scholarly journals Molecular Determinant s Elucidate the Selectivity in Abscisic acid Receptor and HAB1 Protein Interactions

2020 ◽  
Author(s):  
Jing-Fang Yang ◽  
Chun-Yan Yin ◽  
Di Wang ◽  
Chen-Yang Jia ◽  
Ge-Fei Hao ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Protein Interactions ◽  
Binding Free Energy ◽  
Strong Support ◽  
Activation Function ◽  
Dynamics Simulation ◽  
Activation Mechanism ◽  
Energy Calculation ◽  
Selective Activation ◽  
Aba Receptors

Abstract The abscisic acid (ABA), as a pivotal plant hormone, plays a key role in controlling the life cycle and adapting to the environmental stresses. The receptors of ABA are the Pyrabactin Resistance /Pyrabactin Resistance -Like/Regulatory Component of ABA Receptors (PYR/PYL/RCAR, PYLs for simplicity), which regulate the Protein Phosphatase 2Cs (PP2Cs) in the signal pathway. As an important ABA mimicking ligand, Pyrabactin shows the activation function to parts of members of PYLs, such as PYR1 and PYL1. Due to the antagonism of Pyrabactin to PYL2, it was used as a probe to discover a part of ABA receptors. Since then, many researchers have been trying to find out the determinants of the selective regulation of PYLs and PP2Cs interaction. However, the roles of residues on the selective regulation of PYR1/PYL2 and PP2Cs interaction induced by Pyrabactin are still ambiguous. This research investigated the selective activation mechanism of Pyrabactin through the sequence alignment, molecular docking, molecular dynamics simulation, and binding free energy calculation. Furthermore, the electrostatic and hydrophobic interaction differences induced by Pyrabactin and agonists were compared. The results indicate that Leu137/Val114, Ser85/Ser89, and Gly86/Gly90 from the pocket and gate of PYR1/PYL2 are the vital residues for the selective activation of Pyrabactin. Meanwhile, the electrostatic interaction between PP2Cs and PYLs complexed with agonists was improved. This mechanism provides strong support for the design of selective agonists and antagonists.

scholarly journals Scaffold Hopping of α-Rubromycin Enables Direct Access to FDA-Approved Cromoglicic Acid as a SARS-CoV-2 MPro Inhibitor

2021 ◽  
Vol 14 (6) ◽  
pp. 541
Author(s):  
Hani A. Alhadrami ◽  
Ahmed M. Sayed ◽  
Heba Al-Khatabi ◽  
Nabil A. Alhakamy ◽  
Mostafa E. Rateb
Keyword(s):  
Binding Free Energy ◽  
Human Fibroblasts ◽  
Critical Time ◽  
Dynamics Simulation ◽  
Direct Access ◽  
Energy Calculation ◽  
Wide Range ◽  
Normal Human ◽  
Novel Scaffold

The COVID-19 pandemic is still active around the globe despite the newly introduced vaccines. Hence, finding effective medications or repurposing available ones could offer great help during this serious situation. During our anti-COVID-19 investigation of microbial natural products (MNPs), we came across α-rubromycin, an antibiotic derived from Streptomyces collinus ATCC19743, which was able to suppress the catalytic activity (IC50 = 5.4 µM and Ki = 3.22 µM) of one of the viral key enzymes (i.e., MPro). However, it showed high cytotoxicity toward normal human fibroblasts (CC50 = 16.7 µM). To reduce the cytotoxicity of this microbial metabolite, we utilized a number of in silico tools (ensemble docking, molecular dynamics simulation, binding free energy calculation) to propose a novel scaffold having the main pharmacophoric features to inhibit MPro with better drug-like properties and reduced/minimal toxicity. Nevertheless, reaching this novel scaffold synthetically is a time-consuming process, particularly at this critical time. Instead, this scaffold was used as a template to explore similar molecules among the FDA-approved medications that share its main pharmacophoric features with the aid of pharmacophore-based virtual screening software. As a result, cromoglicic acid (aka cromolyn) was found to be the best hit, which, upon in vitro MPro testing, was 4.5 times more potent (IC50 = 1.1 µM and Ki = 0.68 µM) than α-rubromycin, with minimal cytotoxicity toward normal human fibroblasts (CC50 > 100 µM). This report highlights the potential of MNPs in providing unprecedented scaffolds with a wide range of therapeutic efficacy. It also revealed the importance of cheminformatics tools in speeding up the drug discovery process, which is extremely important in such a critical situation.

scholarly journals Hydrogen Bond Stability of Quinazoline Derivatives Compounds in Complex against EGFR using Molecular Dynamics Simulation

