In Silico Prediction and Validation of Oxygen-Regulated Protein N-myc Downstream Regulated Gene 3 and Virtual Screening of Competitive Inhibitors of L-Lactate as Therapeutics

2019 ◽  
Vol 16 (6) ◽  
pp. 637-644
Author(s):  
Hongyu Cao ◽  
Yanhua Wu ◽  
Xingzhi Zhou ◽  
Xuefang Zheng ◽  
Ge Jiang
Keyword(s):  
Active Sites ◽  
Competitive Inhibition ◽  
Hydrophobic Effect ◽  
3D Structure ◽  
Amino Acid Residues ◽  
In Silico Prediction ◽  
Hypoxic Response ◽  
Drug Candidates ◽  
Competitive Inhibitors ◽  
Extracellular Regulated Protein Kinases

Background: N-myc downstream regulated gene 3 (NDRG3) is a newly discovered oxygen-regulated protein which will bind with L-Lactate in hypoxia and further activate Raf (rapidly accelerated fibrosarcoma)-ERK (extracellular regulated protein kinases) pathway, promoting cell growth and angiogenesis. Methods: Competitive inhibition on the binding of NDRG3 and L-Lactate may be potentially a useful strategy for the repression of hypoxic response mediated by NDRG3. The threedimensional (3D) structure of NDRG3 was built by using homology modeling for its crystal structure was not available. Then, L-Lactate was docked into NDRG3, from which we knew it bound with amino acid residues Gln69, His183, Asn189, Ala72 and Pro66 of NDRG3 in the most possible active sites. Approximately 3000 compounds have been virtually screened and the 6 topranked compounds were selected as reference molecules to analyze their interaction relationships, which illustrated that some of them might form electrostatic interaction with Glu70 and Asp187, π-&π stack with Phe75 and Tyr180, hydrogen bonds with Gly71 and Asn189, hydrophobic effect with Ala72 and Ile184. Results: Novel molecules were designed through structural optimization of the 6 top-ranked compounds and subsequently their ADMET properties were predicted. Conclusion: These molecules may be potential drug candidates for the suppression of hypoxic response mediated by NDRG3 and targeted therapy for hypoxia-induced diseases.

scholarly journals Small Angle X-ray Scattering, Molecular Modeling, and Chemometric Studies from a Thrombin-Like (Lmr-47) Enzyme of Lachesis m. rhombeata Venom

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3930
Author(s):  
Salvatore Giovanni De-Simone ◽  
Guilherme Curty Lechuga ◽  
Paloma Napoleão-Pêgo ◽  
Larissa Rodrigues Gomes ◽  
David William Provance ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
3D Structure ◽  
Ph Variation ◽  
Critical Elements ◽  
X Ray Scattering ◽  
Plot Analysis ◽  
Competitive Inhibitors ◽  
Resolution Model ◽  
Lachesis Muta ◽  
Lachesis Muta Rhombeata

Introduction: Snakebite envenomation is considered a neglected tropical disease, and SVTLEs critical elements are involved in serious coagulopathies that occur on envenoming. Although some enzymes of this group have been structurally investigated, it is essential to characterize other proteins to better understand their unique properties such as the Lachesis muta rhombeata 47 kDa (Lmr-47) venom serine protease. Methods: The structure of Lmr-47 was studied in solution, using SAXS, DLS, CD, and in silico by homology modeling. Molecular docking experiments simulated 21 competitive inhibitors. Results: At pH 8.0, Lmr-47 has an Rg of 34.5 ± 0.6 Å, Dmax of 130 Å, and SR of 50 Å, according to DLS data. Kratky plot analysis indicates a rigid shape at pH 8.0. Conversely, the pH variation does not change the center of mass’s intrinsic fluorescence, possibly indicating the absence of fluorescent amino acids in the regions affected by pH variation. CD experiments show a substantially random coiled secondary structure not affected by pH. The low-resolution model of Lmr-47 presented a prolate elongated shape at pH 8.0. Using the 3D structure obtained by molecular modeling, docking experiments identified five good and three suitable competitive inhibitors. Conclusion: Together, our work provided insights into the structure of the Lmr-47 and identified inhibitors that may enhance our understanding of thrombin-like family proteins.

