Discovery of potential Toxoplasma gondii CDPK1 inhibitors with new scaffolds based on the combination of QSAR and scaffold‐hopping method with in vitro validation

To discover drugs for toxoplasmosis with less side‐effects and less probability to get drug resistance is eagerly appealed for pregnant women, infant or immunocompromised patients. In this work, using TgCDPK1 as drug target, we design a method to discover new inhibitors for CDPK1 as potential drug lead for toxoplasmosis with novel scaffolds based on the combination of 2D/3D‐QSAR and scaffold‐hopping methods. All the binding sites of the potential inhibitors were checked by docking method, and only the ones that docked to the most conserved sites of TgCDPK1, which make them have less probability to get drug resistance, were remained. As a result, 10 potential inhibitors within two new scaffolds were discovered for TgCDPK1 with experimentally verified inhibitory activities in micromole level. The discovery of these inhibitors may contribute to the drug development for toxoplasmosis. Besides, the pipeline which is composed in this work as the combination of QSAR and scaffold‐hopping is simple, easy to repeat for researchers without need of in‐depth knowledge of pharmacology to get inhibitors with novel scaffolds, which will accelerate the procedure of drug discovery and contribute to the drug repurposing study.     

1,3,4‐Thiadiazole and its Derivatives: A Review on Recent Progress in Biological Activities

The 1,3,4‐thiadiazole nucleus is one of the most important and well‐known heterocyclic nuclei, which is a common and integral feature of a variety of natural products and medicinal agents. Thiadiazole nucleus is present as a core structural component in an array of drug categories such as antimicrobial, anti‐inflammatory, analgesic, antiepileptic, antiviral, antineoplastic, and antitubercular agents. The broad and potent activity of thiadiazole and their derivatives has established them as pharmacologically significant scaffolds. In this study, an attempt has been made with recent research findings on this nucleus, to review the structural modifications on different thiadiazole derivatives for various pharmacological activities.     

Enhanced composite electrospun nanofiber scaffolds for use in drug delivery

The utility of nanofibrous electrospun composite scaffolds has greatly expanded over the last decade, so that they now serve as viable drug delivery vehicles for a host of different biomedical applications. The material properties of electrospun scaffolds are extremely advantageous for drug delivery, in which site-specificity and lower overall medicinal dosages lead to a potential industry-altering mechanism of delivering therapeutics. Different drugs used to predominantly treat infections and cancers can easily be incorporated and released at therapeutic dosages. Further, the inherent high porosity of these electrospun scaffolds allows for a more precisely controlled degradation which is tunable by polymer composition and fiber morphology, leading to sustained drug release. This review examines the current research and breakthrough discoveries that have elevated electrospun scaffolds to a cutting-edge technology that will dramatically alter the landscape of drug delivery.     

In silico approaches and chemical space of anti‐P‐type ATPase compounds for discovering new antituberculous drugs

Tuberculosis (TB) is one of the most important public health problems around the world. The emergence of multi‐drug‐resistant (MDR) and extensively drug‐resistant (XDR) Mycobacterium tuberculosis strains has driven the finding of alternative anti‐TB targets. In this context, P‐type ATPases are interesting therapeutic targets due to their key role in ion homeostasis across the plasma membrane and the mycobacterial survival inside macrophages. In this review, in silico and experimental strategies used for the rational design of new anti‐TB drugs are presented; in addition, the chemical space distribution based on the structure and molecular properties of compounds with anti‐TB and anti‐P‐type ATPase activity is discussed. The chemical space distribution compared to public compound libraries demonstrates that natural product libraries are a source of novel chemical scaffolds with potential anti‐P‐type ATPase activity. Furthermore, compounds that experimentally display anti‐P‐type ATPase activity belong to a chemical space of molecular properties comparable to that occupied by those approved for oral use, suggesting that these kinds of molecules have a good pharmacokinetic profile (drug‐like) for evaluation as potential anti‐TB drugs.     

Enhanced composite electrospun nanofiber scaffolds for use in drug delivery

The utility of nanofibrous electrospun composite scaffolds has greatly expanded over the last decade, so that they now serve as viable drug delivery vehicles for a host of different biomedical applications. The material properties of electrospun scaffolds are extremely advantageous for drug delivery, in which site-specificity and lower overall medicinal dosages lead to a potential industry-altering mechanism of delivering therapeutics. Different drugs used to predominantly treat infections and cancers can easily be incorporated and released at therapeutic dosages. Further, the inherent high porosity of these electrospun scaffolds allows for a more precisely controlled degradation which is tunable by polymer composition and fiber morphology, leading to sustained drug release. This review examines the current research and breakthrough discoveries that have elevated electrospun scaffolds to a cutting-edge technology that will dramatically alter the landscape of drug delivery.     

