In silico study the interaction of heterocyclic bases with peptide moieties of proteins in the "fragment-to-fragment" approach

The binding affinity of model peptide moieties (Pept) and heterocyclic bases involving 1,3-oxazoles that are condensed with pyridine and pyrimidine as pharmacophores (Pharm) was investigated in silico and analyzed within the «fragment-to-fragment» approach. The anellation of the heterocyclic rings increasing their acceptor properties is accompanied by gaining stability of the [Pharm-Pept] complexes formed by the π,π-stacking interaction. It was found that elongation of the polypeptide chain led to a twofold increase of the stabilization energy of the [Pharm-Pept] complexes. The stability of the hydrogen bonding ([HB]) [Pharm-BioM] complexes formed by means of the interaction between the dicoordinated nitrogen atom of the heterocycle and the functional groups of peptide amino acids (-OH, -NH2, -SH) was evaluated. It was demonstrated that [HB]-complexes that were formed by hydrogen bonds formation with amino acid that contained OH groups had the largest stabilization effect. The anellation with pyridine and pyrimidine rings led to stability increase of the complexes formed by the hydrogen bonding mechanism. The binding energy of [HB]-complexes for compounds 2b and 3 with a «free» peptide bond of the extended part of the protein is lower compared to amino acids with OH-functional groups. On the contrary, the binding energy of compound 4 with peptides was 2 kcal/mol higher. Compound 4 demonstrated the most pronounced biological activity in vitro studies.

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The rate-limiting step of protein synthesis in vivo and in vitro and the distribution of growing peptides between the puromycinlabile and puromycin-non-labile sites on polyribosomes

Biochemical Journal ◽

10.1042/bj1220267 ◽

1971 ◽

Vol 122 (3) ◽

pp. 267-276 ◽

Cited By ~ 10

Author(s):

D. C. N. Earl ◽

Susan T. Hindley

Keyword(s):

Amino Acids ◽

Protein Synthesis ◽

Donor Site ◽

Peptide Bond ◽

Rate Limiting Step ◽

Limiting Step ◽

Donor And Acceptor ◽

Rate Limiting

1. At 3 min after an intravenous injection of radioactive amino acids into the rat, the bulk of radioactivity associated with liver polyribosomes can be interpreted as growing peptides. 2. In an attempt to identify the rate-limiting step of protein synthesis in vivo and in vitro, use was made of the action of puromycin at 0°C, in releasing growing peptides only from the donor site, to study the distribution of growing peptides between the donor and acceptor sites. 3. Evidence is presented that all growing peptides in a population of liver polyribosomes labelled in vivo are similarly distributed between the donor and acceptor sites, and that the proportion released by puromycin is not an artifact of methodology. 4. The proportion released by puromycin is about 50% for both liver and muscle polyribosomes labelled in vivo, suggesting that neither the availability nor binding of aminoacyl-tRNA nor peptide bond synthesis nor translocation can limit the rate of protein synthesis in vivo. Attempts to alter this by starvation, hypophysectomy, growth hormone, alloxan, insulin and partial hepatectomy were unsuccessful. 5. Growing peptides on liver polyribosomes labelled in a cell-free system in vitro or by incubating hemidiaphragms in vitro were largely in the donor site, suggesting that either the availability or binding of aminoacyl-tRNA, or peptide bond synthesis, must be rate limiting in vitro and that the rate-limiting step differs from that in vivo. 6. Neither in vivo nor in the hemidiaphragm system in vitro was a correlation found between the proportion of growing peptides in the donor site and changes in the rate of incorporation of radioactivity into protein. This could indicate that the intracellular concentration of amino acids or aminoacyl-tRNA limits the rate of protein synthesis and that the increased incorporation results from a rise to a higher but still suboptimum concentration.

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Analisa In Silico Kunyit (Curcuma longa) sebagai Inhibitor Murine Double Minute 2 Protein untuk Terapi Glioblastoma Multiforme

Oceana Biomedicina Journal ◽

10.30649/obj.v3i2.61 ◽

2020 ◽

Vol 3 (2) ◽

pp. 82

Author(s):

Benny Iswanto Pantoro ◽

Nancy Margarita Rehatta ◽

Siti Khaerunnisa ◽

Anna Surgean Veterini ◽

Yuani Setiawati

Keyword(s):