The clpB gene of Bifidobacterium breve UCC 2003: transcriptional analysis and first insights into stress induction

Microbiology ◽  
2005 ◽  
Vol 151 (9) ◽  
pp. 2861-2872 ◽  
Author(s):  
Marco Ventura ◽  
John G. Kenny ◽  
Ziding Zhang ◽  
Gerald F. Fitzgerald ◽  
Douwe van Sinderen
Keyword(s):  
3D Structure ◽  
Binding Mode ◽  
Dna Interaction ◽  
Transcriptional Analysis ◽  
Amino Acid Residues ◽  
Mobility Shift ◽  
Bifidobacterium Breve ◽  
Gel Mobility Shift ◽  
Slot Blot Analysis

The so-called clp genes, which encode components of the Clp proteolytic complex, are widespread among bacteria. The Bifidobacterium breve UCC 2003 genome contains a clpB gene with significant homology to predicted clpB genes from other members of the Actinobacteridae group. The heat- and osmotic-inducibility of the B. breve UCC 2003 clpB homologue was verified by slot-blot analysis, while Northern blot and primer extension analyses showed that the clpB gene is transcribed as a monocistronic unit with a single promoter. The role of a hspR homologue, known to control the regulation of clpB and dnaK gene expression in other high G+C content bacteria was investigated by gel mobility shift assays. Moreover the predicted 3D structure of HspR provides further insight into the binding mode of this protein to the clpB promoter region, and highlights the key amino acid residues believed to be involved in the protein–DNA interaction.

scholarly journals Investigation of major amino acid residues of anti-norfloxacin monoclonal antibodies responsible for binding with fluoroquinolones

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Patamalai Boonserm ◽  
Songchan Puthong ◽  
Thanaporn Wichai ◽  
Sajee Noitang ◽  
Pongsak Khunrae ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Amino Acid ◽  
3D Structure ◽  
Cross Reactivity ◽  
Enzyme Linked Immunosorbent Assay ◽  
Amino Acid Residues ◽  
Variable Regions ◽  
Complementarity Determining Regions ◽  
Crucial Part ◽  
Major Amino Acid

AbstractIt is important to understand the amino acid residues that govern the properties of the binding between antibodies and ligands. We studied the binding of two anti-norfloxacins, anti-nor 132 and anti-nor 155, and the fluoroquinolones norfloxacin, enrofloxacin, ciprofloxacin, and ofloxacin. Binding cross-reactivities tested by an indirect competitive enzyme-linked immunosorbent assay indicated that anti-nor 132 (22–100%) had a broader range of cross-reactivity than anti-nor 155 (62–100%). These cross-reactivities correlated with variations in the numbers of interacting amino acid residues and their positions. Molecular docking was employed to investigate the molecular interactions between the fluoroquinolones and the monoclonal antibodies. Homology models of the heavy chain and light chain variable regions of each mAb 3D structure were docked with the fluoroquinolones targeting the crucial part of the complementarity-determining regions. The fluoroquinolone binding site of anti-nor 155 was a region of the HCDR3 and LCDR3 loops in which hydrogen bonds were formed with TYR (H:35), ASN (H:101), LYS (H:106), ASN (L:92), and ASN (L:93). These regions were further away in anti-nor 132 and could not contact the fluoroquinolones. Another binding region consisting of HIS (L:38) and ASP (H:100) was found for norfloxacin, enrofloxacin, and ciprofloxacin, whereas only ASP (H:100) was found for ofloxacin.

scholarly journals Individual subunits of a rhinovirus causing common cold exhibit largely different protein-RNA contact site conformations

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Dieter Blaas
Keyword(s):  
Common Cold ◽  
3D Structure ◽  
Conformational Heterogeneity ◽  
Amino Acid Residues ◽  
Assembly Mechanism ◽  
Gradual Loss ◽  
Density Map ◽  
The Common