Cyclotides: a patent review

INTRODUCTION: Cyclotides are bioactive mini-proteins from plants that have the unique topological feature of a head-to-tail cyclic backbone combined with a cystine knot. Because of this structure they are ultra-stable and have attracted interest as peptide-based templates for drug design applications. Cyclotide biosynthesis involves processing from a genetically encoded precursor protein but methods have been developed for their man-made synthesis using solid phase peptide synthesis as well as recombinant methods. Their natural function in plants is as insecticidal agents and thus they have potential applications in agriculture. However, they have a range of pharmaceutically relevant activities, including anti-HIV, antimicrobial and uterotonic activity. Their exceptional stability and facile synthesis lend them to uses as pharmaceutical templates into which bioactive peptide sequences can be grafted. AREAS COVERED: This article reviews the patent literature associated with cyclotides with a focus on therapeutic applications. These patents are primarily related to the use of cystine knot scaffolds for the production of peptide-based drug leads, molecular probes or diagnostic agents. EXPERT OPINION: Although no cyclotide-related peptide has yet reached clinical trials, proof-of-concept has been obtained that bioactive peptide sequences can be grafted onto a cyclotide framework, maintaining biological activity while becoming resistant to proteolysis. Thus, cyclotides are promising templates in drug development applications and there is increasing interest in them and related cystine knot scaffolds, as well as in the use of other disulfide-rich scaffolds, in drug design.     

Molecular Scaffold Analysis of Natural Products Databases in the Public Domain

Natural products represent important sources of bioactive compounds in drug discovery efforts. In this work, we compiled five natural products databases available in the public domain and performed a comprehensive chemoinformatic analysis focused on the content and diversity of the scaffolds with an overview of the diversity based on molecular fingerprints. The natural products databases were compared with each other and with a set of molecules obtained from in‐house combinatorial libraries, and with a general screening commercial library. It was found that publicly available natural products databases have different scaffold diversity. In contrast to the common concept that larger libraries have the largest scaffold diversity, the largest natural products collection analyzed in this work was not the most diverse. The general screening library showed, overall, the highest scaffold diversity. However, considering the most frequent scaffolds, the general reference library was the least diverse. In general, natural products databases in the public domain showed low molecule overlap. In addition to benzene and acyclic compounds, flavones, coumarins, and flavanones were identified as the most frequent molecular scaffolds across the different natural products collections. The results of this work have direct implications in the computational and experimental screening of natural product databases for drug discovery.     

Dexamethasone loaded multi-layer poly-l-lactic acid/pluronic P123 composite electrospun nanofiber scaffolds for bone tissue engineering and drug delivery

In tissue engineering, it is common to mix drugs that can control proliferation and differentiation of cells into polymeric solutions as part of composite to get bioactive scaffolds. However, direct incorporation of drugs might potentially result in undesired burst release. To overcome this problem, here we developed electrospun multilayer drug loaded poly-l-lactic acid/pluronic P123 (PLLA–P123) composite scaffolds. The drug was loaded into the middle layer. The surface, the mechanical and physiochemical properties of the scaffolds were evaluated. The drug release profiles were monitored. Finally, the osteogenic proliferation and differentiation potential were determined. The scaffolds fabricated here have appropriate surface properties, but with different mechanical strength and osteogenic proliferation and differentiation. Multi-layer scaffolds where the drug was in the middle layer and PLLA-plasma and PLLA–P123 with cover layer showed the best osteogenic proliferation and differentiation than the other groups of scaffolds. The drug release profiles of the scaffolds were completely different: single layer scaffolds showed burst release within the first day, while multilayer scaffolds showed controlled release. Therefore, the multilayer drug loaded scaffolds prepared have dual benefits can provide both better osteogenesis and controlled release of drugs and bioactive molecules at the implant site.     

