Exploiting structural information in patent specifications for key compound prediction

Patent specifications are one of many information sources needed to progress drug discovery projects. Understanding compound prior art and novelty checking, validation of biological assays, and identification of new starting points for chemical explorations are a few areas where patent analysis is an important component. Cheminformatics methods can be used to facilitate the identification of so-called key compounds in patent specifications. Such methods, relying on structural information extracted from documents by expert curation or text mining, can complement or in some cases replace the traditional manual approach of searching for clues in the text. This paper describes and compares three different methods for the automatic prediction of key compounds in patent specifications using structural information alone. For this data set, the cluster seed analysis described by Hattori et al. (Hattori, K.; Wakabayashi, H.; Tamaki, K. Predicting key example compounds in competitors' patent applications using structural information alone. J. Chem. Inf. Model.2008, 48, 135-142) is superior in terms of prediction accuracy with 26 out of 48 drugs (54%) correctly predicted from their corresponding patents. Nevertheless, the two new methods, based on frequency of R-groups (FOG) and maximum common substructure (MCS) similarity measures, show significant advantages due to their inherent ability to visualize relevant structural features. The results of the FOG method can be enhanced by manual selection of the scaffolds used in the analysis. Finally, a successful example of applying FOG analysis for designing potent ATP-competitive AXL kinase inhibitors with improved properties is described.     

Exploring sets of molecules from patents and relationships to other active compounds in chemical space networks

Patents from medicinal chemistry represent a rich source of novel compounds and activity data that appear only infrequently in the scientific literature. Moreover, patent information provides a primary focal point for drug discovery. Accordingly, text mining and image extraction approaches have become hot topics in patent analysis and repositories of patent data are being established. In this work, we have generated network representations using alternative similarity measures to systematically compare molecules from patents with other bioactive compounds, visualize similarity relationships, explore the chemical neighbourhood of patent molecules, and identify closely related compounds with different activities. The design of network representations that combine patent molecules and other bioactive compounds and view patent information in the context of current bioactive chemical space aids in the analysis of patents and further extends the use of molecular networks to explore structure–activity relationships.     

Congenericity of Claimed Compounds in Patent Applications

A method is presented to analyze quantitatively the degree of congenericity of claimed compounds in patent applications. The approach successfully differentiates patents exemplified with highly congeneric compounds of a structurally compact and well defined chemical series from patents containing a more diverse set of compounds around a more vaguely described patent claim. An application to 750 common patents available in SureChEMBL, SureChEMBLccs and ChEMBL is presented and the congenericity of patent compounds in those different sources discussed.     

Diamonds are a chemist's best friend: diamondoid chemistry beyond adamantane

Marilyn Monroe knew that "diamonds are a girl's best friend" but, in the meantime, many chemists have realized that they are also extremely attractive objects in contemporary chemistry. The chemist's diamonds are usually quite small (herein: nanometer-sized "diamondoids") and as a result of their unique structure are unusual chemical building blocks. Since lower diamondoids (up to triamantane) have recently become available in large amounts from petroleum and higher diamondoids (starting from tetramantane) are now also accessible from crude oil new research involving them has begun to emerge. Having well-defined structures makes these cage compounds so special compared to other nanometer-scale diamonds. Selective and high-yielding synthetic approaches to the functionalization of diamondoids gives derivatives that can find applications in, for example, polymers, coating materials, drugs, and molecular electronics.     

Open-access high-resolution mass spectrometry in early drug discovery

Techniques such as mass spectrometry and NMR spectroscopy form an essential part of the medicinal chemist's toolbox for characterizing and assessing the purity of new molecules. Empowering medicinal chemists to gain early insight into their reaction products has a direct impact on productivity. Devolution of cutting-edge techniques from the specialist to the bench chemist also frees the specialist to concentrate on solving the more demanding of analytical problems. For open-access techniques to be taken up, they must be robust and be able to handle differing sample concentrations and varying sample complexities. This paper details the implementation of high-resolution liquid chromatography/mass spectrometry in open access to aid the medicinal chemist in characterizing desired products and identifying unexpected rearrangements, by-products and complete unknowns.     