Abstract Rhinoviruses cause the common cold. They are icosahedral, built from sixty copies each of the capsid proteins VP1 through VP4 arranged in a pseudo T = 3 lattice. This shell encases a ss(+) RNA genome. Three-D classification of single and oligomeric asymmetric units computationally excised from a 2.9 Å cryo-EM density map of rhinovirus A89, showed that VP4 and the N-terminal extension of VP1 adopt different conformations within the otherwise identical 3D-structures. Analysis of up to sixty classes of single subunits and of six classes of subunit dimers, trimers, and pentamers revealed different orientations of the amino acid residues at the interface with the RNA suggesting that local asymmetry is dictated by disparities of the interacting nucleotide sequences. The different conformations escape detection by 3-D structure determination of entire virions with the conformational heterogeneity being only indicated by low density. My results do not exclude that the RNA follows a conserved assembly mechanism, contacting most or all asymmetric units in a specific way. However, as suggested by the gradual loss of asymmetry with increasing oligomerization and the 3D-structure of entire virions reconstructed by using Euler angles selected in the classification of single subunits, RNA path and/or folding likely differ from virion to virion.

scholarly journals Psoromic Acid, a Lichen-Derived Molecule, Inhibits the Replication of HSV-1 and HSV-2, and Inactivates HSV-1 DNA Polymerase: Shedding Light on Antiherpetic Properties

Molecules ◽  
2019 ◽  
Vol 24 (16) ◽  
pp. 2912 ◽  
Author(s):  
Sherif T. S. Hassan ◽  
Miroslava Šudomová ◽  
Kateřina Berchová-Bímová ◽  
Karel Šmejkal ◽  
Javier Echeverría
Keyword(s):  
Dna Polymerase ◽  
Active Sites ◽  
Inhibitory Action ◽  
Inhibitory Concentration ◽  
Competitive Inhibition ◽  
Inhibitory Effect ◽  
Standard Drug ◽  
Key Enzyme ◽  
Hsv 1

Psoromic acid (PA), a bioactive lichen-derived compound, was investigated for its inhibitory properties against herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2), along with the inhibitory effect on HSV-1 DNA polymerase, which is a key enzyme that plays an essential role in HSV-1 replication cycle. PA was found to notably inhibit HSV-1 replication (50% inhibitory concentration (IC50): 1.9 μM; selectivity index (SI): 163.2) compared with the standard drug acyclovir (ACV) (IC50: 2.6 μM; SI: 119.2). The combination of PA with ACV has led to potent inhibitory activity against HSV-1 replication (IC50: 1.1 µM; SI: 281.8) compared with that of ACV. Moreover, PA displayed equivalent inhibitory action against HSV-2 replication (50% effective concentration (EC50): 2.7 μM; SI: 114.8) compared with that of ACV (EC50: 2.8 μM; SI: 110.7). The inhibition potency of PA in combination with ACV against HSV-2 replication was also detected (EC50: 1.8 µM; SI: 172.2). Further, PA was observed to effectively inhibit HSV-1 DNA polymerase (as a non-nucleoside inhibitor) with respect to dTTP incorporation in a competitive inhibition mode (half maximal inhibitory concentration (IC50): 0.7 μM; inhibition constant (Ki): 0.3 μM) compared with reference drugs aphidicolin (IC50: 0.8 μM; Ki: 0.4 μM) and ACV triphosphate (ACV-TP) (IC50: 0.9 μM; Ki: 0.5 μM). It is noteworthy that the mechanism by which PA-induced anti-HSV-1 activity was related to its inhibitory action against HSV-1 DNA polymerase. Furthermore, the outcomes of in vitro experiments were authenticated using molecular docking analyses, as the molecular interactions of PA with the active sites of HSV-1 DNA polymerase and HSV-2 protease (an essential enzyme required for HSV-2 replication) were revealed. Since this is a first report on the above-mentioned properties, we can conclude that PA might be a future drug for the treatment of HSV infections as well as a promising lead molecule for further anti-HSV drug design.