Glioblastoma Multiforme ◽

Binding Energy ◽

In Silico ◽

Curcuma Longa ◽

Double Minute ◽

Murine Double Minute ◽

Autodock 4.2 ◽

Tumor Suppresor Gene

Tumor otak meliputi berbagai kanker yang tumbuh dari sel otak (tumor otak primer) ataupun berasal dari tumor sistemik yang mengalami metastasis ke otak (tumor otak sekunder). Dari seluruh tipe tumor otak primer, Glioblastoma Multiforme merupakan tumor otak yang paling sering dijumpai dan merupakan salah satu yang paling ganas. Pada 85% kasus Glioblastoma Multiforme, umumnya ditemukan kaitan dengan adanya gangguan tingkat molekuler pada jalur tumor suppresor gene p53, sehingga semakin banyak terapi yang dikembangkan dengan berfokus pada jalur ini. Salah satu jalur yang dapat dipakai sebagai model terapi adalah menginhibisi protein murine double minute 2 yang merupakan inhibitor dari p53. Kunyit (curcuma longa) adalah salah satu tanaman tradisional yang sudah sangat sering digunakan dalam dunia medis dan berbagai ekstrak nya telah diteliti mempunyai efek anti-kanker.Penelitian ini adalah sebuah studi in silico yang meneliti potensi berbagai bahan kimia aktif dari kunyit sebagai inhibitor pada protein murine double minute 2 menggunakan AutoDock 4.2 dan berdasarkan prinsip algoritma genetik Lamarckian. Hasil docking menunjukkan binding energy berkisar dari rentang -4.81 kcal/mol sampai -2.34 kcal/mol, dengan senyawa curcumenol mempunyai binding energy yang paling kecil dan curcumin mempunyai binding energy yang paling besar. Studi ini dapat digunakan sebagai dasar untuk melakukan penelitian lebih lanjut (in vivo dan in vitro) terkait bahan kimia aktif kunyit dan efek nya sebagai terapi Glioblastoma Multiforme.

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In Vitro and In Silico Evaluation of Biological Properties of Some 1, 3, 4-Oxadiazole Derivatives Against Streptococcus mutans and Their Interaction With Gbp-C by Molecular Docking

Avicenna Journal of Dental Research ◽

10.34172/ajdr.2021.27 ◽

2021 ◽

Vol 13 (4) ◽

pp. 142-147

Author(s):

Behin Omidi ◽

Yasin SarveAhrabi

Keyword(s):

Amino Acids ◽

Molecular Docking ◽

Hydrogen Bonds ◽

Streptococcus Mutans ◽

In Silico ◽

Antibacterial Properties ◽

Inhibition Zone ◽

Biological Properties ◽

High Concentrations

Background: The need to replace new drug structures for the treatment of resistant strains has become essential. Streptococcus mutans is one of the most important factors in causing tooth decay. Glucan binding protein-C (Gbp-C) is a crucial mobileular floor protein that is worried in biofilm formation, and 1, 3, 4-oxadiazoles are new antibacterial structures. Accordingly, this study focused on assessing in vitro and in silico activity of our previously synthesized compounds of 1, 3, 4-oxadiazole against S. mutans. Methods: To this end, our previously synthesized derivatives were re-synthesized and prepared, and then antibacterial susceptibility tests were used for inhibition zone, minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC) test values. The molecular docking method was also applied to confirm the effect of compounds in interaction with the Gbp-C of S. mutans. Results: All compounds showed different effects against the bacterial sample. Among these, the most effective ones were related to naphthalene (4d), fluorophenyl (4e), and dimethoxyphenyl (4h) derivatives against S. mutans, respectively. Other compounds also had antibacterial properties but to a lesser extent. In the molecular part, compounds 4d and 4h had the highest affinity to inhibit the GbpC-protein. compound 4d with amino acids ASP and GLN established 402 and 391 hydrogen bonds, respectively, and compound 4h with amino acids SER, GLU, THR, and TRP established 347, 360, 449, and 451 hydrogen bonds, respectively. Conclusions: In general, 1, 3, 4-oxadiazoles containing naphthalene and dimethoxy phenyl functional groups in high concentrations can be good alternatives to the existing drugs for eliminating caries-causing tooth mutants that have drug resistance. It seems that more inhibitory effects can be observed on clinical specimens by adding different purposeful groups and increasing the destructive power of oxadiazole-based compounds.

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Differential MMP-14 Targeting by Lumican-Derived Peptides Unraveled by In Silico Approach

Cancers ◽

10.3390/cancers13194930 ◽

2021 ◽

Vol 13 (19) ◽

pp. 4930

Author(s):

Jonathan Dauvé ◽

Nicolas Belloy ◽

Romain Rivet ◽

Nicolas Etique ◽

Pierre Nizet ◽

...