Therapeutic importance of synthetic thiophene

Thiophene and its substituted derivatives are very important class of heterocyclic compounds which shows interesting applications in the field of medicinal chemistry. It has made an indispensable anchor for medicinal chemists to produce combinatorial library and carry out exhaustive efforts in the search of lead molecules. It has been reported to possess a wide range of therapeutic properties with diverse applications in medicinal chemistry and material science, attracting great interest in industry as well as academia. It has been proven to be effectual drugs in present respective disease scenario. They are remarkably effective compounds both with respect to their biological and physiological functions such as anti-inflammatory, anti-psychotic, anti-arrhythmic, anti-anxiety, anti-fungal, antioxidant, estrogen receptor modulating, anti-mitotic, anti-microbial, kinases inhibiting and anti-cancer. Thus the synthesis and characterization of novel thiophene moieties with wider therapeutic activity is a topic of interest for the medicinal chemist to synthesize and investigate new structural prototypes with more effective pharmacological activity. However, several commercially available drugs such as Tipepidine, Tiquizium Bromides, Timepidium Bromide, Dorzolamide, Tioconazole, Citizolam, Sertaconazole Nitrate and Benocyclidine also contain thiophene nucleus. Therefore, it seems to be a requirement to collect recent information in order to understand the current status of the thiophene nucleus in medicinal chemistry research.     

A Review on the Main Phytoconstituents,Traditional Uses,Inventions, and Patent Literature of Gum Arabic Emphasizing Acacia seyal

Acacia seyal is an important source of gum Arabic. The availability, traditional, medicinal, pharmaceutical, nutritional, and cosmetic applications of gum acacia have pronounced its high economic value and attracted global attention. In addition to summarizing the inventions/patents applications related to gum A. seyal, the present review highlights recent updates regarding its phytoconstituents. Traditional, cosmetic, pharmaceutical, and medicinal uses with the possible mechanism of actions have been also reviewed. The patent search revealed the identification of 30 patents/patent applications of A. seyal. The first patent related to A. seyal was published in 1892, which was related to its use in the prophylaxis/treatment of kidney and bladder affections. The use of A. seyal to treat cancer and osteoporosis has also been patented. Some inventions provided compositions and formulations containing A. seyal or its ingredients for pharmaceutical and medical applications. The inventions related to agricultural applications, food industry, cosmetics, quality control of gum Arabic, and isolation of some chemical constituents (L-rhamnose and arabinose) from A. seyal have also been summarized. The identification of only 30 patents/patent applications from 1892 to 15 November 2021 indicates a steadily growing interest and encourages developing more inventions related to A. seyal. The authors recommend exploring these opportunities for the benefit of society.     

Touching proteins with virtual bare hands

The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more effective next generation drugs. It is currently common practice among medicinal chemists while attempting the above to access the information contained in three-dimensional structures by using two-dimensional projections, which can preclude disclosure of useful features. A more accessible and intuitive visualization of the three-dimensional configuration of the atomic geometry in the models can be achieved through the implementation of immersive virtual reality (VR). While bespoke commercial VR suites are available, in this work, we present a freely available software pipeline for visualising protein structures through VR. New consumer hardware, such as the HTC Vive and the Oculus Rift utilized in this study, are available at reasonable prices. As an instructive example, we have combined VR visualization with fast algorithms for simulating intramolecular motions of protein flexibility, in an effort to further improve structure-led drug design by exposing molecular interactions that might be hidden in the less informative static models. This is a paradigmatic test case scenario for many similar applications in computer-aided molecular studies and design.     

Microwave‐activated Synthesis of Pyrroles: A Short Review

In the current scenario for continuous requirement of better drugs, medicinal chemists must visage the challenging task of preparing novel patentable compounds, combining high activity and selectivity, good drug‐likeness, and pharmacokinetic properties. There is an acute need of new molecules in both lead identification and lead optimization. Chemists thoroughly scrutinize ways to simplify synthetic protocols using green chemistry approaches, for example, microwaves. Reduction in the reaction time by the use of microwaves has emerged as a promising method for bringing out new leads in organic synthesis. Among the azaheterocyclic systems, synthesis of pyrrole moiety has been a highly attractive and an inspiring proposition. It has been found to be an inbuilt pharmacophore of various momentous pharmacologically active compounds in medicinal chemistry. This article outlines the basic principles of microwave technology and its use in the synthesis of pyrrole derivatives wherein this technology has made a tremendous impact.     