2019 ◽  
Vol 19 (2) ◽  
pp. 461
Author(s):  
Herlina Rasyid ◽  
Bambang Purwono ◽  
Thomas S Hofer ◽  
Harno Dwi Pranowo
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Binding Free Energy ◽  
Dynamics Simulation ◽  
Inhibition Mechanism ◽  
Energy Calculation ◽  
Protein Receptor ◽  
The Stability

Lung cancer was a second common cancer case due to the high cigarette smoking activity both in men and women. One of protein receptor which plays an important role in the growth of the tumor is Epidermal Growth Factor Receptor (EGFR). EGFR protein is the most frequent protein mutation in cancer and promising target to inhibit the cancer growth. In this work, the stability of the hydrogen bond as the main interaction in the inhibition mechanism of cancer will be evaluated using molecular dynamics simulation. There were two compounds (A1 and A2) as new potential inhibitors that were complexed against the EGFR protein. The dynamic properties of each complexed were compared with respect to erlotinib against EGFR. The result revealed that both compounds had an interaction in the main catalytic area of protein receptor which is at methionine residue. Inhibitor A1 showed additional interactions during simulation time but the interactions tend to be weak. Inhibitor A2 displayed a more stable interaction. Following dynamics simulation, binding free energy calculation was performed by two scoring techniques MM/GB(PB)SA method and gave a good correlation with the stability of the complex. Furthermore, potential inhibitor A2 had a lower binding free energy as a direct consequence of the stability of hydrogen bond interaction.

scholarly journals In-Silico Analysis of nsSNPs Associated with CYP11B2 Gene

2019 ◽  
Author(s):  
Anam Arooj ◽  
Muhammad Tariq Pervez ◽  
Zeeshan Gillani ◽  
Tahir Ali Chohan ◽  
M. Tayyab Chaudhry ◽  
...  
Keyword(s):  
Active Site ◽  
Binding Free Energy ◽  
In Silico Analysis ◽  
The Body ◽  
Dynamics Simulation ◽  
Energy Calculation ◽  
Simulation Techniques ◽  
Functional Aspects ◽  
Excess Production ◽  
Active Site Cavity

AbstractCYP11B2gene is located over the upper layer of the kidney. It produces aldosterone synthase enzyme and thereby has an essential role to balance salt and mineral level in the body. A mutation in this gene can deregulate the production of aldosterone hormone in the body which may lead to many diseases including hypertension and cardiac diseases. To control the excess production of this aldosterone an inhibitor “Fadrozole” is being used which is associated with an active site cavity of CYP11B2. This study has been divided into two parts. In the first part, the four computational tools (SIFT, Polyphen-2, I-Mutant, ConSurf) were used to identify 29 deleterious SNPs out of 1600CYP11B2SNPs. In the second part, five residues (R448G, R141P, W260R, F130S, and F445S) were identified in the active site cavity (out of 29 deleterious CYP11B2 SNPs) at the distance of 5A°. Binding free energy calculation as well as Dynamics simulation techniques were applied to determine the effect of these mutations on the CYP11B2-Fadrozole compound. The results showed thatFadrozolebinding with CYP11B2 became stronger which proved the efficiency of this drug inhibitor with these highly damaging mutations. Our study will be useful for selecting the high priority CYP11B2 mutations, which could be further, investigated in this gene-associated study, for better understanding of the structural and functional aspects of the observed (CYP11B2) protein.

scholarly journals Structure-Based Virtual Screening of Tumor Necrosis Factor-α Inhibitors by Cheminformatics Approaches and Bio-Molecular Simulation

Biomolecules ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 329
Author(s):  
Sobia Ahsan Halim ◽  
Almas Gul Sikandari ◽  
Ajmal Khan ◽  
Abdul Wadood ◽  
Muhammad Qaiser Fatmi ◽  
...  
Keyword(s):  
Tumor Necrosis Factor ◽  
Virtual Screening ◽  
Tumor Necrosis ◽  
Tumor Necrosis Factor Α ◽  
Binding Free Energy ◽  
Dynamics Simulation ◽  
Energy Calculation ◽  
Tnf Α ◽  
Factor Α ◽  
Necrosis Factor

