Research progress of feature-based deep learning for predicting compound-protein interaction / 中国药科大学学报

@#The prediction of compound-protein interaction (CPI) is a critical technological tool for discovering lead compounds and drug repurposing during the process of drug development.In recent years, deep learning has been widely used in CPI research, which has accelerated the development of CPI prediction in drug discovery.This review focuses on feature-based CPI prediction models.First, we described the datasets, as well as typical feature representation methods commonly used for compounds and proteins in CPI prediction.Based on the critical problems in modeling, we discussed models for CPI prediction from two perspectives: multimodal features and attention mechanisms.Then, the performance of 12 selected models was evaluated on 3 benchmark datasets for both classification and regression tasks.Finally, the review summarizes the existing challenges in this field and prospects for future directions.We believe that this investigation will provide some reference and insight for further research on CPI prediction.

Research progress of the screening and generation of lead compounds based on artificial intelligence model / 中国药科大学学报

@#Excellent lead compounds have a profound influence on drug development and can improve the success rate of product launch. It is expensive and time-consuming to discover lead compounds by traditional methods, yet artificial intelligence (AI) can discover good lead compounds efficiently.This article systematically summarizes the research progress of obtaining lead compounds through the screening and generation models of AI, classifies different models according to the type of information input, focuses on drug repurposing by screening model and multi-objective drug design by generation model, and discusses the development prospect of AI in the research field of lead compounds, aiming to provide new research ideas for the application of AI in lead compounds.

Research progress on the biological activity of pyrrole 1,2-α indole alkaloids / 中国基层医药

Pyrrole [1,2-α] indole is a novel fused heterocyclic skeleton, which is also the basic structural unit and synthetic intermediate of many natural active products and drugs. Pyrrole [1,2-α] indole heterocyclic derivatives have attracted much attention in organic synthesis and medicinal chemistry because of their extensive and marked biological activities. Plant extracts have always been an important source of active compounds. At present, the alkaloids based on the pyrrole [1,2-α] indole heterocyclic structure discovered and isolated from plant extracts include isatisine, isoborreverine, flinderoles, polyavolensin and yuremamine. This paper reviews the research progress on the biological activity of pyrrole [1,2-α] indole heterocyclic derivatives and has found that pyrrole [1,2-α] indole heterocyclic derivatives have a good development prospect in screening active compounds and developing candidate drugs.

Validation of compound C19 as a glutaminase C inhibitor / 药学学报

The mitochondrial enzyme glutaminase C (GAC) is highly expressed in a variety of cancer cells, resulting in increased glutamine metabolism and cancer development. Therefore, GAC has become a potential target for anti-tumor drug development. However, current GAC inhibitors shared similar structural characteristics, few new scaffolds were reported. By conducting a prokaryotic Escherichia coli expression system, human GAC protein of high-purity was obtained through lysozyme digestion combined with ultrasound dissociation, and cobalt magnetic beads purification, Moreover, we performed studies to validate interaction between small molecules and GAC protein through thermal shift assay, drug affinity responsive target stability assay, protein crosslinking and GAC enzyme activity detection. Meanwhile, a comprehensive small molecule-protein interaction confirmation and systematic pharmacodynamic study in vitro were carried out on compound C19, which was a reported GAC inhibitor screened from the Enamine database. Results showed that C19 directly bind to GAC protein, disturbed GAC tetramers formation, and inhibited its enzyme catalytic activity. By interfering GAC function, C19 dose-dependently suppressed GAC-mediated glutamine metabolism, reduced glutamate in cancer cells, and thus alleviated A549 and NCI-H1299 non-small cell lung cancer cell growth. Together, C19 was identified as a lead compound, providing a new strategy for the structural design of drugs targeting GAC.

Lead compound optimization strategy (8) - drug transporters and related drug design strategies / 药学学报

Transporters have a great influence on the transportation and distribution of drugs in the body. On the one hand, solute carrier transporters could transport drugs into tissues and organs, which may improve the oral bioavailability or change the tissue-distribution of the drugs. On the other hand, the ATP-binding cassette could pump some drugs out of the cell, which decreases the intracellular drug concentrations and leads to drug resistance. This paper summarizes the distribution, substrate characteristics and drug design strategies of several important drug transporters, such as improving bioavailability by prodrug design, introducing acid group to improve hepatic selectivity and adjusting the polarity of compounds to decrease efflux ratio.