Virtual screening and library enumeration of new hydroxycinnamates based antioxidant compounds: A complete framework

Designing of molecules for drugs is important topic from many decades. The search of new drugs is very hard, and it is expensive process. Computer assisted framework can provide the fastest way to design and screen drug-like compounds. In present work, a multidimensional approach is introduced for the designing and screening of antioxidant compounds. Antioxidants play a crucial role in ensuring that the body's oxidizing and reducing species are kept in the proper balance, minimizing oxidative stress. Machine learning models are used to predict antioxidant activity. Three hydroxycinnamates are selected as standard antioxidants. Similar compounds are searched from ChEMBL database using chemical structural similarity method. The libraries of new compounds are generated using evolutionary method. New compounds are also designed using automatic decomposition and construction building blocks. The antioxidant activity of all designed and searched compounds is predicted using machine learning models. The chemical space of searched and generated compounds is envisioned using t-distributed stochastic neighbor embedding (t-SNE) method. Best compounds are shortlisted, and their synthetic accessibility is predicted to further facilitate the experimental chemists. The chemical similarity between standard and selected compounds is also studied using fingerprints and heatmap.     

Intuitive patent Markush structure visualization tool for medicinal chemists

A Markush, or generic structure, is a widely used convention in chemical and pharmaceutical patents. The flexibility and complexity of this format, however, preclude an easy understanding and analysis of chemical space. In this paper, an application package called MarVis (Markush Visualization) is introduced to help chemists visualize Markush structures in chemical patents. MarVis can output a report with the Markush structure showing the query substructure and also an R-group table of all the possible R-groups described in the patent. MarVis also has a unique interactive interface that allows chemists to explore and zoom in the chemical space to find a subset of interest. SMILES, with minimal extensions, was used to facilitate a variety of patent Markush structure studies.     

Fluorine chemistry statistics: numbers of organofluorine compounds and publications associated with fluorine chemistry

Data are presented which demonstrate the considerable growth in the numbers of new organofluorine compounds produced annually, and also the numbers of papers and patents published concerned with fluorine chemistry. An overview of some information sources of relevance to fluorine chemists is also presented.     

Fast log P determination by ultra-high-pressure liquid chromatography coupled with UV and mass spectrometry detections

Ultra-high-pressure liquid chromatography (UHPLC) systems able to work with columns packed with sub-2 μm particles offer very fast methods to determine the lipophilicity of new chemical entities. The careful development of the most suitable experimental conditions presented here will help medicinal chemists for high-throughput screening (HTS) log P _oct measurements. The approach was optimized using a well-balanced set of 38 model compounds and a series of 28 basic compounds such as β-blockers, local anesthetics, piperazines, clonidine, and derivatives. Different organic modifiers and hybrid stationary phases packed with 1.7-μm particles were evaluated in isocratic as well as gradient modes, and the advantages and limitations of tested conditions pointed out. The UHPLC approach offered a significant enhancement over the classical HPLC methods, by a factor 50 in the lipophilicity determination throughput. The hyphenation of UHPLC with MS detection allowed a further increase in the throughput. Data and results reported herein prove that the UHPLC-MS method can represent a progress in the HTS-measurement of lipophilicity due to its speed (at least a factor of 500 with respect to HPLC approaches) and to an extended field of application. Figure The UHPLC approach described here greatly enhanced the time required for log P determination (5' min by compound using UV detection) and, at least, 8 compounds measured in a 5' run when Mass Spectrometry detection in used. These developments offer to medicinal chemists a high-throughput method to estimate the lipophilicity of NCEs Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Experimental section for capillary electrophoresis (CE) measurements, list of the 38 compounds of the calibration set and solvatochromic analyses of the extrapolated retention factors and partition coefficients.     

Using bibliometric analyses of patent literature for predicting the clinical fates of developing drugs.

Certain bibliometric features of the early literatures of developing drugs can be used to predict their ultimate clinical fates. The chronological sequence of publications is expressed as a binary vector with 1 for a patent and 0 for a nonpatent. The decimal equivalents for standardized vector lengths provide scalar values for comparing one drug with another. In order to incorporate concordant patents, fuzzy subsets are employed, with the number of attempts required to achieve transitive closure being the values for comparison. The methods involved are described using minoxidil as an example.     

Iranian chemist’s efforts to provide various effective methods for the synthesis of xanthenes

Xanthenes and their derivatives as very important classes of organic compounds are key structural elements of many biologically active compounds. These materials are important heterocyclic nucleus of various dyes and drugs. Because of their wide range of pharmacological, industrial and synthetic applications, many methods for the preparation of xanthenes are reported in the literature. In recent years, among the other chemists, introduction of new methods for the preparation of these types of compounds has attracted the attention of Iranian chemists. The result of these efforts is the introduction of appropriate, effective and efficient methods. In this paper, we have a brief review on these methods and their main advantages and important applicabilities.     

