Current Enzyme Inhibition - Volume 13, Issue 3, 2017

Background: Inhibition of Dipeptidyl peptidase IV (DPP IV) enzyme is an attractive and appropriate target for the treatment of type 2 diabetes. In order to discover for potent DPP IV inhibitors a chemoinformatics studies were performed on fifty nine trifluorophenyl β-aminoamide derivatives using Sybyl X 2.1.1. Methods: The comparative molecular field analysis (CoMFA), comparative molecular similarity index analysis (CoMSIA) and hologram quantitative structural activity relationship (HQSAR) and docking techniques were selected, validated and optimized by a test set of fifteen compounds in order to design new molecules. Result: The values of cross validated r2 (q2), non cross validated r2 and predicted r2 were for CoMFA (q2=0.854, r2=0.928, pred. r2=0. 932), CoMSIA (q2 =0. 864, r2=0. 924, pred. r2=0.922) and HQSAR (q2=0.826, r2=0.942, pred. r2=0.705), respectively. Conclusion: The structure activity relationship of selected analysis suggested that bulky and electron withdrawing substituents at 2nd and 3rd position of piperazine ring; bulky and electron withdrawing substituent at R position and less bulky and electron donating substituent at 5th position of piperazine ring were favorable for inhibition of DPP IV enzyme. In docking analysis (3W2T pdb) amino group and carbonyl group of compound 44 formed hydrogen bond interactions with Glu 206, Tyr 662 and Arg 125 respectively at active site of DPP IV enzyme. The present work finding may be helpful in the designing and optimization of novel DPP IV inhibitors.

Background: The glyoxylate shunt of fatty acid metabolism is critical to the survival of Mycobacterium tuberculosis (Mtb) during the dormant stage. The two enzymes of glyoxylate shunt pathway, isocitrate lyase (ICL) and malate synthase (MS), have been identified to be involved in Mtb persistence and become the attractive targets to intervene with the pathway. Methods: In order to search novel MS inhibitors, molecular docking in autodock Vina was employed for the first time to virtually screen Fragment-Like subset of ZINC database against MS crystal structure. Results: Total 11 candidates were screened out based on binding score, binding conformation, and structural diversity. Conclusion: The interaction mode analysis, binding affinity reassessment and ADME predictions of these candidates indicate they all can be treated as potential MS inhibitors. Their skeletons can be classified into four novel types, i.e., pyrrolo[3,4-d]pyrimidine, chromen-2-one, hetero biphenyl and phenyl substituted chiral cyclic diketone, which will bring an encouraging enlightenment to enrich the category of MS inhibitors and broaden their research scope.

Background: The glycolytic pathway plays an important role in tumor cells. Triosephosphate isomerase (TIM) catalyzes the reversible isomerization of D-glyceraldehyde-3-phosphate (GAP) to dihydroxyacetone phosphate (DHAP) in the glycolysis. Proteomics of a human prostate adenocarcinoma cell line revealed the presence of the G233D TIM variant, a new allelic type whose biochemical properties have not been reported [1]. Objective: Provide the first biochemical and biophysical characterization of the allelic variant G233D of TIM. Methods: The Michaelis-Menten curves using both substrates of TIM were obtained. Also the effect of the competitive inhibitor phosphoenolpyruvate (PEP) was assessed in presence of GAP and DHAP. The thermal stability in absence and presence of PEP was analyzed by circular dichroism spectroscopy. For comparison purposes, all the measurements were carried out on the wild type TIM and variant G233D. Results: The G233D variant exhibited a kcat value 4-fold lower than that of the WT enzyme in the GAP isomerization to DHAP, which is the reverse reaction of the glycolytic pathway. The G233D variant exhibited Ki and IC50 values of 120 μM and 356 μM in the presence of several concentrations of GAP and 0.3 mM DHAP, respectively. These inhibition parameters are similar to those exhibited by the WT enzyme. The thermal unfolding cooperativity of G233D variant was significantly increased upon PEP binding, suggesting that the ligand-bound enzyme was trapped in a rigid conformation. Conclusion: We suggest that the flow of GAP through glycolysis could be enhanced by the decreased activity of the G233D variant in the formation of DHAP.