Keyword(s):

Amino Acids ◽

In Silico ◽

Primary Melanoma ◽

Direct Interaction ◽

Inhibitory Effect ◽

Melanoma Tumor ◽

And Migration ◽

Key Residues

Lumican, a small leucine-rich proteoglycan (SLRP) of the extracellular matrix (ECM), displays anti-tumor properties through its direct interaction with MMP-14. Lumican-derived peptides, such as lumcorin (17 amino acids) or L9M (10 amino acids), are able to inhibit the proteolytic activity of MMP-14 and melanoma progression. This work aimed to visualize the interactions of lumican-derived peptides and MMP-14. Molecular modeling was used to characterize the interactions between lumican-derived peptides, such as lumcorin, L9M, and cyclic L9M (L9Mc, 12 amino acids), and MMP-14. The interaction of L9Mc with MMP-14 was preferential with the MT-Loop domain while lumcorin interacted more with the catalytic site. Key residues in the MMP-14 amino acid sequence were highlighted for the interaction between the inhibitory SLRP-derived peptides and MMP-14. In order to validate the in silico data, MMP-14 activity and migration assays were performed using murine B16F1 and human HT-144 melanoma cells. In contrast to the HT-144 melanoma cell line, L9Mc significantly inhibited the migration of B16F1 cells and the activity of MMP-14 but with less efficacy than lumican and lumcorin. L9Mc significantly inhibited the proliferation of B16F1 but not of HT-144 cells in vitro and primary melanoma tumor growth in vivo. Thus, the site of interaction between the domains of MMP-14 and lumcorin or L9Mc were different, which might explain the differences in the inhibitory effect of MMP-14 activity. Altogether, the biological assays validated the prediction of the in silico study. Possible and feasible improvements include molecular dynamics results.

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Bio-Mechanism of Catechin as Pheromone Signal Inhibitor: Prediction of Antibacterial Agent Action Mode by In Vitro and In Silico Study

Molecules ◽

10.3390/molecules26216381 ◽

2021 ◽

Vol 26 (21) ◽

pp. 6381

Author(s):

Dikdik Kurnia ◽

Zenika Febian Ramadhanty ◽

Aprilina Mora Ardani ◽

Achmad Zainuddin ◽

Hendra Dian Adhita Dharsono ◽

...

Keyword(s):

Antibiotic Resistance ◽

Binding Energy ◽

Serine Protease ◽

In Silico ◽

Antibacterial Agent ◽

Antibacterial Agents ◽

Chemical Structures ◽

In Silico Study ◽

And Control

The utilization of medicinal plants has long been explored for the discovery of antibacterial agents and the most effective mechanisms or new targets that can prevent and control the spread of antibiotic resistance. One kind of bacterial cell wall inhibition is the inactivation of the MurA enzyme that contributes to the formation of peptidoglycan. Another approach is to interfere with the cell–cell communication of bacteria called the Quorum sensing (QS) system. The blocking of auto-inducer such as gelatinase biosynthesis-activating pheromone (GBAP) can also suppress the virulence factors of gelatinase and serine protease. This research, in particular, aims to analyze lead compounds as antibacterial and anti-QS agents from Gambir (Uncaria gambir Roxburgh) through protein inhibition by in silico study. Antibacterial agents were isolated by bioactivity-guided isolation using a combination of chromatographic methods, and their chemical structures were determined by spectroscopic analysis methods. The in vitro antibacterial activity was evaluated by disc diffusion methods to determine inhibitory values. Meanwhile, in the in silico analysis, the compound of Uncaria gambir was used as ligand and compared with fosfomycin, ambuic acid, quercetin, and taxifolin as the standard ligand. These ligands were attached to MurA, GBAP, gelatinase, and serine proteases using Autodock Vina in PyRx 0.8 followed by PYMOL for combining the ligand conformation and proteins. plus programs to explore the complex, and visualized by Discovery Studio 2020 Client program. The antibacterial agent was identified as catechin that showed inhibitory activity against Enterococcus faecalis ATCC 29212 with inhibition zones of 11.70 mm at 10%, together with MIC and MBC values of 0.63 and 1.25 μg/mL, respectively. In the in silico study, the molecular interaction of catechin with MurA, GBAP, and gelatinase proteins showed good binding energy compared with two positive controls, namely fosfomycin and ambuic acid. It is better to use catechin–MurA (−8.5 Kcal/mol) and catechin–gelatinase (−7.8 Kcal/mol), as they have binding energies which are not marginally different from quercetin and taxifolin. On the other hand, the binding energy of serine protease is lower than quercetin, taxifolin, and ambuic acid. Based on the data, catechin has potency as an antibacterial through the inhibition of GBAP proteins, gelatinase, and serine protease that play a role in the QS system. This is the first discovery of the potential of catechin as an alternative antibacterial agent with an effective mechanism to prevent and control oral disease affected by antibiotic resistance.

