Identification of a dihydroorotate dehydrogenase inhibitor thatinhibits cancer cell growth by proteomic profiling

Dihydroorotate dehydrogenase(DHODH)is a central enzyme of the de novo pyrimidine biosynthesis pathway and is a promising drug target for the treatment of cancer and autoimmune diseases.This study presents the identification of a potent DHODH inhibitor by proteomic profiling.Cell-based screening revealed that NPD723,which is reduced to H-006 in cells,strongly induces myeloid differentiation and inhibits cell growth in HL-60 cells.H-006 also suppressed the growth of various cancer cells.Proteomic profiling of NPD723-treated cells in ChemProteoBase showed that NPD723 was clustered with DHODH inhibitors.H-006 potently inhibited human DHODH activity in vitro,whereas NPD723 was approximately 400 times less active than H-006.H-006-induced cell death was rescued by the addition of the DHODH product orotic acid.Moreover,metabolome analysis revealed that H-006 treatment promotes marked accumulation of the DHODH substrate dihydroorotic acid.These results suggest that NPD723 is reduced in cells to its active metabolite H-006,which then targets DHODH and suppresses cancer cell growth.Thus,H-006-related drugs represent a potentially powerful treatment for cancer and other diseases.

GTD MODEL-BASED TIME-SHIFT INVARIANT TARGET IDENTIFICATION USING MATCHING PURSUITS AND LIKELIHOOD RATIO TESTS

In order to improve the identification capability of ultra wide-band radar,this paper in-troduces a step-variant multiresolution approach for the time-shift parameter estimation. Subsequently,combining with the approach,a Geometrical Theory of Diffraction(GTD) model-based time-shift Invariant method to target identification using Matching Pursuits and Likelihood Ratio Test(IMPLRT) is developed. Simulation results using measured scattering signatures of two targets in an ultra wide-band chamber are presented contrasting the performance of the IMPLRT to the Wang's MPLRT technique.

Simplified Modeling and Mathematical Analysis in Cardiac Electric Field Propagation for Human and Animals

The different characteristics of cardiac electric field(CEF)radiation in humans and other animals are presented in this paper.Physical modeling and mathematical analysis are developed to comprehensively unveil the properties of CEF,based on typical heartbeat waveforms.Our numerical simulation results demonstrate that the frequency bandwidths and the cycle durations of CEF are different for healthy humans versus humans on the verge of death and for humans versus other animals.The results indicate that the present study may extensively contribute towards recognizing human beings or other animal targets quickly and accurately with CEF in dangerous situations or in other applications.

Artificial Intelligence in Pharmaceutical Sciences

Drug discovery and development affects various aspects of human health and dramatically impacts the pharmaceutical market.However,investments in a new drug often go unrewarded due to the long and complex process of drug research and development(R&D).With the advancement of experimental technology and computer hardware,artificial intelligence(AI)has recently emerged as a leading tool in analyzing abundant and high-dimensional data.Explosive growth in the size of biomedical data provides advantages in applying AI in all stages of drug R&D.Driven by big data in biomedicine,AI has led to a revolution in drug R&D,due to its ability to discover new drugs more efficiently and at lower cost.This review begins with a brief overview of common AI models in the field of drug discovery;then,it summarizes and discusses in depth their specific applications in various stages of drug R&D,such as target discovery,drug discovery and design,preclinical research,automated drug synthesis,and influences in the pharmaceutical market.Finally,the major limitations of AI in drug R&D are fully discussed and possible solutions are proposed.

Natural products against hematological malignancies and identification of their targets

Naturally occurring molecules derived from higher plants, animals, microorganisms and minerals play an important role in the discovery and development of novel therapeutic agents. The identification of molecular targets is of interest to elucidate the mode of action of these compounds, and it may be employed to set up target-based assays and allow structure-activity relationship studies to guide medicinal chemistry efforts toward lead optimization. In recent years, plant-derived natural compounds possessing potential anti-tumor activities have been garnering much interest and efforts are underway to identify their molecular targets. Here, we attempt to summarize the discoveries of several natural compounds with activities against hematological malignancies, such as adenanthin, oridonin, gambogic acid and wogonoside, the identification of their targets, and their modes of actions.