Background: Type 2 diabetes (T2D) is a swiftly growing disease which affects human health seriously around the world. So far, nine DPP-4 inhibitors have been launched on the markets for patients with T2D. The aminomethyl biaryl derivatives, with a novel structure scaffold, have been proved as potential DPP-4 inhibitors. Our team focused on the modification of aminomethyl biaryl derivatives through the pharmacophore model. Method: A series of aminomethyl biaryl derivatives, which were designed according to the pharmacophore model, were synthesized and evaluated as inhibitors of dipeptidyl peptidase 4 (DPP-4) for the treatment of type 2 diabetes. Results: A novel series of DPP-4 inhibitors with biaryl scaffold designed by pharmacophore model, has been synthesized and identified. The IC50 level of compound A7, A25 and A26 in potency was comparable to Sitagliptin. A25 showed more than 100-fold selectivity over DPP-7 and DPP-8. Conclusion: The substitution 1,2,4-triazolyl group was proved to be a key discovery in increasing the potency of this structural class of inhibitors.

Background: Biosurfactants are natural extracellular products that are produced by several microorganisms. These compounds are highly developed during recent years for industrial, medical, and environmental applications. Although, the majority of microbial biosurfactants were originated from bacterial species, some studies have shown that Rhodotorula muciliginosa and Candida rugosa are fungal sources for biosurfactants production. The aim of the present study was to evaluate anti- Candida activity of biosurfactant produced by R. paludigena. In addition, the combination of biosurfactant and several antifungal drugs was also investigated against Candida isolates. Materials and Methods: In the present study, R. paludigena was subjected for the production of biosurfactant and yielded product was confirmed using several specific tests. Biosurfactant was produced using Sabouraud dextrose broth at 29°C for 5-7 days. Cell-free supernatants were collected and extracted using chloroform-methanol solvent. Checkerboard microdilution method was used to assess antifungal susceptibility and combination interaction. Results: Out of 80 suspected isolates to Rhodotorula, only one strain (R. paludigena) has been found to be predominant for biosurfactant production. Our results show that produced biosurfactant has anti- Candida activity at the range of 1-8 mg/mL. Furthermore, it showed a synergistic effect with antifungal drugs caspofungin. Conclusion: It is concluded that R. paludigena has great potential for biosurfactant production with valuable antifungal effect against C. albicans. On the other hand, the synergistic effect was found when a combination of biosurfactant and caspofungin were applied against C. albicans.

Introduction: Broad spectrums of antibiotics are widely used in the treatment of bacterial infections, particularly causing Staphylococcus aureus. These drugs have high acute renal injury (AKI) potency due to an increase in nitric oxide level. In this study, potency of nitric oxide synthase inhibition of some antibiotics was investigated according to vancomycin which was used as a reference antibiotic in renal injury. Methods and Results: Nitric oxide synthase (NOS) enzyme was purified by using 2'5'-ADP Sepharose 4B affinity chromatography from bovine kidney tissue in a single step with a yield of 3.58% and 1217- fold. Native and subunit molecular weights of the purified kidney NOS enzyme were calculated as 215 kDa and 114.8 kDa. Optimum pH, optimum ionic strength, optimum temperature and stable pH values for purified enzyme were determined as 7.5, 50 mM, 10°C and a pH range of 5.5-6.5, respectively. In vitro effects of antibiotics on purified enzyme activity were investigated by drawing Lineweaver-Burk plots. Enrofloxacin, kanamycin, chloramphenicol, gentamicin, vancomycin, cefazolin, streptomycin and ampicillin inhibited enzyme activity. IC50 values of these compounds were determined as 0.189 mM, 0.295 mM, 1.509 mM, 6.614 mM, 16.579 mM, 18.679 mM, 28.171 mM and 30.394 mM, respectively. Conclusion: Enrofloxacin and kanamycin were observed to have stronger NOS inhibitory effects as compared to vancomycin and may be more reliable antibiotics for use in renal infections as an alternative to vancomycin.