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Endophytic Fungi Penicillium species BCt Phytochemicals Inhibit Replication of Enzymes of Human Immuno-deficiency Virus 1 in in vitro and in silico Studies

International Journal of Pharmaceutical Sciences and Nanotechnology ◽

10.37285/ijpsn.2021.14.5.6 ◽

2021 ◽

Vol 14 (5) ◽

pp. 5624-5633

Author(s):

Govindappa M ◽

Channabasava ◽

Ritu Pawar ◽

Chandrasekhar Srinivasa ◽

Chandan Shivamallu ◽

...

Keyword(s):

Amino Acids ◽

Endophytic Fungi ◽

In Silico ◽

Methanol Extract ◽

Penicillium Species ◽

Ms Analysis ◽

In Silico Studies ◽

Hiv 1

The present investigation was aimed to know the coumarins in the methanol extract of endophytic fungi, Penicillium species BCt isolated from Calophyllum tomentosum bark tissues using qualitative and GC-MS analysis. The endophytic extract was evaluated for anti-HIV activity on three replicating enzymes in vitro and in silico. The methanol extract of Penicillium species confirmed the presence of coumarins in four qualitative methods and yielded four different types of coumarins in GC-MS. In GC-MS analysis, totally seven different phytochemicals were identified based on retention time and compared with available library data. The four coumarins are coumarin (2H-1-benzopyran-2-one), coumaric acid (3-benzofuran-carboxylic acid), hynecromone (coumarin 4), 4-hydroxy-9-(3-methyl-2-butyl) furo (3,2-g) chloronen-7-one) and other three are common phytochemicals. The HIV-1 RT (98) was strongly inhibited by the endophytic fungal extract compared to integrase (118) and protease (158) in vitro analysis. Highest inhibition of integrase was observed with coumarilic acid (-17.62) when attached to Glu-35, Asn-38, Ser-39 amino acids. The protease was inhibited strongly by hymecromone (-16.39) when attached to amino acids of Val-77, Glu-34, Pro-79, Gly-78. The inhibition of RT was observed with coumarilic acid by attaching to Ala-445, Arg-567, Asp-456, Glu-478, Ser-499, Asn-474 (-23.54) significantly. Based on above results, the endophytic fungal coumarins have the ability to inhibit the three replicating enzymes of HIV-1 significantly. The in-silico results are evidence for how coumarins inhibiting the HIV replicating proteins by binding at specific amino acids. The results will help to understand how and where phytochemicals bind to target proteins to inhibit their action and it may help to identification of drugs to treat HIV. To validate our results, the in vivo research is needed.

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In Vitro Apatite Formation on Polymer Substrates Irradiated by the Simultaneous Use of Oxygen Cluster and Monomer Ion Beams

MRS Proceedings ◽

10.1557/proc-1020-gg07-10 ◽

2007 ◽

Vol 1020 ◽

Author(s):

Masakazu Kawashita ◽

Rei Araki ◽

Gikan H Takaoka

Keyword(s):

Functional Groups ◽

Silicone Rubber ◽

Silicon Oxide ◽

Ion Beams ◽

Phosphate Solution ◽

Apatite Formation ◽

Oh Groups ◽

Oxygen Cluster ◽

Simultaneous Use

AbstractPolyethylene (PE) and silicone rubber substrates were irradiated at an acceleration voltage of 7kV and a dose of 1×1015 ions/cm2 by the simultaneous use of oxygen cluster and monomer ion beams, and then soaked in CaCl2 solution. Apatite-forming ability of the substrates was examined using a metastable calcium phosphate solution that had 1.5 times the ion concentrations of a normal simulated body fluid (1.5SBF). After the irradiation, the hydrophilic functional groups such as COOH and silicon oxide cluster (SiOx) were formed at the PE and silicone rubber surfaces, respectively. The hydrophilicity of the substrates was remarkably improved by the irradiation. The irradiated PE and silicone rubber substrates formed apatite in 1.5SBF, whereas unirradiated ones did not form it. These results suggest that the functional groups such as COOH groups and Si-OH groups induced apatite nucleation in 1.5SBF.

