scholarly journals In Silico Structural Modeling of Wildtype and Mutant PRODH Proteins Involved in Psychiatric Disorder.

2021 ◽  
Author(s):  
Muhammad Muzammal ◽  
Sumra Wajid Abbasi ◽  
Ansar Ahmad Abbasi ◽  
Muzammil Ahmad Khan
Keyword(s):  
In Silico ◽  
Active Sites ◽  
3D Models ◽  
Protein Docking ◽  
The Body ◽  
Proline Dehydrogenase ◽  
Discovery Studio ◽  
Dehydrogenase Enzyme ◽  
Binding Residues ◽  
Excess Quantity

Abstract Proline dehydrogenase is an important mitochondrial enzyme that is encoded by the PRODH gene. Biologically, a mutation in this gene affects the activity of proline dehydrogenase enzyme that is normally involved in conversion of proline to glutamate. However, its reduced or null activity leads to excess quantity of proline in the body, which results in different psychiatric phenotypes along with intellectual disability. In the present study, we performed in silico analysis on all reported mutations of PRODH. The 3D models of normal and mutant PRODH were predicted using I-TASSER. The predicted structures were visualized and superimposed using chimera 1.13.1. The CASTp was used to identify active sites in modelled proteins. Protein-protein docking was done with Cluspro, while protein-substrate docking was done with Auto Dock 1.5.6 and-MGL tools and the results were visualized using LigPlus+ v.2.2 and Discovery studio 2020 respectively. Alignment of 3D models (mutant with wildtype) revealed that Arg185Gln (73.83 % ) and Gln19Ter (6.25% ) had the highest and lowest similarity indices, respectively. Enzyme pocket prediction identified three largest sites, with the second largest active site pocket containing substrate proline binding residues Leu527, Tyr548, and Arg563. Moreover, docking of mutant and wildtype PRODH with its close interactor “ALDH4A1” showed differences with respect to number, position, and nature of interacting amino acids residues. We observed that the nature of amino acid substitution and the number of bonds affect the binding of proline molecule with proline dehydrogenase enzyme, and therefore, affect its biological activity.

scholarly journals In silico Analysis of Phytochemicals from Cocoa against Ribitol-5-Phosphate 2-Dehydrogenase of Streptococcus pneumoniae Causing Pneumonia

2020 ◽  
pp. 1-5
Author(s):  
Sunanya Das ◽  
Suchismita Khatei ◽  
Saismita Sahoo ◽  
Sitaram Swain ◽  
Dipankar Bhattacharyay
Keyword(s):  
Molecular Docking ◽  
Streptococcus Pneumoniae ◽  
Vanillic Acid ◽  
In Silico ◽  
Metabolic Pathways ◽  
In Silico Analysis ◽  
Discovery Studio ◽  
Dehydrogenase Enzyme ◽  
High Possibility ◽  
Silico Analysis

This analysis aims at evaluating the effects of Cocoa extract on Pneumonia. Pneumonia is caused by Streptococcus pneumoniae. Caffeine, Chorogenic acid, Ferulic acid, Iso- Orientin, luteolin, Naringenin and Vanillic acid of Cocoa were interacted with ribitol-5-phosphate 2-dehydrogenase which is involved in pentose and glucorunate interconversion pathways of Streptococcus pneumoniae. The enzyme was taken as receptor and phytochemicals were considered as ligands. All the interactions were done in Biovia discovery Studio 2020 and the process is known as molecular Docking. Molecular Docking provides us an opportunity to identify the potential phytochemical or component which can act as powerful tool against the pathogen. Out of all the phytochemicals, Luteolin of Cocoa inhibits or blocks the mechanism or action of ribitol-5-phosphate 2-dehydrogenase enzyme of Streptococcus pneumoniae. There is high possibility that these phytochemicals can potentially inhibit others enzymes involved in various metabolic pathways of Streptococcus pneumoniae.

scholarly journals In silico Identification of Characteristics Spike Glycoprotein of SARS-CoV-2 in the Development Novel Candidates for COVID-19 Infectious Diseases

2020 ◽  
Vol 6 (2) ◽  
pp. 48-52
Author(s):  
Taufik Muhammad Fakih ◽  
Mentari Luthfika Dewi
Keyword(s):  
Infectious Diseases ◽  
In Silico ◽  
Three Dimensional ◽  
Protein Docking ◽  
Dimensional Structure ◽  
Spike Glycoprotein ◽  
Angiotensin Converting Enzyme 2 ◽  
Docking Simulations ◽  
Discovery Studio ◽  
Identification Evaluation

