Insight into Structural Characteristics of Protein-Substrate Interaction in Pimaricin Thioesterase

As a polyene antibiotic of great pharmaceutical significance, pimaricin has been extensively studied to enhance its productivity and effectiveness. In our previous studies, pre-reaction state (PRS) has been validated as one of the significant conformational categories before macrocyclization, and is critical to mutual recognition and catalytic preparation in thioesterase (TE)-catalyzed systems. In our study, molecular dynamics (MD) simulations were conducted on pimaricin TE-polyketide complex and PRS, as well as pre-organization state (POS), a molecular conformation possessing a pivotal intra-molecular hydrogen bond, were detected. Conformational transition between POS and PRS was observed in one of the simulations, and POS was calculated to be energetically more stable than PRS by 4.58 kcal/mol. The structural characteristics of PRS and POS-based hydrogen-bonding, and hydrophobic interactions were uncovered, and additional simulations were carried out to rationalize the functions of several key residues (Q29, M210, and R186). Binding energies, obtained from MM/PBSA calculations, were further decomposed to residues, in order to reveal their roles in product release. Our study advanced a comprehensive understanding of pimaricin TE-catalyzed macrocyclization from the perspectives of conformational change, protein-polyketide recognition, and product release, and provided potential residues for rational modification of pimaricin TE.

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Conformational Change of H64 and Substrate Transportation: Insight Into a Full Picture of Enzymatic Hydration of CO2 by Carbonic Anhydrase

Frontiers in Chemistry ◽

10.3389/fchem.2021.706959 ◽

2021 ◽

Vol 9 ◽

Author(s):

Yuzhuang Fu ◽

Fangfang Fan ◽

Yuwei Zhang ◽

Binju Wang ◽

Zexing Cao

Keyword(s):

Free Energy ◽

Carbonic Anhydrase ◽

Proton Transfer ◽

Energy Barrier ◽

Conformational Transition ◽

Md Simulations ◽

Nucleophilic Attack ◽

Free Energy Barrier ◽

Full Picture ◽

Key Residues

The enzymatic hydration of CO2 into HCO3− by carbonic anhydrase (CA) is highly efficient and environment-friendly measure for CO2 sequestration. Here extensive MM MD and QM/MM MD simulations were used to explore the whole enzymatic process, and a full picture of the enzymatic hydration of CO2 by CA was achieved. Prior to CO2 hydration, the proton transfer from the water molecule (WT1) to H64 is the rate-limiting step with the free energy barrier of 10.4 kcal/mol, which leads to the ready state with the Zn-bound OH−. The nucleophilic attack of OH− on CO2 produces HCO3− with the free energy barrier of 4.4 kcal/mol and the free energy release of about 8.0 kcal/mol. Q92 as the key residue manipulates both CO2 transportation to the active site and release of HCO3−. The unprotonated H64 in CA prefers in an inward orientation, while the outward conformation is favorable energetically for its protonated counterpart. The conformational transition of H64 between inward and outward correlates with its protonation state, which is mediated by the proton transfer and the product release. The whole enzymatic cycle has the free energy span of 10.4 kcal/mol for the initial proton transfer step and the free energy change of −6.5 kcal/mol. The mechanistic details provide a comprehensive understanding of the entire reversible conversion of CO2 into bicarbonate and roles of key residues in chemical and nonchemical steps for the enzymatic hydration of CO2.

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Key Interacting Residues Between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamic Simulation and Density Functional Calculation

10.26434/chemrxiv.14582484.v1 ◽

2021 ◽

Author(s):

Bahaa Jawad ◽

Puja Adhikari ◽

Rudolf Podgornik ◽

Wai-Yim Ching

Keyword(s):