scholarly journals Evaluation of the Spider (Phlogiellus genus) Phlotoxin 1 and Synthetic Variants as Antinociceptive Drug Candidates

Toxins ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 484 ◽  
Author(s):  
Gonçalves ◽  
Lesport ◽  
Kuylle ◽  
Stura ◽  
Ciolek ◽  
...  
Keyword(s):  
Mouse Model ◽  
3D Structure ◽  
Computational Modelling ◽  
Marked Change ◽  
Disulfide Bridge ◽  
Voltage Gated ◽  
Drug Candidates ◽  
Analgesic Effects ◽  
Kv Channels ◽  
Whole Cell Patch Clamp

Over the two last decades, venom toxins have been explored as alternatives to opioids to treat chronic debilitating pain. At present, approximately 20 potential analgesic toxins, mainly from spider venoms, are known to inhibit with high affinity the NaV1.7 subtype of voltage-gated sodium (NaV) channels, the most promising genetically validated antinociceptive target identified so far. The present study aimed to consolidate the development of phlotoxin 1 (PhlTx1), a 34-amino acid and 3-disulfide bridge peptide of a Phlogiellus genus spider, as an antinociceptive agent by improving its affinity and selectivity for the human (h) NaV1.7 subtype. The synthetic homologue of PhlTx1 was generated and equilibrated between two conformers on reverse-phase liquid chromatography and exhibited potent analgesic effects in a mouse model of NaV1.7-mediated pain. The effects of PhlTx1 and 8 successfully synthetized alanine-substituted variants were studied (by automated whole-cell patch‐clamp electrophysiology) on cell lines stably overexpressing hNaV subtypes, as well as two cardiac targets, the hCaV1.2 and hKV11.1 subtypes of voltage-gated calcium (CaV) and potassium (KV) channels, respectively. PhlTx1 and D7A-PhlTx1 were shown to inhibit hNaV1.1–1.3 and 1.5–1.7 subtypes at hundred nanomolar concentrations, while their affinities for hNaV1.4 and 1.8, hCaV1.2 and hKV11.1 subtypes were over micromolar concentrations. Despite similar analgesic effects in the mouse model of NaV1.7-mediated pain and selectivity profiles, the affinity of D7A-PhlTx1 for the NaV1.7 subtype was at least five times higher than that of the wild-type peptide. Computational modelling was performed to deduce the 3D-structure of PhlTx1 and to suggest the amino acids involved in the efficiency of the molecule. In conclusion, the present structure–activity relationship study of PhlTx1 results in a low improved affinity of the molecule for the NaV1.7 subtype, but without any marked change in the molecule selectivity against the other studied ion channel subtypes. Further experiments are therefore necessary before considering the development of PhlTx1 or synthetic variants as antinociceptive drug candidates.

Suramin could block the activity of Arabinono-1, 4-lactone oxidase enzyme from Leishmania donovani: structure-based screening and molecular dynamics analyses

2019 ◽  
Vol 114 (3) ◽  
pp. 162-172 ◽  
Author(s):  
Keivan Adinehbeigi ◽  
Minoo Shaddel ◽  
Saeed Khalili ◽  
Alireza Zakeri
Keyword(s):  
Active Sites ◽  
Leishmania Donovani ◽  
3D Structure ◽  
Current Treatment ◽  
Model Assessment ◽  
Docking Analysis ◽  
Oxidase Enzyme ◽  
Inhibitory Molecules ◽  
Dynamics Analyses

