Rationalizing Structure and Target Relationships between Current Drugs

A recent analysis of structure and target relationships between current drugs and bioactive compounds has revealed that only a small fraction of drugs that are active against the same or overlapping targets are involved in substructure relationships and/or share the same topology. By contrast, structurally related drugs displayed a tendency to preferentially act against different targets. For bioactive compounds, opposite trends were observed. These surprising findings arising from the global analysis have now been examined in detail by analyzing structure and target relationships between drugs at the level of individual targets and individual drugs and by comparing the results of local (target- or drug-based) and global relationship analysis. On the basis of target-based analysis, on average, only 14% of drugs active against a given target form well-defined structural relationships. In addition, drug-based analysis revealed that on average 72% of all structurally related drugs have no or at most 20% target overlap. Taken together, the results of our current analysis at the level of single targets and drugs rationalize their unexpected structure and target relationships in a consistent manner. These findings also have implications for ligand binding characteristics of popular drug targets and for frequently observed polypharmacological drug behavior.     

HierS: hierarchical scaffold clustering using topological chemical graphs

An exhaustive ring-based algorithm, HierS, has been developed in order to provide an intuitive approach to compound clustering for analyzing high-throughput screening results. The recursive algorithm rapidly identifies all possible ring-delimited substructures within a set of compounds. Molecules are grouped by shared ring substructures (scaffolds) so that common scaffolds obtain higher membership. Once all of the scaffolds for a set of compounds are identified, the hierarchical structural relationships between the scaffold structures are established. The complex network of hierarchical relationships is then utilized to navigate compounds in a structurally directed fashion. When the scaffold hierarchy is traversed, over-represented structural features can be rapidly identified so that excess compounds that contain them can be removed without significantly impacting the structural diversity landscape of the compound set. Furthermore, the removed compounds can provide the opportunity to follow-up on active compounds that had previously been discarded because of practical limitations on follow-up capacity. A Web-based interface has been developed that incorporates this algorithm in order to allow for an interactive analysis. In addition, biological data are coupled to scaffolds by the inclusion of activity histograms, which indicate how the compounds in each scaffold class performed in previous high-throughput screening campaigns.     

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.     

Many Approved Drugs Have Bioactive Analogs With Different Target Annotations

Close structural relationships between approved drugs and bioactive compounds were systematically assessed using matched molecular pairs. For structural analogs of drugs, target information was assembled from ChEMBL and compared to drug targets reported in DrugBank. For many drugs, multiple analogs were identified that were active against different targets. Some of these additional targets were closely related to known drug targets while others were not. Surprising discrepancies between reported drug targets and targets of close structural analogs were often observed. On one hand, the results suggest that hypotheses concerning alternative drug targets can often be formulated on the basis of close structural relationships to bioactive compounds that are easily detectable. It is conceivable that such obvious structure–target relationships are frequently not considered (or might be overlooked) when compounds are developed with a focus on a primary target and a few related (or undesired) ones. On the other hand, our findings also raise questions concerning database content and drug repositioning efforts.     

How Promiscuous Are Pharmaceutically Relevant Compounds? A Data-Driven Assessment

Given the increasing notion of target promiscuity of bioactive compounds and polypharmacological drug behavior, a detailed analysis of publicly available compound activity data from medicinal chemistry sources was carried out to determine and quantify the degree of promiscuity of active compounds across all known human target families. The results are surprising. Approximately 62% of currently available compounds with high-confidence activity data are only annotated with a single biological target, whereas 36% are known to act against multiple targets within the same family (i.e., closely related targets). However, only ～2% of bioactive compounds are promiscuous across different target families. Thus, despite general data sparseness, these findings indicate that highly promiscuous bioactive compounds only rarely occur. Because pharmaceutically relevant active compounds represent the pool from which drug candidates emerge, one might extrapolate from these results and conclude that there is a low statistical probability to obtain drugs that act against multiple targets belonging to distinct families.     