Tumor necrosis factor-α (TNF-α) is a drug target in rheumatoid arthritis and several other auto-immune disorders. TNF-α binds with TNF receptors (TNFR), located on the surface of several immunological cells to exert its effect. Hence, the use of inhibitors that can hinder the complex formation of TNF-α/TNFR can be of medicinal significance. In this study, multiple chem-informatics approaches, including descriptor-based screening, 2D-similarity searching, and pharmacophore modelling were applied to screen new TNF-α inhibitors. Subsequently, multiple-docking protocols were used, and four-fold post-docking results were analyzed by consensus approach. After structure-based virtual screening, seventeen compounds were mutually ranked in top-ranked position by all the docking programs. Those identified hits target TNF-α dimer and effectively block TNF-α/TNFR interface. The predicted pharmacokinetics and physiological properties of the selected hits revealed that, out of seventeen, seven compounds (4, 5, 10, 11, 13–15) possessed excellent ADMET profile. These seven compounds plus three more molecules (7, 8 and 9) were chosen for molecular dynamics simulation studies to probe into ligand-induced structural and dynamic behavior of TNF-α, followed by ligand-TNF-α binding free energy calculation using MM-PBSA. The MM-PBSA calculations revealed that compounds 4, 5, 7 and 9 possess highest affinity for TNF-α; 8, 11, 13–15 exhibited moderate affinities, while compound 10 showed weaker binding affinity with TNF-α. This study provides valuable insights to design more potent and selective inhibitors of TNF-α, that will help to treat inflammatory disorders.

scholarly journals De novo ssRNA Aptamers against the SARS-CoV-2 Main Protease: In Silico Design and Molecular Dynamics Simulation

2021 ◽  
Vol 22 (13) ◽  
pp. 6874
Author(s):  
Francesco Morena ◽  
Chiara Argentati ◽  
Ilaria Tortorella ◽  
Carla Emiliani ◽  
Sabata Martino
Keyword(s):  
De Novo ◽  
Binding Free Energy ◽  
3D Structure ◽  
Dynamics Simulation ◽  
Stable Complex ◽  
Therapeutic Drug ◽  
Energy Calculation ◽  
Potential Candidate ◽  
Initial Sequence ◽  
Main Protease

Herein, we have generated ssRNA aptamers to inhibit SARS-CoV-2 Mpro, a protease necessary for the SARS-CoV-2 coronavirus replication. Because there is no aptamer 3D structure currently available in the databanks for this protein, first, we modeled an ssRNA aptamer using an entropic fragment-based strategy. We refined the initial sequence and 3D structure by using two sequential approaches, consisting of an elitist genetic algorithm and an RNA inverse process. We identified three specific aptamers against SARS-CoV-2 Mpro, called MAptapro, MAptapro-IR1, and MAptapro-IR2, with similar 3D conformations and that fall in the dimerization region of the SARS-CoV-2 Mpro necessary for the enzymatic activity. Through the molecular dynamic simulation and binding free energy calculation, the interaction between the MAptapro-IR1 aptamer and the SARS-CoV-2 Mpro enzyme resulted in the strongest and the highest stable complex; therefore, the ssRNA MAptapro-IR1 aptamer was selected as the best potential candidate for the inhibition of SARS-CoV-2 Mpro and a perspective therapeutic drug for the COVID-19 disease.

scholarly journals A Drug Repurposing Approach to Identify Therapeutics by Screening Medicines for Malaria Ventures Exploiting SARS-CoV-2 Main Protease

2021 ◽  
Author(s):  
Rashmi Tyagi ◽  
Anubrata Paul ◽  
V. Samuel Raj ◽  
Krishna Kumar Ojha ◽  
Manoj Kumar Yadav
Keyword(s):  
Free Energy ◽  
Catalytic Domain ◽  
Binding Free Energy ◽  
Dynamics Simulation ◽  
Radius Of Gyration ◽  
Energy Calculation ◽  
High Morbidity ◽  
Molecular Docking Study ◽  
Virus Propagation ◽  
Main Protease

<p>COVID-19 pandemic makes the human-kind standstill and results in high morbidity and mortality cases worldwide. Still, there are no approved antiviral drugs with proven efficacy nor any therapeutic vaccines to combat the disease as per the current date. In the present study, SARS-CoV-2 main protease (Mpro) has been taken as a potential drug target considering its crucial role in virus propagation. We have used 400 diverse bioactive inhibitors with proven antibacterial and antiviral properties for screening against Mpro target. Our screening result identifies ten compounds with higher binding affinity than N3 (used as a reference compound to validate the experiment). All the compounds possess desire physicochemical properties. Later on, in-depth docking and superimposition of selected complexes confirm that only three compounds (MMV1782211, MMV1782220 and MMV1578574) are actively interacting with the catalytic domain of Mpro. </p> <p>Furthermore, the selected three molecules complexed with Mpro and N3-Mpro as control are subjected to molecular dynamics simulation study (root means square deviation, root mean square fluctuation, hydrogen bonding, solvent-accessible area and radius of gyration). MMV1782211-Mpro complex shows a strong and stable interaction as compared to others. The MM/PBSA free energy calculation shows the highest binding free energy of –115.8 kJ/mol for MMV1782211 compound also cross-confirms our molecular docking study. Therefore, our <i>in silico</i> findings become very interesting towards developing alternative medicine against SARS-CoV-2 Mpro target. So, we can expect prompt actions in this direction to combat the COVID-19.</p>

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