Abstract Background Leishmania donovani, a parasitic protozoan causing visceral leishmaniasis, can lead to a dangerous and often fatal disease in humans. Current treatment for leishmaniasis may have severe side effects, low efficacy and high cost, hence an immediate need for new efficient drugs is essential. Arabinono-1, 4-lactone oxidase enzyme from Leishmania donovani (LdALO), which catalyzes the last step of the ascorbate biosynthesis pathway, has been considered as a potential target for antileishmanial drugs design. Methods The current study was performed with an in silico approach to predict novel inhibitory molecules against the LdALO enzyme. Various modeling and refinement processes were employed to obtain a reliable 3D structure. Results The best LdALO model with the highest qualitative model energy analysis score was predicted by the Robetta server and subsequently refined by 3D refine and ModLoop servers. The high quality of the final LdALO model was confirmed using model assessment software. Based on docking analysis results, we predicted 10 inhibitory molecules of a US Food and Drug Administration-approved library, with appropriate criteria regarding energy binding and interaction with the main functionally active sites of LdALO, indicating that they could be significant targets for further drug design investigations against L. donovani. Conclusion Suramin is used to treat the first stage of African sleeping sickness and its mechanism of action is unknown. Our results showed that suramin was the best-predicted inhibitor compound for LdALO enzyme activity.

The dynamic behaviour of nitrifying Activated sludge systems influenced by inhibiting wastewater compounds

1995 ◽  
Vol 31 (2) ◽  
pp. 115-124 ◽  
Author(s):  
O. Nowak ◽  
K. Svardal ◽  
P. Schweighofer
Keyword(s):  
Activated Sludge ◽  
Treatment Process ◽  
Dynamic Behaviour ◽  
Competitive Inhibition ◽  
Nitrification Inhibition ◽  
Peak Loads ◽  
Inhibitory Compounds ◽  
Competitive Inhibitors ◽  
Nitrification Process ◽  
Activated Sludge Systems

More or less severe nitrification inhibition was observed in several pilot and full-scale activated sludge plants treating industrial wastewaters. In order to control the treatment process under inhibiting conditions, extended nitrification models have been developed on base of the ‘Activated sludge model No. 1’. In the case of temperatures between 25 and 30°C, the nitrification process has been expressed as a two-step reaction with nitrite as intermediate. Model elements for competitive and non-competitive inhibition as well as for biodegradation of the inhibitor were added, if required. The dynamic behaviour of the investigated activated sludge systems indicates that there are biodegradable non-competitive inhibitors. Operational as well as simulation results show that nitrifying activated sludge plants may become acclimatized to inhibitory compounds but have to be protected from peak loads of both nitrogen and inhibitory compounds.

scholarly journals Molecular Interactions of Renin with Chikusetsusaponin IV and Momordin IIc

2019 ◽  
Vol 2019 ◽  
pp. 1-7 ◽  
Author(s):  
Hai-Ling Zhang ◽  
Gui-Lan Zhu ◽  
Xiao-Tian Chen
Keyword(s):  
Hydrogen Bonding ◽  
Binding Sites ◽  
Driving Forces ◽  
Hydrophobic Interactions ◽  
Hydrophobic Effect ◽  
Energy Calculation ◽  
Total Binding Energy ◽  
Interaction Energies ◽  
Amino Acid Residues ◽  
Poisson Boltzmann

The paper dealt with the molecular mechanism for the binding sites and driving forces of renin with chikusetsusaponin IV and momordin IIc by means of molecular docking and free energy calculation based on the crystal structure. The result showed that renin and the saponins fit well. As shown by LigPlot + software analyzing the hydrogen bonding and hydrophobic effect between renin and the saponins, the amino acid residues such as Ser230, Tyr85, and Tyr201 form the hydrogen bonds, with S3sp, S3, and S2′ being the active pockets. In addition, there are relatively strong hydrophobic interactions of renin with saponins in S3sp, S3, S2, S1, S1′, and S2′, with Gly228, Val36, Ala229, Gln19, Met303, Gln135, Ser41, Ile137, Asp38, Arg82, and Tyr83 being the key amino acids. The dynamics reached equilibration after about 1000 ps simulation with average root-mean-square deviations of 0.222 nm and 0.217 nm. The molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) yielded −1.10812 kcal/mol and −39.0587 kcal/mol total binding energy for the two complexes, respectively, which were primarily contributed by electrostatic and van der Waals interaction energies, and the binding was strongly unfavored by polar solvation energy, a further confirmation that momordin IIc has stronger hydrogen bonding and hydrophobic effect in the inhibition of renin than the chikusetsusaponin IV.

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