微球在组织工程中的应用

组织工程一直是生命科学领域研究的热点,存在着不少亟待解决的难题,如种子细胞的扩增、工程支架的制备、组织工程所需药物的控制释放等。在解决这些难题时,常要用到微球技术,如微球可以用作微载体培养种子细胞、也可用于制备支架或直接用作支架、还可作为控制药物释放的载体。本文主要介绍微球在组织工程中的应用概况,并总结有关微载体性能改良、微球制成支架,以及载药微球加入支架技术方法的研究进展。     

Reviews on 1,4-naphthoquinones from Diospyros L

The genus Diospyros is one of the most important sources of bioactive compounds, exclusively 1,4-naphthoquinones. The following information is an attempt to cover the developments in the biology and phytochemistry of 1,4-naphthoquinones isolated from this genus, as well as the studies done and the suggested mechanisms regarding their activities. During the past 60 years, many of these agents have been isolated from Diospyros L. Twelve considerable bioactive structures are reported in this review. The basic 1,4-naphthoquinone skeletons, on which a large number of studies have been done, are plumbagin and diospyrin. Today, the potential for development of leads from 1,4-naphthoquinones obtained from Diospyros L. is growing dramatically, mainly in the area of anticancer and antibacterial investigations. The data prepared and described here are intended to be served as a reference tool to the natural products and chemistry specialists in order to expand the rational drug design.     

Molecular basis for covalent inhibition of glyceraldehyde‐3‐phosphate dehydrogenase by a 2‐phenoxy‐1,4‐naphthoquinone small molecule

Glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) has recently gained attention as an antiprotozoan and anticancer drug target. We have previously identified 2‐phenoxy‐1,4‐naphthoquinone as an inhibitor of both Trypanosoma brucei and human GAPDH. Herein, through multiple chemical, biochemical, and biological studies, and through the design of analogs, we confirmed the formation of a covalent adduct, we clarified the inhibition mechanism, and we demonstrated antitrypanosomal, antiplasmodial, and cytotoxic activities in cell cultures. The overall results lent support to the hypothesis that 2‐phenoxy‐1,4‐naphthoquinone binds the GAPDH catalytic cysteine covalently through a phenolate displacement mechanism. By investigating the reactivity of 2‐phenoxy‐1,4‐naphthoquinone and its analogs with four GAPDH homologs, we showed that the covalent inhibition is not preceded by the formation of a strong non‐covalent complex. However, an up to fivefold difference in inactivation rates among homologs hinted at structural or electrostatic differences of their active sites that could be exploited to further design kinetically selective inhibitors. Moreover, we preliminarily showed that 2‐phenoxy‐1,4‐naphthoquinone displays selectivity for GAPDHs over two other cysteine‐dependent enzymes, supporting its suitability as a warhead starting fragment for the design of novel inhibitors.     

Evaluation of Natural and Synthetic 1,4‐naphthoquinones as Inhibitors of Monoamine Oxidase

Previous reports have documented that 1,4‐naphthoquinones act as inhibitors of the monoamine oxidase (MAO) enzymes. In particular, fractionation of the extracts of cured tobacco leafs has led to the characterization of 2,3,6‐trimethyl‐1,4‐naphthoquinone, a non‐selective MAO inhibitor. To derive structure–activity relationships for MAO inhibition by the 1,4‐naphthoquinone class of compounds, this study investigates the human MAO inhibitory activities of fourteen structurally diverse 1,4‐naphthoquinones of natural and synthetic origin. Of these, 5,8‐dihydroxy‐1,4‐naphthoquinone was found to be the most potent inhibitor with an IC₅₀ value of 0.860 μm for the inhibition of MAO‐B. A related compound, shikonin, inhibits both the MAO‐A and MAO‐B isoforms with IC₅₀ values of 1.50 and 1.01 μm , respectively. It is further shown that MAO‐A and MAO‐B inhibition by these compounds is reversible by dialysis. In this respect, kinetic analysis suggests that the modes of MAO inhibition are competitive. This study contributes to the discovery of novel MAO inhibitors, which may be useful in the treatment for disorders such as Parkinson's disease, depressive illness, congestive heart failure and cancer.     

Tagged fragment method for evolutionary structure-based de novo lead generation and optimization

Here we describe a computer-assisted de novo drug design method, EAISFD, which combines the de novo design engine EA-Inventor with a scoring function featuring the molecular docking program Surflex-Dock. This method employs tagged fragments, which are preserved substructures in EA-Inventor used for base fragment matching in Surflex-Dock, for constructing ligand structures under specific binding motifs. In addition, a target score mechanism is adopted that allows EAISFD to deliver a diverse set of desired structures. This method can be used to design novel ligand scaffolds (lead generation) or to optimize attachments on a fixed scaffold (lead optimization). EAISFD has successfully suggested many known inhibitor scaffolds as well as a number of new scaffold types when applied to p38 MAP kinase.     

