QSAR,virtual Screening And Interaction Mechanism Of Inhibitors Targeting New Delhi Metallo-?-lactamase-1

Food-borne pathogens,which leading to food poisoning and food contamination seriously threat human health.With the overuse of antibiotics in the aquaculture industry,pathogens has been detected in various food products,especially in animal food,then transmitted to human by food chain,which leading to food poisoning and food-borne diseases in humans.?-lactam antibiotics is the important weapon to fight for pathogens infections due to its broad spectrum,high efficiency of antibacterial and low toxicity.Unfortunately,the emergence of resistant strains severely restricted the application of?-lactam antibiotics.With the increasing awareness of food safety and the rising infection of food-borne pathogens in worldwide,it is urgent to developing the strategy against the drug-resistant pathogen infection.One of the most important resistance mechanisms for?-lactam antibiotics is the expression of?-lactamase,which can catalyze the hydrolysis of the?-lactam ring leading to drug inactivation.Of these,New Delhi metallo-?-lactamase-1?NDM-1?represents the most troubling development due to its efficient hydrolysis of almost all kinds of?-lactam antibiotics,including the latest antibiotics,cephamycins and the ability of mediated pathogen resistance to almost?-lactam antibiotics.Despite ongoing efforts to identify NDM-1inhibitors,approved drugs in clinic are not yet available.Therefore,the research and development of antimicrobial agents against food-borne pathogens infection targeting NDM-1 is in an urgent need.Herein,we report a study on inhibitors against NDM-1 using a combined computational approach,which provide a new idea of developing novel drug-resistant inhibitors and effective control of drug-resistant pathogen infections.The specific research results are as follows:1.The inhibition mechanism of 2,6-dipicolinic acid and its derivatives to NDM-1.Based on molecular modelling and binding free energy calculations,it was confirmed that the inhibitors DPA and compound 36 can bind to the catalytically active region of NDM-1.In details,the residues His189,Cys208,Lys211,Met248,Ser249,His250,and Ser251 play critical roles in the binding of compound 36 with NDM-1.Of these,His189,Ser249,His250,and Ser251 can form four stable hydrogen bonds with compound 36,because of the strong interaction of Lys211 with the aniline group of compound 36.However,because of the lack of the aniline group,DPA can only form weak interactions with the residues around the binding site?Phe70,Asp124,Lys125,and Lys211?,leading to the decreased inhibitory activity.2.3D-QSAR and design of 2,6-dipicolinic acid derivatives as NDM-1inhibitors.In this study,a 3D-QSAR for DPA as NDM-1 inhibitors was established using Topomer CoMFA.Then,statistical results illustrate the fitting ability and internal prediction of the model.Topomer Search was used to virtual screening and design 10new molecules that had comparatively high activities against NDM-1.Furthermore,from molecular modeling and binding free-energy calculation,it was found that the newly designed molecules can bind to the catalytic region of NDM-1.Additionally,the newly designed inhibitors formed strong interactions with Ile35,Met67,Phe70,Trp93,His122,His189,Cys208,and His250 around the Zn²⁺-centered active region of NDM-1.3.3D-QSAR and design of Captopril Derivatives as NDM-1inhibitors.In this research,3D-QSAR for Captopril as NDM-1 inhibitors was established using Topomer CoMFA.According to statistical analysis of the model,it has enough fitting ability and internal prediction.Further,Topomer Search was used to virtual screening and design 40 new molecules and 38 of these showed higher activity than all inhibitors in the training set.Molecular docking,molecular modeling and binding free energies were calculated to explore the binding mode and mechanism of the newly designed inhibitors.The results indicated that these molecules interacted with the Ile35,Met67,Phe70,Val73,Trp93,Asn220,His250 sites around Zn²⁺ions.4.Discovery of the novel inhibitor against NDM-1 based on virtual screening.In this study,ZINC05683641 and ZINC25558277 were screened as potential NDM-1 inhibitor by virtual screening and enzyme inhibition assay.The enzyme inhibition assay shown that the IC50 values of the two compound were 13.59±0.52and 18.933±1.03?M,respectively.Moreover,the two inhibitors significantly restored the effectiveness of meropenem in vitro with NDM-expressing isolates in antibacterial activity assays.Further,the binding mode of ZINC05683641 and ZINC25558277 with NDM-1 was obtained by molecular modeling,binding free energy calculation,mutagenesis assays and fluorescence-quenching assays.As results,Ile35,Val73,Asp199,Asn220,Lys242 and His 250 play the key roles in the binding of NDM-1 with ZINC05683641,while Ile35,Met67,Phe70,Val73,Trp93,Gly219and His250 are the key residues of NDM-1-ZINC25558277 complex.Interestingly,these key residues were exactly located in the catalytic activity region of NDM-1,implying that the inhibitor mechanism of ZINC05683641 and ZINC25558277 against NDM-1 were the competitive inhibition.In this research,the novel efficient inhibitors targeting NDM-1 were identified using computer-aided drug design?CADD?strategy and the inhibition mechanisms were revealed at atom level,which laid a foundation for further study on drug-resistant inhibitors of food-borne pathogens.