药物分子设计的策略：论药效团和骨架迁越

药物分子是由药效团和结构骨架构成的，药效团是由不连续的离散的原子、基团或片断所构成，但需结合在分子骨架上，形成具体的分子。骨架具有连续性，相同的药效团附着在不同的分子骨架上，构成了作用于同一靶标而结构多样的化合物。骨架依据受体的柔性和可塑性形成了“杂乱性”的空间。显示了受体结合部位的杂乱性。杂乱性越大，可容纳的配体分子的结构多样性就越多，意味着结构修饰与变换的余地大，成药的机会多。由苗头化合物演化成先导物，进而优化成候选药物，这由化合物变革成安全、有效、稳定、可控的药物过程就是保持药效团、变换分子骨架、修饰基团和边链的过程。结构骨架的变化可分为3个层次：以电子等排原理变换骨架结构；以优势结构为导向变换骨架结构；以结构一活性演化的方式变换骨架结构，即骨架迁越。骨架迁越的目的是改善分子的物化、药代、稳定性和赋予分子的结构新颖性。该文以实例阐述了骨架变换的方法与技巧。     

2-Phenylindole and Arylsulphonamide: Novel Scaffolds Bactericidal against Mycobacterium tuberculosis

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Classification of scaffold-hopping approaches

The general goal of drug discovery is to identify novel compounds that are active against a preselected biological target with acceptable pharmacological properties defined by marketed drugs. Scaffold hopping has been widely applied by medicinal chemists to discover equipotent compounds with novel backbones that have improved properties. In this article we classify scaffold hopping into four major categories, namely heterocycle replacements, ring opening or closure, peptidomimetics and topology-based hopping. We review the structural diversity of original and final scaffolds with respect to each category. We discuss the advantages and limitations of small, medium and large-step scaffold hopping. Finally, we summarize software that is frequently used to facilitate different kinds of scaffold-hopping methods.     

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.     

ScafBank: a public comprehensive Scaffold database to support molecular hopping

Aim:

The search for molecules whose bioactivities are similar to those of given compounds or to optimize the initial lead compounds from high throughput screening has attracted increasing interest in recent years. Our goal is to provide a publically searchable database of scaffolds out from a large collection of existing chemical molecules.

Results:

Although a number of in silico methods have emerged to facilitate this process, which has become known as ”scaffold hopping” or “molecular hopping”, there is an urgent need for a database system to provide such valuable data in the drug design field. Here we have systematically analyzed a collection of commercially available small molecule databases and a bioactive compound database to identify unique scaffolds and we have built apublically searchable database. The analysis of approximately 4 800 000 of these compounds identified 241 824 unique scaffolds, which are stored in a relational database (http://202.127.30.184:8080/db.html). Each entry in the database is associated with a molecular occurrence and includes its distribution of molecular properties, such as molecular weight, logP, hydrogen bond acceptor number, hydrogen bond donor number, rotatable bond number and ring number. More importantly, for scaffolds derived from the bioactive compounds database, it also contains the original compounds and their target information.

Conclusion:

This Web-based database system could help researchers in the fields of medicinal and organic chemistry to design novel molecules with properties similar to the original compounds, but built on novel scaffolds.     

Electrospun nanofibrous polymeric scaffold with targeted drug release profiles for potential application as wound dressing

We have successfully fabricated a dual drug release electrospun scaffold containing an anesthetic, lidocaine, and an antibiotic, mupirocin. Two drugs with different lipophilicities were electrospun from a poly-l-lactic acid (PLLA) solution with a dual spinneret electrospinning apparatus into a single scaffold. The release of the drugs from the scaffold showed different profiles for the two drugs. Lidocaine hydrochloride exhibited an initial burst release (80% release within an hour) followed by a plateau after the first few hours. Mupirocin exhibited only a 5% release in the first hour before experiencing a more sustained release to provide antibacterial action for over 72 h. For comparative purposes, both drugs were spun from a single spinneret and evaluated to determine their release profiles. The scaffold maintained its antibiotic activity throughout the processes of electrospinning and gas sterilization and supported cell viability. It has been reported in the literature that interactions between polymer and drug are known to govern the pattern of drug release from electrospun scaffolds. Here, it was found that the presence of the two drugs in the same polymer matrix altered the release kinetics of at least one drug. Based on the release profiles obtained, the dual spinneret technique was the preferred method of scaffold fabrication over the single spinneret technique to obtain a prototype wound healing device.     