Lead compound optimization strategy (7) —— modification strategies for peptides / 药学学报

Most peptides have high binding affinity and good selectivity for endogenous receptors and are good lead compounds to develop into drugs. Many approved drugs are derived from the structural optimization of peptide molecules, such as the antihypertensive drug captopril and the anti-hepatitis C drug telaprevir. At present, the main problems in the development of peptide drugs include poor stability, short half-life, and high plasma clearance rate; lack of oral availability and poor patient compliance, a complex production process, and high production cost. Therefore, rational modification of peptides can not only reduce the production cost, but also improve the druggability of the peptides. Here we review structural modification strategies for peptides from the perspective of improving their physicochemical properties. These modification strategies are divided into two parts: one is modification of the peptide backbone, including unnatural amino acid modification, pseudopeptide strategy, inverse-peptide strategy, cyclization strategy, and terminal structure modification. Another is modification of the side chains of peptides, including fatty acid conjugation, polyethylene glycol conjugation, protein fusion strategy, and cholesterol conjugation.

Advances in the study of antiviral natural products / 药学学报

Long-term use of approved antiviral drugs can lead to drug resistance and side effects. On the other hand, there are currently no antiviral drugs or vaccines available to treat some newly emerging virus infections. Therefore, antiviral drugs research has always been a hot research topic in the field of medicinal chemistry. Natural products are an important source of antiviral drugs. This article reviews the progress of antiviral natural products discovered in the past decade to provide potential lead compounds for drug development.

Screening of anti-depressant active ingredients in Acori Tatarinowii Rhizoma based on molecular docking technique / 中草药

Objective: To screen the anti-depressant active ingredients in Acori Tatarinowii Rhizoma by molecular docking technique. Methods: All the chemical constituents of Acori Tatarinowii Rhizoma were obtained by Traditional Chinese Medicine Pharmacology Database (TCMSP). Combined with oral bioavailability, 65 candidate compounds were obtained. The studied anti-depressant targets included monoamine oxidase A, dopamine transporter, serotonin transporter, and histamine H1 receptor. AutoDock Vina was used to explore the affinity and binding modes of the candidate compounds with the above targets. Results: There were 18 compounds from Acori Tatarinowii Rhizoma that could bind to the above four targets. Among them, four compounds could bind to four targets, three compounds could bind to two targets, and the other 11 compounds could interact with one target. Conclusion: Molecular docking technology can be used to investigate the molecular mechanism of Acori Tatarinowii Rhizoma and determine the active ingredients, which provides an alternative method for the discovery of novel anti-depressants and lead compounds from Chinese herbal medicines.

Discovery of lead compounds to inhibit proliferation of cervical cancer cells based on privileged structure of 6,11-dihydro-5H-benzoacarbazole / 上海交通大学学报（医学版）

Objective • To discover lead compounds with 6,11-dihydro-5H-benzo[a]carbazole as core scaffold that can inhibit the proliferation of cervical cancer cells. Methods • A series of 6,11-dihydro-5H-benzo[a]carbazole derivatives and analogs were synthesized using Fischer indole synthesis method, and their anticancer activity against HeLa cells was tested in vitro by CCK8 test. Results • 2-Methoxy-6,11-dihydro-5H-benzo[a]carbazole and 8-chloro-2- methoxy-6,11-dihydro-5H-benzo[a]carbazole could significantly inhibit the proliferation of HeLa cells with the half maximal inhibitory concentration (IC50) values of 9.61 μmol/L and 16.52 μmol/L, respectively. Conclusion • Two objective lead compounds were found. Among 6,11-dihydro-5H-benzo[a]carbazole derivatives, compounds with methoxy group at the C-2 position of the core scaffold show better activity against proliferation of cervical cancer cells.