Density Functional ◽

Vaccine Development ◽

Hydrophobic Interactions ◽

Binding Free Energy ◽

Tight Binding ◽

Md Simulations ◽

Functional Theory ◽

Generalized Born ◽

The Density Functional Theory ◽

Key Residues

The spike protein of SARS-CoV-2 binds to ACE2 receptor via its receptor-binding domain (RBD), with the RBD-ACE2 complex presenting an essential molecular target for vaccine development to stall the virus infection proliferation. The computational analysis at molecular, amino acid (AA) and atomic levels have been performed systematically to identify the key interacting AAs in the formation of the RBD-ACE2 complex, including the MD simulations with molecular mechanics generalized Born surface area (MM-GBSA) method to predict binding free energy (BFE) and to determine the actual interacting AAs, as well as two ab initio quantum chemical protocols based on the density functional theory (DFT) implementation. Based on MD results, Q493, Y505, Q498, N501, T500, N487, Y449, F486, K417, Y489, F456, Y495, and L455 have been identified as hotspots in RBD, while those in ACE2 are K353, K31, D30, D355, H34, D38, Q24, T27, Y83, Y41, E35, and E37. Both the electrostatic and hydrophobic interactions are the main driving force to form the AA-AA binding pairs. We confirm that Q493, N501, F486, K417, and F456 in RBD are the key residues responsible for the tight binding of SARS-CoV-2 with ACE2 compared to SARS-CoV. The DFT results reveal that N487, Q493, Y449, T500, G496, G446 and G502 in RBD form pairs via specific hydrogen bonding with Q24, H34, E35, D38, Y41, Q42 and K353 in ACE2.

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Key Interacting Residues Between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamic Simulation and Density Functional Calculation

10.26434/chemrxiv.14582484 ◽

2021 ◽

Author(s):

Bahaa Jawad ◽

Puja Adhikari ◽

Rudolf Podgornik ◽

Wai-Yim Ching

Keyword(s):

Density Functional ◽

Vaccine Development ◽

Hydrophobic Interactions ◽

Binding Free Energy ◽

Tight Binding ◽

Md Simulations ◽

Functional Theory ◽

Generalized Born ◽

The Density Functional Theory ◽

Key Residues

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Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type

Biomolecules ◽

10.3390/biom11070919 ◽

2021 ◽

Vol 11 (7) ◽

pp. 919

Author(s):

Anwar Mohammad ◽

Fahd Al-Mulla ◽

Dong-Qing Wei ◽

Jehad Abubaker

Keyword(s):

Rna Polymerase ◽

Molecular Conformation ◽

Antiviral Drug ◽

Md Simulations ◽

Binding Energies ◽

Wild Type ◽

Rna Dependent Rna Polymerase ◽

Dynamic Motion ◽

Similar Dynamic ◽

Insight Into

SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) protein is the target for the antiviral drug Remdesivir (RDV). With RDV clinical trials on COVID-19 patients showing a reduced hospitalisation time. During the spread of the virus, the RdRp has developed several mutations, with the most frequent being A97V and P323L. The current study sought to investigate whether A97V and P323L mutations influence the binding of RDV to the RdRp of SARS-CoV-2 compared to wild-type (WT). The interaction of RDV with WT-, A97V-, and P323L-RdRp were measured using molecular dynamic (MD) simulations, and the free binding energies were extracted. Results showed that RDV that bound to WT- and A97V-RdRp had a similar dynamic motion and internal residue fluctuations, whereas RDV interaction with P323L-RdRp exhibited a tighter molecular conformation, with a high internal motion near the active site. This was further corroborated with RDV showing a higher binding affinity to P323L-RdRp (−24.1 kcal/mol) in comparison to WT-RdRp (−17.3 kcal/mol). This study provides insight into the potential significance of administering RDV to patients carrying the SARS-CoV-2 P323L-RdRp mutation, which may have a more favourable chance of alleviating the SARS-CoV-2 illness in comparison to WT-RdRp carriers, thereby suggesting further scientific consensus for the usage of Remdesivir as clinical candidate against COVID-19.

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Biochemical study of fibrinolytic protease from Euphausia superba possessing multifunctional serine protease activity

Protein and Peptide Letters ◽

10.2174/0929866527666201112123714 ◽

2020 ◽

Vol 27 ◽

Author(s):

Guo-Ying Qian ◽

Gyutae Lim ◽

Shang-Jun Yin ◽

Jun-Mo Yang ◽

Jinhyuk Lee ◽

...