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.     

Synthesis,analgesic and anti-inflammatory activities of new methyl-imidazolyl-1,3,4-oxadiazoles and 1,2,4-triazoles

Background

Long-term clinical employment of nonsteroidal anti-inflammatory drugs (NSAIDs) is associated with significant side effects including gastrointestinal (GI) lesions and kidney toxicity. In this paper we designed and synthesized new imidazolyl-1,3,4-oxadiazoles and 1,2,4-triazoles by molecular hybridization of previously described anti-inflammatory compounds in the hope of obtaining new safer analgesic and anti-inflammatory agents.

Methods

The target structures were synthesized by preparation of 5-methyl-1H-imidazole-4-carboxylic acid ethyl ester 5. The reaction of hydrazine hydrate with this ester afforded the 5-methyl-1H-imidazole-4-carboxylic acid hydrazide 6 which was converted to target compounds 7-15 according to the known procedures. In silico toxicity risk assessment and drug likeness predictions were done, in order to consider the privileges of the synthesized structures as drug candidates.

Results and discussion

The analgesic and anti-inflammatory profile of the synthesized compounds were evaluated by writhing and carrageenan induced rat paw edema tests respectively. Compounds 8, 9 and 11-13 and 15 were active analgesic agents and compounds 8, 9 and 11-13 showed significant anti-inflammatory response in comparison with control. Compounds 11 and 13 were screened for their ulcerogenic activities and none of them showed significant ulcerogenic activity. The active Compounds 11 and 12 showed the highest drug likeness and drug score.

Conclusions

The analgesic and anti-inflammatory activities of title compounds were comparable to that of standard drug indomethacin with a safer profile of activity. The results revealed that both of oxadiazole and triazole scaffolds can be determined as pharmacophores. The in silico predictions and pharmacological evaluations showed that compounds 11 and 12 can be chosen as lead for further investigations.     

Solid-phase synthesis of a library of amphipatic hydantoins. Discovery of new hits for TRPV1 blockade

Some heterocyclic systems, called privileged scaffolds, appear frequently in bioactive products and marketed drugs. The combination of a recognized privileged scaffold (hydantoin) and a functional group with high incidence in bioactive molecules (guanidine) guided the design of a library of amphipatic compounds, which allowed the discovery of novel TRPV1 ion channel blockers. The library was synthesized by parallel solid-phase synthesis from an orthogonally protected resin-bound Lys-Lys skeleton. Key steps of the synthetic procedure were the construction of the hydantoin ring, by reaction of the N-terminal amino group with N,N-disuccinimidyl carbonate (DSC) and subsequent base-induced cyclization, and the guanidinylation of the C-terminal Lys side-chain after removal of the Alloc protecting-group. The preliminary biological studies have allowed the identification of some of the key structural features directing the blockage of capsaicin-induced Ca(2+) influx through TRPV1 channels, particularly, the strong preference showed for highly lipophilic acyl groups and substituted guanidine moieties. Active compounds based on this new pharmacophoric scaffold that display in vitro and in vivo inhibitory activity.     