Discovery of lead compounds to inhibit proliferation of cervical cancer cells based on privileged structure of 6,11-dihydro-5H-benzoacarbazole / 上海交通大学学报（医学版）

Objective·To discover lead compounds with 6,11-dihydro-5H-benzo[a]carbazole as core scaffold that can inhibit the proliferation of cervical cancer cells. Methods?·?A series of 6,11-dihydro-5H-benzo[a]carbazole derivatives and analogs were synthesized using Fischer indole synthesis method, and their anticancer activity against HeLa cells was tested in vitro by CCK8 test. Results?·?2-Methoxy-6,11-dihydro-5H-benzo[a]carbazole and 8-chloro-2-methoxy-6,11-dihydro-5H-benzo[a]carbazole could significantly inhibit the proliferation of HeLa cells with the half maximal inhibitory concentration ( IC50) values of 9.61?μmol/L and 16.52?μmol/L, respectively. Conclusion?·?Two objective lead compounds were found. Among 6,11-dihydro-5H-benzo[a]carbazole derivatives, compounds with methoxy group at the C-2 position of the core scaffold show better activity against proliferation of cervical cancer cells.

Lead compound optimization strategy (6)-improving the plasma stability / 药学学报

Plasma stability plays an important role in the druggability of lead compound. Improving the plasma stability of compounds by structural modification can lead to good pharmacokinetic and pharmacodynamics properties. This review provides a summary of varieties of structure modification strategies for improving plasma stability including bioisosterism, increasing steric hindrance, ring closure, scaffold hopping and etc.

A Progress on the Key Technologies for Discovery of Bioactive Compounds from Traditional Chinese Medicines / 世界科学技术-中医药现代化

Traditional Chinese medicines (TCM) is one of the most important sources of new drugs.The rapid development of modern science and technology has brought new opportunities for TCM.Admittedly,new academic theory is getting into a golden period of innovation.Key technologies that enbody TCM features and adapt to modern drug-screening requirements are urgently needed.After five years' endeavor,the authors' group has made great progress in the new theories and methodologies for the discovery of bioactive compounds from TCM.In this review,a total of five key technologies:library-bioactivity-structure integration,biological and chemical fishing technology,ligand-and receptor-based virtual screening,profile-bioactivity relationship and the technology for discovering bioactive equivalent combinatorial components (BECCs),were introduced.In the text,several valuable demonstrations over the TCM-based drug discovery were provided,for uncovering the scientific basis of TCM and accelerating the process of TCM modernization.

Active derivatives based on the resveratrol scaffold: Research advances / 国际药学研究杂志

Natural product resveratrol has antioxidation, cardiovascular protection and many other useful biological activities. In recent years, many researchers have paid more and more attention to it. However it cannot be used as candidate for the development of new drug due to its poor druggability. Novel resveratrol derivates with improved water solubility and highly potent biological activity could be obtained by chemical modifying of chemical structure of resveratrol. Researches have shown that resveratrol derivatives exhibit many kinds of attractive activities, including antitumor, reducing blood fat, antiviral, anti-neurodegenerative diseases and so on, which makes them could be used as leads for the further developing of new drugs. This review discusses the development of novel resveratrol derivatives by chemical modification in recent years.

Lead compound optimization strategy (5)-reducing the hERG cardiac toxicity in drug development / 药学学报

The potassium channel encoded by the human ether-a-go-go related gene (hERG) plays a very important role in the physiological and pathological processes in human. hERG potassium channel determines the outward currents which facilitate the repolarization of the myocardial cells. Some drugs were withdrawn from the market for the serious side effect of long QT interval and arrhythmia due to blockade of hERG channel. The strategies for lead compound optimization are to reduce inhibitory activity of hERG potassium channel and decrease cardiac toxicity. These methods include reduction of lipophilicity and basicity of amines, introduction of hydroxyl and acidic groups, and restricting conformation.

Active derivatives based on the resveratrol scaffold:research advances / 国际药学研究杂志

Natural product resveratrol has antioxidation,cardiovascular protection and many other useful biological activities. In recent years,many researchers have paid more and more attention to it. However it cannot be used as candidate for the development of new drug due to its poor druggability. Novel resveratrol derivates with improved water solubility and highly potent biological activity could be obtained by chemical modifying of chemical structure of resveratrol. Researches have shown that resveratrol derivatives exhib?it many kinds of attractive activities,including antitumor,reducing blood fat,antiviral,anti-neurodegenerative diseases and so on, which makes them could be used as leads for the further developing of new drugs. This review discusses the development of novel resve?ratrol derivatives by chemical modification in recent years..