通过鉴定关键靶标蛋白探究青蒿素抗疟机制

The widespread use of artemisinin(ART)and its derivatives has significantly reduced the global burden of malaria;however,malaria still poses a serious threat to global health.Although significant progress has been achieved in elucidating the antimalarial mechanisms of ART,the most crucial target proteins and pathways of ART remain unknown.Knowledge on the exact antimalarial mechanisms of ART is urgently needed,as signs of emerging ART resistance have been observed in some regions of the world.Here,we used a combined strategy involving mass spectrometry-coupled cellular thermal shift assay(MS-CETSA)and transcriptomics profiling to identify a group of putative antimalarial targets of ART.We then conducted a series of validation experiments on five prospective protein targets,demonstrating that ART may function against malaria parasites by interfering with redox homeostasis,lipid metabolism,and protein synthesis processes.Taken together,this study provides fresh perspectives on the antimalarial mechanisms of ART and identifies several crucial proteins involved in parasite survival that can be targeted to combat malaria.

Doppler shift of a laser pulse beam scattered by a rotating cone and cylinder

Based on laser radar equations, a Doppler shift model of a laser pulse beam scattered by a rotating arbitrary convex target is reported in this paper. The boundary relations between an incident pulse beam and the detected area elements are analyzed by geometric methods. The Doppler shift characteristics of the rotating cone and cylinder are discussed and the difference between the laser pulse beam and the plane wave scattered from the same rotating target is compared accordingly. Numerical simulations show that the Doppler shift is tightly relevant to their dimensions, speeds, and so on. In the same incidence conditions, the pulse beam and plane wave have difference peak values and the same Doppler shift bandwidth. If the waist radius of the pulse beam is larger, the peak value is higher, and the Doppler shifts are proportional to the speed of the rotating target. By virtue of our theoretical model, we probe into the scattered characteristics of the Doppler shifts of a laser pulse beam, which would benefit target identification in national defense.

The New Method for Calculating Poles of a Scattering Object

The natural resonances (poles) of a scattering object are important for the target identification. A new method for calculating poles of a scattering object is proposed in this paper. It is shown that the zeros of the Fast Fourier Transform of the integral kernel function are the poles of the scattering object. As an example, the poles of a thin wire conductor are obtained with high precision in very short time by using this method.

Discovery and identification of EIF2AK2 as a direct key target of berberine for anti-inflammatory effects

Using chemoproteomic techniques,we first identified EIF2AK2,eEF1A1,PRDX3 and VPS4B as direct targets of berberine(BBR)for its synergistically anti-inflammatory effects.Of them,BBR has the strongest affinity with EIF2AK2 via two ionic bonds,and regulates several key inflammatory pathways through EIF2AK2,indicating the dominant role of EIF2AK2.Also,BBR could subtly inhibit the dimerization of EIF2AK2,rather than its enzyme activity,to selectively modulate its downstream pathways including JNK,NF-κB,AKT and NLRP3,with an advantage of good safety profile.In EIF2AK2 gene knockdown mice,the inhibitory IL-1β,IL-6,IL-18 and TNF-a secretion of BBR was obviously attenuated,confirming an EIF2AK2-dependent anti-inflammatory efficacy.The results highlight the BBR's network mechanism on anti-inflammatory effects in which EIF2AK2 is a key target,and inhibition of EIF2AK2 dimerization has a potential to be a therapeutic strategy against inflammationrelated disorders.

Chemical proteomic profling with photoaffinity labeling strategy identifies antimalarial targets of artemisinin

Present research on the antimalarial mechanisms of artemisinin(ART)is mainly focused on covalent drug binding targets alkylated by free radicals,while non-covalent binding targets have rarely been reported.Here,we developed a novel photoaffinity probe of ART to globally capture and identify the antimalarial target proteins of ART through chemical proteomics.The results demonstrated that ART can bind to par-asite proteins by both covalent and non-covalent modification,and these may jointly contribute to the antimalarial effects.Our work enriches the research on the antimalarial targets of ART,and provides a new perspective for further exploring the antimalarial mechanism of ART.

Drug Target Identification Using Affinity Core-Shell Magnetic Nanoparticles and Mass Spectrometry

Affinity core-shell magnetic nanoparticles （MNPs） were prepared for identifying the target proteins of drugs in the cell lysate when used in combination with nano-high-performance liquid chromatography tandem mass spectrometry （HPLC-MS/MS）-based shotgun proteomic analysis. A number of new potential targets of cyclosporine A （CsA） could be identified, owing to the high efficacy of the affinity MNPs in drug target identification. To the best of our knowledge, this is the first time to reveal such an abundant target spectrum of CsA.