Background: The emergence of infectious diseases caused by SARS-CoV-2 has resulted in more than 90,000 infections and 3,000 deaths. The coronavirus spike glycoprotein encourages the entry of SARS-CoV-2 into cells and is the main target of antivirals. SARS-CoV-2 uses ACE2 to enter cells with an affinity similar to SARS-CoV, correlated with the efficient spread of SARS-CoV-2 among humans.Objective: In the research, identification, evaluation, and exploration of the structure of SARS-CoV and SARS-CoV-2 spike glycoprotein macromolecules and their effects on Angiotensin-Converting Enzyme 2 (ACE-2) using in silico studies.Methods: The spike glycoproteins of the two coronaviruses were prepared using the BIOVIA Discovery Studio 2020. Further identification of the three-dimensional structure and sequencing of the macromolecular spike glycoprotein structure using Chimera 1.14 and Notepad++. To ensure the affinity and molecular interactions between the SARS-CoV and SARS-CoV-2 spike glycoproteins against ACE-2 protein-protein docking simulations using PatchDock was accomplished. The results of the simulations were verified using the BIOVIA Discovery Studio 2020.Results: Based on the results of the identification of the macromolecular structure of the spike glycoprotein, it was found that there are some similarities in characteristics between SARS-CoV and SARS-CoV-2. Protein-protein docking simulations resulted that SARS-COV-2 spike glycoprotein has the strongest bond with ACE-2, with an ACE score of −1509.13 kJ/mol.Conclusion: Therefore, some information obtained from the results of this research can be used as a reference in the development of SARS-CoV-2 spike glycoprotein inhibitor candidates for the treatment of infectious diseases of COVID-19.

scholarly journals In silico studies of selected xanthophylls as potential candidates against SARS-CoV-2 targeting main protease (Mpro) and papain-like protease (PLpro)

2021 ◽  
Vol 67 (2) ◽  
pp. 1-8
Author(s):  
Tomasz M. Karpiński ◽  
Marek Kwaśniewski ◽  
Marcin Ożarowski ◽  
Rahat Alam
Keyword(s):  
Binding Energy ◽  
Active Site ◽  
In Silico ◽  
Active Sites ◽  
Data Bank ◽  
Pharmacokinetic Parameters ◽  
Discovery Studio ◽  
Main Protease ◽  
In Silico Studies ◽  
Potential Inhibitors

Summary Introduction: The main protease (Mpro) and the papain-like protease (PLpro) are essential for the replication of SARS-CoV-2. Both proteases can be targets for drugs acting against SARS-CoV-2. Objective: This paper aims to investigate the in silico activity of nine xanthophylls as inhibitors of Mpro and PLpro. Methods: The structures of Mpro (PDB-ID: 6LU7) and PLpro (PDB-ID: 6W9C) were obtained from RCSB Protein Data Bank and developed with BIOVIA Discovery Studio. Active sites of proteins were performed using CASTp. For docking the PyRx was used. Pharmacokinetic parameters of ADMET were evaluated using SwissADME and pkCSM. Results: β-cryptoxanthin exhibited the highest binding energy: –7.4 kcal/mol in the active site of Mpro. In PLpro active site, the highest binding energy had canthaxanthin of –9.4 kcal/mol, astaxanthin –9.3 kcal/mol, flavoxanthin –9.2 kcal/mol and violaxanthin –9.2 kcal/mol. ADMET studies presented lower toxicity of xanthophylls in comparison to ritonavir and ivermectin. Conclusion: Our findings suggest that xanthophylls can be used as potential inhibitors against SARS-CoV-2 main protease and papain-like protease.

scholarly journals The potential role of caffeic acid in coffee as cyclooxygenase-2 (COX-2) inhibitor: in silico study

2019 ◽  
Vol 9 (5) ◽  
pp. 4424-4427 ◽  
Keyword(s):  
Caffeic Acid ◽  
In Silico ◽  
Positive Impact ◽  
The Body ◽  
Ligand Interaction ◽  
Discovery Studio ◽  
In Silico Study ◽  
Cox 2

Caffeic acid was formed from hydrolyzation chlorogenic acid caused roasting coffee. Caffeic acid has anti-inflammatory properties by in vitro and in vivo analysis. Inflammation is the body will be activator COX-2 as mediator inflammation. This study purpose to prediction, investigate and analyze caffeic acid as potential theuraphic to inhibit COX-2 by in silico study. The method of this research using in silico compound interaction models. COX-2 Protein data was taken from Protein Data Bank, caffeic acid from PubChem. Protein-ligand interaction docking using HEX 8.0.0. Although visualization and analysis of the molecular interactions of caffeic acid and COX-2 conducted by the Discovery Studio software 4.1. Caffeic acid is a potential therapist because easily absorbed and has high permeability. The results show that interacted between COX-2 and caffeic acid. The interactions showed by seven amino acid residues, which bind with the caffeic acid with hydrogen bond type. Energy binding formed from ligand and protein -210.23cal/mol. Interaction caffeic acid and COX-2 has a positive impact which potential as inhibitor COX-2.