Toward an Efficient Approach to Identify Molecular Scaffolds Possessing Selective or Promiscuous Compounds

The concept of a recurrent scaffold present in a series of structures is common in medicinal drug discovery. We present a scaffold analysis of compounds screened across 100 sequence‐unrelated proteins to identify scaffolds that drive promiscuity or selectivity. Selectivity and promiscuity play a major role in traditional and poly‐pharmacological drug design considerations. The collection employed here is the first publicly available data set containing the complete screening profiles of more than 15 000 compounds from different sources. In addition, no scaffold analysis of this data set has been reported. The protocol described here employs the Molecular Equivalence Index tool to facilitate the selection of Bemis–Murcko frameworks in the data set, which contain at least five compounds and Scaffold Hunter to generate a hierarchical tree of scaffolds. The annotation of the scaffold tree with protein‐binding profile data enabled the successful identification of mostly highly specific compounds, due to data set constraints. We also applied this approach to a public set of 1497 small molecules screened non‐uniformly across a panel of 172 protein kinases. The approach is general and can be applied to any other data sets and activity readout.     

Searching for new antimalarial therapeutics amongst known drugs

The need to discover and develop new antimalarial therapeutics is overwhelming. The annual mortality attributed to malaria, currently approximately 2.5 million, is increasing due primarily to widespread resistance to currently used drugs. One strategy to identify new treatment alternatives for malaria is to examine libraries of diverse compounds for the possible identification of novel scaffolds. Beginning with libraries of drug or drug-like compounds is an ideal starting point because, in the case of approved drugs, substantial pharmacokinetic and toxicologic data should be available for each compound series. We have employed a high-throughput screen of the MicroSource Spectrum and Killer Collections, a library of known drugs, bioactive compounds, and natural products. Our screening assay identifies compounds that inhibit growth of Plasmodium falciparum cultured in human erythrocytes. We have identified 36 novel inhibitors of P. falciparum, of which 19 are therapeutics, and five of these drugs exhibit effective 50% inhibitory concentrations within similar ranges to therapeutic serum concentrations for their recently indicated uses: propafenone, thioridazine, chlorprothixene, perhexiline, and azlocillin. The findings we report here indicate that this is an effective strategy to identify novel scaffolds and therefore aid in antimalarial drug discovery efforts.     

Beyond Topoisomerase Inhibition: Antitumor 1,4‐Naphthoquinones as Potential Inhibitors of Human Monoamine Oxidase

Monoamine oxidase (MAO) action has been involved in the regulation of neurotransmitters levels, cell signaling, cellular growth, and differentiation as well as in the balance of the intracellular polyamine levels. Although so far obscure, MAO inhibitors are believed to have some effect on tumors progression. 1,4‐naphthoquinone (1,4‐NQ) has been pointed out as a potential pharmacophore for inhibition of both MAO and DNA topoisomerase activities, this latter associated with antitumor activity. Herein, we demonstrated that certain antitumor 1,4‐NQs, including spermidine‐1,4‐NQ, lapachol, and nor‐lapachol display inhibitory activity on human MAO‐A and MAO‐B. Kinetic studies indicated that these compounds are reversible and competitive MAO inhibitors, being the enzyme selectivity greatly affected by substitutions on 1,4‐NQ ring. Molecular docking studies suggested that the most potent MAO inhibitors are capable to bind to the MAO active site in close proximity of flavin moiety. Furthermore, ability to inhibit both MAO‐A and MAO‐B can be potentialized by the formation of hydrogen bonds between these compounds and FAD and/or the residues in the active site. Although spermidine‐1,4‐NQs exhibit antitumor action primarily by inhibiting topoisomerase via DNA intercalation, our findings suggest that their effect on MAO activity should be taken into account when their application in cancer therapy is considered.     

Structural and Activity Profile Relationships Between Drug Scaffolds

Core structures of current drugs have been assembled and their structural relationships and activity profiles have been explored. Drug scaffolds were frequently involved in different types of structural relationships. In addition, a variety of activity profile relationships between structurally related drug scaffolds were detected, ranging from closely overlapping to distinct profiles. Furthermore, when structural and activity profile relationships of scaffolds from drugs and bioactive compounds were compared, systematic differences were detected. Consensus activity profiles were introduced as a new approach for the qualitative and quantitative assessment of activity similarity of structurally related drugs represented by the same scaffold. On the basis of consensus activity profiles, scaffolds representing drugs active against distinct targets can be distinguished from drugs having similar target profiles and target hypotheses can be derived for individual drugs. Given the results of our analysis, drug scaffolds have been systematically organized according to structural and activity profile criteria. Our scaffold sets and the associated information are made freely available.

Electronic supplementary material

The online version of this article (doi:10.1208/s12248-015-9737-5) contains supplementary material, which is available to authorized users.KEY WORDS: activity profiles, bioactive compounds, approved drugs, scaffolds, structural relationships