Recent advances in antiviral activity of benzo/heterothiadiazine dioxide derivatives

Benzo/heterothiadiazine dioxides have been identified as important fused heterocyclic systems possessing a broad spectrum of biological activities and potential pharmacological applications. Recently, a large number of structurally novel compounds derived from these heterocycle scaffolds were identified as antiviral agents. Especially, substituted benzo/heterothiadiazine dioxide derivatives have been shown to inhibit the replication of HCMV, VZV, HCV and HIV. Of particular interest, some potent HCV polymerase inhibitors possess a benzothiadiazine dioxide scaffold, which is critical for the anti-HCV potency through strong hydrogen bond formation of the SO(2)NH group with the active site of the enzyme, as shown by X-ray crystallography. Also, some compounds belonging to the benzothiadiazine dioxide class have been found to be potent antiviral agents against HCMV and VZV. Moreover, some novel heterothiadiazine dioxide derivatives have been synthesized and evaluated as potential HIV inhibitors with lower toxicity and/or increased activity against drug-resistant virus strains. No systematic review is available in the literature on these thiadiazine derivatives in the design of potent antiviral inhibitors. In this article, we review the recent advances in the antiviral profile of this kind of compounds, as well as the impact of structural modifications and the structure-activity relationship (SAR).     

Enhancing marine natural product structural diversity and bioactivity through semisynthesis and biocatalysis

In the last several decades the plants, animals and microbes from the marine environment have revealed a portion of what is clearly a tremendous resource for structurally diverse and bioactive secondary metabolites. Many of these extraordinarily sophisticated and bioactive natural products can be isolated in significant quantities without great difficulty. As a result these readily available bioactive natural products provide valuable starting materials for the rational generation of libraries of compounds prepared through semisynthesis and biocatalysis. A review of our work using marine natural products to generate rationally designed compound libraries and their biological activity against infectious diseases, cancer and neurological targets is presented. The marine natural products utilized to date as starting materials consist of compounds from a variety of structural classes and include: aureol, puupehenone, sarcophine, palinurin, and the manzamine alkaloids. The possibility to generate diverse bioactive products beginning with a marine natural product scaffold is a direct result of improvements made in the technologies to harvest samples from the ocean, purify and characterize complex natural products quickly and complete chemical reactions and biotransformations in parallel. As a result the vast resources of the ocean can now be utilized routinely to design and produce countless products to be evaluated as part of drug discovery and development programs.     

Composite polymer-bioceramic scaffolds with drug delivery capability for bone tissue engineering

Introduction: Next-generation scaffolds for bone tissue engineering (BTE) should exhibit the appropriate combination of mechanical support and morphological guidance for cell proliferation and attachment while at the same time serving as matrices for sustained delivery of therapeutic drugs and/or biomolecular signals, such as growth factors. Drug delivery from BTE scaffolds to induce the formation of functional tissues, which may need to vary temporally and spatially, represents a versatile approach to manipulating the local environment for directing cell function and/or to treat common bone diseases or local infection. In addition, drug delivery from BTE is proposed to either increase the expression of tissue inductive factors or to block the expression of others factors that could inhibit bone tissue formation. Composite scaffolds which combine biopolymers and bioactive ceramics in mechanically competent 3D structures, including also organic–inorganic hybrids, are being widely developed for BTE, where the affinity and interaction between biomaterials and therapeutic drugs or biomolecular signals play a decisive role in controlling the release rate.

Areas covered: This review covers current developments and applications of 3D composite scaffolds for BTE which exhibit the added capability of controlled delivery of therapeutic drugs or growth factors. A summary of drugs and biomolecules incorporated in composite scaffolds and approaches developed to combine biopolymers and bioceramics in composites for drug delivery systems for BTE is presented. Special attention is given to identify the main challenges and unmet needs of current designs and technologies for developing such multifunctional 3D composite scaffolds for BTE.

Expert opinion: One of the major challenges for developing composite scaffolds for BTE is the incorporation of a drug delivery function of sufficient complexity to be able to induce the release patterns that may be necessary for effective osseointegration, vascularization and bone regeneration. Loading 3D scaffolds with different biomolecular agents should produce a codelivery system with different, predetermined release profiles. It is also envisaged that the number of relevant bioactive agents that can be loaded onto scaffolds will be increased, whilst the composite scaffold design should exploit synergistically the different degradation profiles of the organic and inorganic components.