The synthesis of PROTAC molecule and new target KAT6A identification of CDK9 inhibitor i CDK9

Cyclin-dependent kinases(CDKs) have become potential targets for treating various diseases, especially cancer. Compound i CDK9 is an excellent and selective CDK9 inhibitor, but its major limitation is the potential toxicity and poor understanding of the underlying mechanism. The PROTAC(proteolysis targeting chimera) degraders of bioactive molecules can significantly induce in vitro and in vivo degradation of their target protein with high selectivity and effectively reduce the dose-limiting toxicity of small molecule drugs. Therefore, we designed and synthesized the bifunctional PROTAC molecules of i CDK9, being used for identifying its previously unknown target and revealing the underlying pharmacological mechanism.The PROTAC bifunctional molecule CD-5 could selectively and significantly degrade CDK9 with low cell toxicity. Therefore, we selected CD-5 as a chemical prober in the SILAC quantitative proteomic analysis, which disclosed that CD-5 could enormously lessen the lysine acetyltransferase KAT6A. Furthermore,KAT6A degradation induced by CD-5 repressed the levels of H3K14Ac and H3K23Ac. Lastly, the streptavidin immunoprecipitation(IP) assay confirmed a direct interaction between KAT6A and i CDK9. Collectively, our results uncover that KAT6A is a potential non-kinase target of i CDK9. Notably, this study also demonstrates that the PROTAC-SILAC strategy is an alternative approach for cellular target identification of bioactive molecules.

A new class of HIV-1 inhibitors and the target identification via proteomic profiling

Anti-HIV screening with the MT-4/MTT assay on a focused library of structurally diverse natural products has led to the discovery of a group of steroids with potent activities, which include four new ergostane-type steroids, named amotsterols A-D （1-4）, together with two known analogs. Among them, the most potent amotsterol D （4） exhibited anti-HIV activity against wild- type and some clinically relevant multidrug resistant HIV-I strains. Subsequent studies on its target identification through a proteomic approach found that compound 4 might target PKM2, a rate limiting enzyme ofglycolysis, in host cells to restrict HIV replication. The docking model of compound 4 to PKM2 showed that the two hydroxyl groups of 4 form hydrogen bonds with the two parallel Y390 in each subunit of PKM2 separately, and the ring C of 4 is sandwiched between the two parallel aromatic rings ofF26. The identified hit compound may have the potential to be further developed as a novel anti-HIVagent. These results demonstrated that an integrated approach, which combines new chemical structures and phenotypic screening with a proteomic approach, could not only identify novel HIV-1 inhibitors, but also elucidate the unknown targets of compound interactions in antiviral drug discovery.

Challenges and Perspectives in Target Identification and Mechanism Illustration for Chinese Medicine

Chinese medicine(CM)is an important resource for human life understanding and discovery of drugs.However,due to the unclear pharmacological mechanism caused by unclear target,research and international promotion of many active components have made little progress in the past decades of years.CM is mainly composed of multi-ingredients with multi-targets.The identification of targets of multiple active components and the weight analysis of multiple targets in a specific pathological environment,that is,the determination of the most important target is the main obstacle to the mechanism clarification and thus hinders its internationalization.In this review,the main approach to target identification and network pharmacology were summarized.And BIBm(Bayesian inference modeling),a powerful method for drug target identification and key pathway determination was introduced.We aim to provide a new scientific basis and ideas for the development and international promotion of new drugs based on CM.

Click chemistry and natural products

The 2022 Nobel Prize in Chemistry was awarded to American scientists Carolyn Bertozzi,K.Barry Sharpless,and Danish scientist Morten P.Merdahl for their contributions to the development of click chemistry and bioorthogonal chemistry.

ETCM v2.0:An update with comprehensive resource and rich annotations for traditional Chinese medicine

Existing traditional Chinese medicine(TCM)-related databases are still insufficient in data standardization,integrity and precision,and need to be updated urgently.Herein,an Encyclopedia of Traditional Chinese Medicine version 2.0(ETCM v2.0,http://www.tcmip.cn/ETCM2/front/#/)was constructed as the latest curated database hosting 48,442 TCM formulas recorded by ancient Chinese medical books,9872 Chinese patent drugs,2079 Chinese medicinal materials and 38,298 ingredients.To facilitate the mechanistic research and new drug discovery,we improved the target identification method based on a two-dimensional ligand similarity search module,which provides the confirmed and/or potential targets of each ingredient,as well as their binding activities.Importantly,five TCM formulas/Chinese patent drugs/herbs/ingredients with the highest Jaccard similarity scores to the submitted drugs are offered in ETCM v2.0,which may be of significance to identify prescriptions/herbs/ingredients with similar clinical efficacy,to summarize the rules of prescription use,and to find alternative drugs for endangered Chinese medicinal materials.Moreover,ETCM v2.0 provides an enhanced Java Script-based network visualization tool for creating,modifying and exploring multi-scale biological networks.ETCM v2.0 may be a major data warehouse for the quality marker identification of TCMs,the TCM-derived drug discovery and repurposing,and the pharmacological mechanism investigation of TCMs against various human diseases.