Role of 4-O Galloylchlorogenic Acid in Lung Cancer- An Insilico Approach

2017 ◽  
Vol 9 (5) ◽  
Author(s):  
Jaynthy C. ◽  
N. Premjanu ◽  
Abhinav Srivastava
Keyword(s):  
Lung Cancer ◽  
Cell Proliferation ◽  
In Silico ◽  
Computational Study ◽  
Regulation Mechanism ◽  
Down Regulation ◽  
Fruit Extract ◽  
In Vitro Techniques ◽  
Discovery Studio

Cancer is a major disease with millions of patients diagnosed each year with high mortality around the world. Various studies are still going on to study the further mechanisms and pathways of the cancer cell proliferation. Fucosylation is one of the most important oligosaccharide modifications involved in cancer and inflammation. In cancer development increased core fucosylation by FUT8 play an important role in cell proliferation. Down regulation of FUT8 expression may help cure lung cancer. Therefore the computational study based on the down regulation mechanism of FUT8 was mechanised. Sapota fruit extract, containing 4-Ogalloylchlorogenic acid was used as the inhibitor against FUT-8 as target and docking was performed using in-silico tool, Accelrys Discovery Studio. There were several conformations of the docked result, and conformation 1 showed 80% dock score between the ligand and the target. Further the amino acids of the inhibitor involved in docking were studied using another tool, Ligplot. Thus, in-silico analysis based on drug designing parameters shows that the fruit extract can be studied further using in-vitro techniques to know its pharmacokinetics.

Ruthenium Complexes for 1- and 2-Photon Photodynamic Therapy: From In Silico Prediction to In Vivo Applications

2020 ◽  
Author(s):  
Johannes Karges ◽  
Shi Kuang ◽  
Federica Maschietto ◽  
Olivier Blacque ◽  
Ilaria Ciofini ◽  
...  
Keyword(s):  
Photodynamic Therapy ◽  
In Silico ◽  
Aqueous Solubility ◽  
The Body ◽  
Photon Absorption ◽  
Multicellular Tumor Spheroids ◽  
Spectral Window ◽  
Photon Excitation ◽  
Polypyridine Complexes

<div>The use of photodynamic therapy (PDT) against cancer has received increasing attention overthe recent years. However, the application of the currently approved photosensitizers (PSs) is somehow limited by their poor aqueous solubility, aggregation, photobleaching and slow clearance from the body. To overcome these limitations, there is a need for the development of new classes of PSs with ruthenium(II) polypyridine complexes currently gaining momentum. However, these compounds generally lack significant absorption in the biological spectral window, limiting their application to treat deep-seated or large tumors. To overcome this drawback, ruthenium(II) polypyridine complexes designed in silico with (E,E’)-4,4´-bisstyryl 2,2´-bipyridine ligands showed impressive 1- and 2-Photon absorption up to a magnitude higher than the ones published so far. While non-toxic in the dark, these compounds were found phototoxic in various 2D monolayer cells, 3D multicellular tumor spheroids and be able to eradicate a multiresistant tumor inside a mouse model upon clinically relevant 1-Photon and 2 Photon excitation.</div>

Novel Thiazole-Based Thiazolidinones as Potent Anti-infective Agents: In silico PASS and Toxicity Prediction, Synthesis, Biological Evaluation and Molecular Modelling

2020 ◽  
Vol 23 (2) ◽  
pp. 126-140 ◽  
Author(s):  
Christophe Tratrat
Keyword(s):  
In Silico ◽  
Antimicrobial Agents ◽  
Target Identification ◽  
Biological Evaluation ◽  
Microbial Infection ◽  
Toxicity Prediction ◽  
Discovery Studio ◽  
Bacteria And Fungi ◽  
Multiple Drugs ◽  
Antibacterial And Antifungal

Aims and Objective: The infectious disease treatment remains a challenging concern owing to the increasing number of pathogenic microorganisms associated with resistance to multiple drugs. A promising approach for combating microbial infection is to combine two or more known bioactive heterocyclic pharmacophores in one molecular platform. Herein, the synthesis and biological evaluation of novel thiazole-thiazolidinone hybrids as potential antimicrobial agents were dissimilated. Materials and Methods: The preparation of the substituted 5-benzylidene-2-thiazolyimino-4- thiazolidinones was achieved in three steps from 2-amino-5-methylthiazoline. All the compounds have been screened in PASS antibacterial activity prediction and in a panel of bacteria and fungi strains. Minimum inhibitory concentration and minimum bacterial concentration were both determined by microdilution assays. Molecular modeling was conducted using Accelrys Discovery Studio 4.0 client. ToxPredict (OPEN TOX) and ProTox were used to estimate the toxicity of the title compounds. Results: PASS prediction revealed the potentiality antibacterial property of the designed thiazolethiazolidinone hybrids. All tested compounds were found to kill and to inhibit the growth of a vast variety of bacteria and fungi, and were more potent than the commercial drugs, streptomycin, ampicillin, bifomazole and ketoconazole. Further, in silico study was carried out for prospective molecular target identification and revealed favorable interaction with the target enzymes E. coli MurB and CYP51B of Aspergillus fumigatus. Toxicity prediction revealed that none of the active compounds was found toxic. Conclusion: Substituted 5-benzylidene-2-thiazolyimino-4-thiazolidinones, endowing remarkable antibacterial and antifungal properties, were identified as a novel class of antimicrobial agents and may find a potential therapeutic use to eradicate infectious diseases.

