activity and structure–activity relationship profiles, we selected 50 compounds for retesting in the two ARE assays and in an additional follow-up assay that employed a mutated ARE linked to β-lactamase. Using this strategy, we identified 30 compounds that demonstrated activity in the ARE-bla and ARE-luc assays and were able to determine structural features conferring compound activity across assays.Conclusions: Our results support the robustness of using two different cell-based approaches for identifying compounds that induce ARE signaling. Together, these methods are useful for prioritizing chemicals for further in-depth mechanism-based toxicity testing.