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 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 Screening marine algae metabolites as high-affinity inhibitors of SARS-CoV-2 main protease (3CLpro): an in silico analysis to identify novel drug candidates to combat COVID-19 pandemic

2020 ◽  
Vol 63 (1) ◽  
Author(s):  
Ghazala Muteeb ◽  
Adil Alshoaibi ◽  
Mohammad Aatif ◽  
Md. Tabish Rehman ◽  
M. Zuhaib Qayyum
Keyword(s):  
Hydrophobic Interactions ◽  
In Silico Analysis ◽  
Salt Bridge ◽  
Competitive Inhibitor ◽  
Binding Energies ◽  
Dynamics Simulation ◽  
In Vivo Studies ◽  
Energy Calculation

AbstractThe recent dissemination of SARS-CoV-2 from Wuhan city to all over the world has created a pandemic. COVID-19 has cost many human lives and created an enormous economic burden. Although many drugs/vaccines are in different stages of clinical trials, still none is clinically available. We have screened a marine seaweed database (1110 compounds) against 3CLpro of SARS-CoV-2 using computational approaches. High throughput virtual screening was performed on compounds, and 86 of them with docking score <  − 5.000 kcal mol−1 were subjected to standard-precision docking. Based on binding energies (< − 6.000 kcal mol−1), 9 compounds were further shortlisted and subjected to extra-precision docking. Free energy calculation by Prime-MM/GBSA suggested RC002, GA004, and GA006 as the most potent inhibitors of 3CLpro. An analysis of ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties of RC002, GA004, and GA006 indicated that only RC002 (callophysin A, from red alga Callophycus oppositifolius) passed Lipinski’s, Veber’s, PAINS and Brenk’s filters and displayed drug-like and lead-like properties. Analysis of 3CLpro-callophysin A complex revealed the involvement of salt bridge, hydrogen bonds, and hydrophobic interactions. callophysin A interacted with the catalytic residues (His41 and Cys145) of 3CLpro; hence it may act as a mechanism-based competitive inhibitor. Docking energy and docking affinity of callophysin A towards 3CLpro was − 8.776 kcal mol−1 and 2.73 × 106 M−1, respectively. Molecular dynamics simulation confirmed the stability of the 3CLpro-callophysin A complex. The findings of this study may serve as the basis for further validation by in vitro and in vivo studies.

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 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>

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 Structural and computational insights into the SARS-CoV-2 Omicron RBD-ACE2 interaction

2022 ◽  
Author(s):  
xinquan wang ◽  
Tong Wang ◽  
Jiwan Ge ◽  
Linqi Zhang ◽  
Jun Lan ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Immune Escape ◽  
Binding Free Energy ◽  
Viral Fitness ◽  
Dynamics Simulation ◽  
Energy Calculation ◽  
Structural Comparison ◽  
Antibody Recognition ◽  
Markov State Model ◽  
Local Conformation

Since SARS-CoV-2 Omicron variant (B.1.1.529) was reported in November 2021, it has quickly spread to many countries and outcompeted the globally dominant Delta variant in several countries. The Omicron variant contains the largest number of mutations to date, with 32 mutations located at spike (S) glycoprotein, which raised great concern for its enhanced viral fitness and immune escape[1-4]. In this study, we reported the crystal structure of the receptor binding domain (RBD) of Omicron variant S glycoprotein bound to human ACE2 at a resolution of 2.6 angstrom. Structural comparison, molecular dynamics simulation and binding free energy calculation collectively identified four key mutations (S477N, G496S, Q498R and N501Y) for the enhanced binding of ACE2 by the Omicron RBD compared to the WT RBD. Representative states of the WT and Omicron RBD-ACE2 systems were identified by Markov State Model, which provides a dynamic explanation for the enhanced binding of Omicron RBD. The effects of the mutations in the RBD for antibody recognition were analyzed, especially for the S371L/S373P/S375F substitutions significantly changing the local conformation of the residing loop to deactivate several class IV neutralizing antibodies.

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