Nanoscale Drug Delivery Systems for Glaucoma: Experimental and In Silico Advances

2020 ◽  
Vol 20 ◽  
Author(s):  
Smriti Sharma ◽  
Vinayak Bhatia
Keyword(s):  
Drug Delivery ◽  
In Silico ◽  
Drug Delivery Systems ◽  
Delivery Systems ◽  
Ocular Drug Delivery ◽  
The Body ◽  
Single Wall Carbon Nanotubes ◽  
Blood Retinal Barrier ◽  
Novel Drugs ◽  
Blood Aqueous Barrier

: In this review nanoscale based drug delivery systems particularly in relevance to the antiglaucoma drugs have been discussed. In addition to that, the latest computational/in silico advances in this field are examined in brief. Using nanoscale materials for drug delivery, is an ideal option to target tumours and drug can be released at areas of the body where traditional drugs may fail to act. Nanoparticles, polymeric nanomaterials, single-wall carbon nanotubes (SWCNTs), quantum dots (QDs), liposomes and graphene are the most important nanomaterials used for drug delivery. Ocular drug delivery is one of the most common and difficult tasks faced by pharmaceutical scientists because of many challenges like circumventing the blood–retinal barrier, corneal epithelium and the blood–aqueous barrier. Authors found compelling empirical evidence of scientists relying on in-silico approaches to develop novel drugs and drug delivery systems for treating glaucoma. This review in nanoscale drug delivery systems will help us in understand the existing queries and evidence gaps and will pave way for effective design of novel ocular drug delivery systems

1'-methylspiro[indoline-3,4'-piperidine] Derivatives: Design, Synthesis, Molecular Docking and Anti-tumor Activity Studies

2020 ◽  
Vol 17 ◽  
Author(s):  
Junjian Li ◽  
Lianbao Ye ◽  
Yuanyuan Wang ◽  
Ying Liu ◽  
Xiaobao Jin ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Cell Lines ◽  
Active Sites ◽  
Biological Activities ◽  
Significant Inhibition ◽  
Alkaline Condition ◽  
Discovery Studio ◽  
Hela Cell Lines ◽  
Antiproliferative Activities

Background: Spirocyclic indoline compounds widely exist in numerous natural products with good biological activities and some drug molecules in many aspects. In recent years, it has attracted extensive attention as potent anti-tumor agents in the fields of pharmacology and chemistry. Objective: In this study, we focused on designing and synthesizing a set of novel 1'-H-spiro[indole-3,4'-piperidine] derivatives, which were evaluated by preliminary bioactivity experiment in vitro and molecular docking. Method: The key intermediate 1'-methylspiro[indoline-3,4'-piperidine] (B4) reacted with benzenesulfonyl chloride with different substituents under alkaline condition to obtain its sulfonyl derivatives (B5-B10). We evaluated their antiproliferative activities against A549, BEL-7402 and HeLa cells by MTT assay. We performed the CDOCKER module in Discovery Studio 2.5.5 software for molecular modeling of compound B5, and investigated the binding of compound B5 with the target proteins from PDB database. Results: The results indicated that compounds B4-B10 exhibited good antiproliferative activities against the above three types of cells, in which compound B5 with chloride atom as electron-withdrawing substituent on a phenyl ring showed the highest potency against BEL-7402 cells (IC50=30.03±0.43 μg/mL). By binging of the prominent bioactive compound B5 to CDK, c-Met, EGFR protein crystals, The binding energy of B5 with these three types receptors are -44.3583 kcal/mol, - 38.3292 kcal/mol, -33.3653 kcal/mol respectively. Conclusion: Six 1'-methylspiro[indoline-3,4'-piperidine] derivatives were synthesized and evaluated against BEL-7402, A- 549, HeLa cell lines. Compound B5 showed significant inhibition on BEL-7402 cell lines. Molecular docking revealed that B5 showed good affinity by the good fitting between B5 and these three targets with amino acid residues in active sites which encourage us to conduct further evaluation such as the kinase experiment.

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