PROTAC technology as a novel tool to identify the target of lathyrane diterpenoids

To the Editor:Proteolysis Targeting Chimera(PROTAC)is an emerging approach to selectively degrading target proteins by utilizing endogenous proteasome.Since PROTACs can degrade target proteins without high affinity,it is natural to speculate that this technology can be used to identify the targets of natural products。Although a recent study reported the employment of PROTACs to explore the unknown non-kinase target of a multi-kinase inhibitor sorafenib,whether PROTACs can be used to find the potential targets of natural products remains unexplored.

Pharmacologically targeting molecular motor promotes mitochondrial fission for anti-cancer

Mitochondrial shape rapidly changes by dynamic balance of fusion and fission to adjust to constantly changing energy demands of cancer cells.Mitochondrial dynamics balance is exactly regulated by molecular motor consisted of myosin and actin cytoskeleton proteins.Thus,targeting myosin eactin molecular motor is considered as a promising strategy for anti-cancer.In this study,we performed a proof-of-concept study with a natural-derived small-molecule J13 to test the feasibility of anti-cancer therapeutics via pharmacologically targeting molecular motor.Here,we found J13 could directly target myosin-9(MYH9)eactin molecular motor to promote mitochondrial fission progression,and markedly inhibited cancer cells survival,proliferation and migration.Mechanism study revealed that J13 impaired MYH9 eactin interaction to inactivate molecular motor,and caused a cytoskeleton-dependent mitochondrial dynamics imbalance.Moreover,stable isotope labeling with amino acids in cell culture(SILAC)technology-coupled with pulldown analysis identified HSPA9 as a crucial adaptor protein connecting MYH9 eactin molecular motor to mitochondrial fission.Taken together,we reported the first natural small-molecule directly targeting MYH9 eactin molecular motor for anti-cancer translational research.Besides,our study also proved the conceptual practicability of pharmacologically disrupting mitochondrial fission/fusion dynamics in human cancer therapy.

A novel PGAM5 inhibitor LFHP-1c protects bloodebrain barrier integrity in ischemic stroke

Bloodebrain barrier(BBB)damage after ischemia significantly influences stroke outcome.Compound LFHP-1 c was previously discovered with neuroprotective role in stroke model,but its mechanism of action on protection of BBB disruption after stroke remains unknown.Here,we show that LFHP-1 c,as a direct PGAM5 inhibitor,prevented BBB disruption after transient middle cerebral artery occlusion(tMCAO)in rats.Mechanistically,LFHP-1 c binding with endothelial PGAM5 not only inhibited the PGAM5 phosphatase activity,but also reduced the interaction of PGAM5 with NRF2,which facilitated nuclear translocation of NRF2 to prevent BBB disruption from ischemia.Furthermore,LFHP-1 c administration by targeting PGAM5 shows a trend toward reduced infarct volume,brain edema and neurological deficits in nonhuman primate Macaca fascicularis model with t MCAO.Thus,our study identifies compound LFHP-1 c as a firstly direct PGAM5 inhibitor showing amelioration of ischemia-induced BBB disruption in vitro and in vivo,and provides a potentially therapeutics for brain ischemic stroke.

Unmodified methodologies in target discovery for small molecule drugs:A rising star

Target discovery,involving target identification and validation,is the prerequisite for drug discovery and screening.Novel methodologies and technologies for the precise discovery and confirmation of drug targets are powerful tools in understanding the disease,looking for a drug and elucidating the mechanism of drug treatment.Among the common target identification and confirmation methods,the modified method is time-consuming and laborious,which may reduce or change the activity of natural products.The unmodified methods developed in recent years without chemical modification have gradually become an important means of studying drug targets.A wide range of unmodified approaches have been reported,introducing and analyzing the recent emerging methodologies and technologies.This review highlights the advantages and limitations of these methods for the application of drug target discovery and presents an overview of their contributions to the target discovery of small molecule drugs.The application and future development trends of methodologies in target discovery are also prospected to provide a reference for drug target research.