Keyword(s):

Defense Mechanisms ◽

Fluorescence Spectra ◽

Biochemical Study ◽

Euphausia Superba ◽

Md Simulations ◽

Time Interval ◽

Serine Residue ◽

Catalytic Function ◽

Serine Protease Activity ◽

Key Residues

Background: Background: Fibrinolytic protease from Euphausia superba (EFP) was isolated. Objective: Biochemical distinctions, regulation of the catalytic function, and the key residues of EFP were investigated. Methods: The serial inhibition kinetic evaluations coupled with measurements of fluorescence spectra in the presence of 4- (2-aminoethyl) benzene sulfonyl fluoride hydrochloride (AEBSF) was conducted. The computational molecular dynamics (MD) simulations were also applied for a comparative study. Results: The enzyme behaved as a monomeric protein with a molecular mass of about 28.6 kD with Km BApNA = 0.629 ± 0.02 mM and kcat/Km BApNA = 7.08 s-1 /mM. The real-time interval measurements revealed that the inactivation was a first-order reaction, with the kinetic processes shifting from a monophase to a biphase. Measurements of fluorescence spectra showed that serine residue modification by AEBSF directly caused conspicuous changes of the tertiary structures and exposed hydrophobic surfaces. Some osmolytes were applied to find protective roles. These results confirmed that the active region of EFP is more flexible than the overall enzyme molecule and serine, as the key residue, is associated with the regional unfolding of EFP in addition to its catalytic role. The MD simulations were supportive to the kinetics data. Conclusion: Our study indicated that EFP has an essential serine residue for its catalyst function and associated folding behaviors. Also, the functional role of osmolytes such as proline and glycine that may play a role in defense mechanisms from environmental adaptation in a krill’s body was suggested.

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Closing the gap: an atomistic structural and functional perspective of S. mansoni universal stress G4LZI3 protein in complex with phenolic compounds

Current Drug Discovery Technologies ◽

10.2174/1570163817666201001122436 ◽

2020 ◽

Vol 17 ◽

Author(s):

Priscilla Masamba ◽

Geraldene Munsamy ◽

Abidemi Paul Kappo

Keyword(s):

Phenolic Compounds ◽

Conformational Changes ◽

Stress Protein ◽

Md Simulations ◽

Binding Energies ◽

Developmental Cycle ◽

Structure Based Drug Design ◽

Bioinformatic Tools ◽

Drug Of Choice ◽

Functional Perspective

Background: For decades, Praziquantel has been the undisputed drug of choice for all schistosome infections, but rising concerns due to the unelucidated mechanism of action of the drug and unavoidable reports of emerging drug resistant strains has necessitated the need for alternative treatment drug. Moreover, current apprehension has been reinforced by total dependence on the drug for treatment hence, the search for novel and effective anti-schistosomal drugs. Uses: This study made use of bioinformatic tools to determine the structural binding of the Universal G4LZI3 stress protein (USP) in complex with ten polyphenol compounds, thereby highlighting the effectiveness of these recently identified ‘lead’ molecules in the design of novel therapeutics targeted against schistosomiasis. Upregulation of the G4LZI3 USP throughout the schistosome multifaceted developmental cycle sparks interest in its potential role as a druggable target. The integration of in silico tools provides an atomistic perspective into the binding of potential inhibitors to target proteins. Conclusion: This study therefore, implemented the use of molecular dynamic (MD) simulations to provide functional and structural insight into key conformational changes upon binding of G4ZLI3 to these key phenolic compounds. Post-MD analyses revealed unique structural and conformational changes in the G4LZI3 protein in complex with curcumin and catechin respectively. These systems exhibited the highest binding energies, while the major interacting residues conserved in all the complexes provides a route map for structure-based drug design of novel compounds with enhanced inhibitory potency against the G4LZI3 protein. This study suggests an alternative approach for the development of anti-schistosomal drugs using natural compounds.

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Hydrophobic interactions in human casein micelle formation: β-casein aggregation

Journal of Dairy Research ◽

10.1017/s0022029900028909 ◽

1989 ◽

Vol 56 (3) ◽

pp. 427-433 ◽

Cited By ~ 22

Author(s):

Charles W. Slattery ◽

Satish M. Sood ◽

Pat Chang

Keyword(s):