Open-access liquid chromatography/mass spectrometry in a drug discovery environment

The use of open-access mass spectrometry to monitor synthetic chemistry reactions, and also the integrity and purity of new chemical entities, has been a part of the medicinal chemist's tool-box for more than 5 years. Originally in our group at Wyeth Research there were two open-access methods available to the chemists, flow injection analysis (FIA) and liquid chromatography/mass spectrometry (LC/MS). The FIA method was approximately 3 min long, while the LC/MS method was approximately 20 min long (including an 8 min gradient). Within the first 2 years, the total number of open-access analyses increased by approximately 125%. It is interesting, however, that the number of LC/MS analyses increased by more than 285%. This is attributed to the fact that the chemists began using the LC/MS data to monitor reactions and also to check final product integrity and purity. In addition, the number of chemists performing parallel synthesis reactions has increased; thus, individual chemists can produce sample sets of up to 100 vials. This paper describes the implementation of new methodology, which accommodates the need for much faster run times and also the ability to acquire alternating positive and negative ion spectra within the same run. In addition, the instrument has been configured to e-mail the resulting processed data report to the submitting chemist. Several methods have been developed, including structure elucidation using in-source collision-induced dissociation (CID) and night-time analysis. The LC/MS methods for this system are described herein and are applicable to both industrial and academic synthetic chemistry optimization efforts.     

Terahertz spectroscopy: a powerful new tool for the chemical sciences?

Terahertz spectroscopy is only now beginning to make its transition from initial development by physicists and engineers to broader use by chemists, materials scientists and biologists, thanks to the increasing availability of commercial terahertz spectrometers. With the unique insights that terahertz spectroscopy can provide into intermolecular bonding and crystalline matter, it could prove to be an invaluable addition to the chemist's analytical toolset. This tutorial review aims to give an introduction to terahertz spectroscopy, its techniques, equipment, current applications and potential for the chemical sciences to a broad readership.     

Preparative Scale Applications of C−H Activation in Medicinal Chemistry

C−H activation is an attractive methodology to increase molecular complexity without requiring substrate prefunctionalization. In contrast to well-established cross-coupling methods, C−H activation is less explored on large scales and its use in the production of pharmaceuticals faces substantial hurdles. However, the inherent advantages, such as shorter synthetic routes and simpler starting materials, motivate medicinal chemists and process chemists to overcome these challenges, and exploit C−H activation steps for the synthesis of pharmaceutically relevant compounds. In this review, we will cover examples of drugs/drug candidates where C−H activation has been implemented on a preparative synthetic scale (range between 355 mg and 130 kg). The optimization processes will be described, and each example will be examined in terms of its advantages and disadvantages, providing the reader with an in-depth understanding of the challenges and potential of C−H activation methodologies in the production of pharmaceuticals.     

LeadScope: software for exploring large sets of screening data

Modern approaches to drug discovery have dramatically increased the speed and quantity of compounds that are made and tested for potential potency. The task of collecting, organizing, and assimilating this information is a major bottleneck in the discovery of new drugs. We have developed LeadScope a novel, interactive computer program for visualizing, browsing, and interpreting chemical and biological screening data that can assist pharmaceutical scientists in finding promising drug candidates. The software organizes the chemical data by structural features familiar to medicinal chemists. Graphs are used to summarize the data, and structural classes are highlighted that are statistically correlated with biological activity.     

Computational platform Way2Drug: from the prediction of biological activity to drug repurposing

The Way2Drug informational-computational platform (www.way2drug.com/dr) provides access to the data on drugs approved for medicinal use in the USA and Russian Federation, as well as computational possibilities for the prediction of biological activity of drug-like organic compounds. Currently realized computational tools of the platform, which allow one to predict several thousands of biological activity types, including the interaction with molecular targets, pharmacotherapeutic and side effects, metabolism, acute toxicity for rats, cytotoxicity, influence on gene expression, and other properties characterizing the evaluation how promising are particular drug-like compounds as potential pharmaceuticals, are reviewed. Using the Way2Drug platform, one can not only select the most promising "hits" for the synthesis and testing of biological activity but also reveal new indications for the launched drugs.