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LEAD MOLECULE IDENTIFICATION FROM VITEX TRIFOLIA LINN FOR HELMINTHIASIS USING IN VITRO AND IN SILICO METHODS

International Journal of Pharmacy and Pharmaceutical Sciences ◽

10.22159/ijpps.2020v12i2.36353 ◽

2020 ◽

pp. 95-103

Author(s):

SOUNDARARAJAN MUTHUKRISHNAN ◽

RAGUNATH G. ◽

BLESSY SUSAN VARGHESE

Keyword(s):

Binding Energy ◽

In Silico ◽

Anthelmintic Activity ◽

Petri Dish ◽

Docking Studies ◽

Diffusion Method ◽

Organ Bath ◽

Active Constituents ◽

Intermolecular Energy

Objective: The study was an attempt to discover a lead molecule to treat helminthiasis using Vitex trifolia. Linn (V. folia Linn) through sterile effect, in vitro and in silico evaluation. Methods: The antibacterial activity was done by Kirby-Bauer disc diffusion method in three different concentrations of extract and in vitro anthelmintic activity was carried out by petri dish and organ bath method. Further, the in silico docking studies were carried out by 11 phytoconstituents against phosphoethanolamine methyltransferase (4FGZ) using Auto Dock 4.2, it was working based on the principle of Lamarckian genetic algorithm. In docking studies, three important parameters such as binding energy, inhibition constant and intermolecular energy are determined. Results: The extracts showed an antibacterial effect in three different concentrations. At 16 mcg/disc a significant effect was observed when compared to blank and ciprofloxacin 5 mcg/disc. The anthelmintic activity in the petri dish method, means paralyzing time of Pheretimaposthuma with the dose of 25, 50 and 100 mg/ml were 13.78, 5.79 and 4.57 min respectively and Piperazine citrate (10 mg/ml) showed paralysis in 21.58 min. In the organ bath method, the time for paralysis of the worm was recorded on a slow-moving Sherrington rotating drum and the study report showed that paralyzing time was decreased at increasing concentrations of the extract. The results of in silico studies exhibited a binding energy of-10.25kcal/mol, inhibitory constant (Ki) 30.91nM, intermolecular energy,-10.84kcal/mol for abietatriene-3-ol which is lesser than the standard ligand phosphoethanolamine (-6.03kcal/mol, 38.29µM,-7.82kcal/mol) respectively. Conclusion: The study reports conclude that the active constituents in V. folia Linn having better anthelmintic activity, thus the active constituents may be optimized and make way to a new moiety for the treatment of helminthiasis.

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An immunoinformatics study: designing multivalent T-cell epitope vaccine against canine circovirus

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-021-00220-4 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Pankaj Jain ◽

Amit Joshi ◽

Nahid Akhtar ◽

Sunil Krishnan ◽

Vikas Kaushik

Keyword(s):

Molecular Dynamics ◽

Amino Acids ◽

Molecular Docking ◽

In Silico ◽

Cell Epitope ◽

Cost Effective ◽

Dynamics Simulation ◽

Cloning And Expression

Abstract Background Canine circovirus is a deadly pathogen of dogs and causes vasculitis and hemorrhagic enteritis. It causes lethal gastroenteritis in pigs, fox, and dogs. Canine circovirus genome contains two main (and opposite) transcription units which encode two open reading frames (ORFs), a replicase-associated protein (Rep) and the capsid (Cap) protein. The replicase protein and capsid protein consist of 303 amino acids and 270 amino acids respectively. Several immuno-informatics methods such as epitope screening, molecular docking, and molecular-dynamics simulations were used to craft peptide-based vaccine construct against canine circovirus. Results The vaccine construct was designed by joining the selected epitopes with adjuvants by suitable linker. The cloning and expression of the vaccine construct was also performed using in silico methods. Screening of epitopes was conducted by NetMHC server that uses ANN (Artificial neural networking) algorithm. These methods are fast and cost-effective for screening epitopes that can interact with dog leukocyte antigens (DLA) and initiate an immune response. Overall, 5 epitopes, YQHLPPFRF, YIRAKWINW, ALYRRLTLI, HLQGFVNLK, and GTMNFVARR, were selected and used to design a vaccine construct. The molecular docking and molecular dynamics simulation studies show that these epitopes can bind with DLA molecules with stability. The codon adaptation and in silico cloning studies show that the vaccine can be expressed by Escherichia coli K12 strain. Conclusion The results suggest that the vaccine construct can be useful in preventing the dogs from canine circovirus infections. However, the results need further validation by performing other in vitro and in vivo experiments.

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