Background: Pyrazolo[3,4-d]pyrimidine compounds are reported to exhibit various pharmacological activities including antitubercular. The mycobacterium trifunctional enzyme_mtTFE is a vital constituent of β-oxidation pathway for lipid metabolism of tubercle bacillus. Method: In this article, the quantum polarized ligand docking of some pyrazolo[3,4-d]pyrimidine molecules have been conducted within the active site of mtTFE of tubercle bacillus and the effect of the polarization of ligands in the active site resulting from the residues of the binding site have been investigated. The charges of the ligands were calculated using density functional B3LYP/6-31G** level. Binding free energy calculations have been carried out through MM/GBSA method. Results: This study examines comparative performance of fixed point charge based Glide SP docking and the quantum polarized ligand docking strategies. Because of the polarization of charges, significant changes in docking scores have been detected. MM/GBSA free energy calculations of the ligands with mtTFE show good agreement with experimental observations reported in literature. Conclusion: Electrostatic interaction play important role in binding between ligand and receptor. Molecules 2 and 6 have better binding capabilities with mycobacterial β-oxidation trifunctional enzyme_ mtTFE satisfying ADME parameters.

Abstract: Background: Present world is badly affected by AIDS. The chief causative agent for AIDS is HIV. The essential milk proteins; bovine lactoferrin (bLF) and human lactoferrin (hLF) are known to obstruct the interaction between HIV gp120 and DC-SIGN protein after sexual transmission. Earlier several research studies have been performed to document the active participation of gp120 protein and lactoferrins, but the molecular-level analysis for lactoferrins (bLF and hLF) and gp120 interaction was never explored. Methodology: Firstly, three essential proteins (hLF, bLF and gp120) were analyzed and demonstrated for their experimentally validated x-ray crystallographic structures. The bLF-gp120 and hLF-gp120 protein complexes were formed. After energy minimization and simulation, the residual participation was observed. Additionally, thermodynamic properties and stability of the proteins were evaluated for the individual complexes. Results, Discussion and Conclusion: Residual interactions showed the predominant ionic-ionic interactions to be double for bLF-gp120 complex than hLF-gp120 complex. 4 ionic-ionic interactions by Glu residues from bLF protein were strong enough to accommodate gp120 protein into the pocket formed in bLF protein. Net area for solvent accessibility and electrostatic surface potential were observed to satisfy better interaction with bLF. Fascinatingly, increased percentage of β-sheets in gp120 after interacting with bLF depicted that gp120 adopted a steadier conformation, whereas; upon interaction with hLF, flexibility of gp120 got increased with increased percentage of residues forming coils. From ΔG evaluations, hLF protein was observed to interact less spontaneously with gp120 protein than bLF protein, thereby allowing the flexibility in the gp120 protein to interact with other host cells in human. Altogether, it affirms gp120 to have weaker interaction with hLF. Therefore, bLF acts as a stronger proficient HIV inhibitor. Thus, this probe provides a coherent outlook for investigating into the mutational impacts on bLF and hLF protein and further interaction with gp120.

Background: Vascular Endothelial Growth Factor Receptor-2 (VEGFR-2) is one of the proangiogenic factors that promotes endothelial cell proliferation, migration, differentiation, tube formation and thus helps in the angiogenesis and progression of cancers. Considering the VEGFR-2 as a prominent target for angiogenesis inhibition, the present study was focused to a potent phytochemical shikonin as potential lead molecule. Method: Different computational analysis like docking, QM/MM (Quantum Mechanics/Molecular Mechanics), stochastic dynamics simulation, mutagenesis and ADME/T with SoM predictions were employed to understand the binding behavior of shikonin with VEGFR-2 and also its toxicity and metabolic profile. Results: From the docking, QM/MM and in silico mutagenesis analysis, it was concluded that the residues like ASP1046, GLU885, LEU889, LEU1019, and LYS868 are major for ligand binding and inhibition. Moreover, shikonin processed strong binding with VEGFR-2 by forming non bonded interactions, and revealed as a non ATP non-competitive inhibitor; which was further confirmed by stochastic dynamics simulations. And also, it is less toxic and has moderate oral absorption rate. Conclusion: This study will be useful for the designing of new inhibitor against VEGFR-2, by selecting shikonin as a lead molecule, and also for the development of shikonin's derivatives for single or combination therapy against angiogenesis and cancer.