Light Scattering ◽

Conformational Transition ◽

Hydrophobic Interactions ◽

Micelle Formation ◽

Tryptophan Fluorescence ◽

Phosphate Esters ◽

Casein Micelle ◽

Protein Association ◽

P Protein ◽

Micelle Size

SummaryThe association of non-phosphorylated (0-P) and fully phosphorylated (5-P) human β-caseins was studied by fluorescence spectroscopy and laser light scattering. The tryptophan fluorescence intensity (FI) level increased between 20 and 35 °C, indicating a change in the environment of that residue. A similar transition occurred when ANS was used as a probe. Transition temperatures were slightly lower in 10 mM-CaCl2 but were not affected by an equivalent increase in ionic strength caused by NaCl. The magnitude of the FI change was less for the 5-P than the 0-P protein but was increased for both by CaCl2 addition. These FI data were characteristic of a conformational change and this was supported by fluorescence polarization which indicated that with CaCl2, tryptophan and ANS mobility increased at the transition temperature even though the extent of protein association also increased. Light scattering suggested that protein association proeeeded with the primary formation of submicellar aggregates containing 20–30 monomers which then associated further to form particles of minimum micelle size (12–15 submicelles), and eventually larger. The temperature of precipitation of the 5-P form in the presence of CaCl2 was lower than the conformational transition and suggested that both hydrophobic interactions and Ca bridges between phosphate esters on adjacent molecules are important in micelle formation.

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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

Applied Biological Chemistry ◽

10.1186/s13765-020-00564-4 ◽

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.

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Exploration of Novel Xanthine Oxidase Inhibitors Based on 1,6-Dihydropyrimidine-5-Carboxylic Acids by an Integrated in Silico Study

International Journal of Molecular Sciences ◽

10.3390/ijms22158122 ◽

2021 ◽

Vol 22 (15) ◽

pp. 8122

Author(s):

Na Zhai ◽

Chenchen Wang ◽

Fengshou Wu ◽

Liwei Xiong ◽

Xiaogang Luo ◽

...

Keyword(s):

Xanthine Oxidase ◽

Carboxylic Acids ◽

Hydrophobic Interactions ◽

Pharmacophore Model ◽

3D Qsar ◽

Md Simulations ◽

Pharmacophore Modeling ◽

Binding Modes ◽

Comfa Model ◽

Validation Parameters

Xanthine oxidase (XO) is an important target for the effective treatment of hyperuricemia-associated diseases. A series of novel 2-substituted 6-oxo-1,6-dihydropyrimidine-5-carboxylic acids (ODCs) as XO inhibitors (XOIs) with remarkable activities have been reported recently. To better understand the key pharmacological characteristics of these XOIs and explore more hit compounds, in the present study, the three-dimensional quantitative structure–activity relationship (3D-QSAR), molecular docking, pharmacophore modeling, and molecular dynamics (MD) studies were performed on 46 ODCs. The constructed 3D-QSAR models exhibited reliable predictability with satisfactory validation parameters, including q2 = 0.897, R2 = 0.983, rpred2 = 0.948 in a CoMFA model, and q2 = 0.922, R2 = 0.990, rpred2 = 0.840 in a CoMSIA model. Docking and MD simulations further gave insights into the binding modes of these ODCs with the XO protein. The results indicated that key residues Glu802, Arg880, Asn768, Thr1010, Phe914, and Phe1009 could interact with ODCs by hydrogen bonds, π-π stackings, or hydrophobic interactions, which might be significant for the activity of these XOIs. Four potential hits were virtually screened out using the constructed pharmacophore model in combination with molecular dockings and ADME predictions. The four hits were also found to be relatively stable in the binding pocket by MD simulations. The results in this study might provide effective information for the design and development of novel XOIs.

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Polypharmacology of Some Medicinal Plant Metabolites Against SARS-CoV-2 and Host Targets: Molecular Dynamics Evaluation of NSP9 RNA Binding Protein

10.26434/chemrxiv.12945833 ◽

2020 ◽

Author(s):

Suritra Bandyopadhyay ◽

Omobolanle Abimbola Abiodun ◽

Blessing Chinweotito Ogboo ◽

Adeola Tawakalitu Kola-Mustapha ◽

Emmanuel Ifeanyi Attah ◽

...

Keyword(s):

Molecular Dynamics ◽

Medicinal Plants ◽

Active Sites ◽

Rna Binding ◽

Hydrophobic Interactions ◽

Binding Energies ◽

Dynamics Simulation ◽

Receptor Interaction ◽

Plant Metabolites ◽

Structure Comparison

Background: Medicinal plants, as rich sources of bioactive compounds with antiviral properties, are now being explored for the development of drugs against SARS-CoV-2.Aims: Identification of promising compounds for the treatment of COVID-19 from natural products via molecular modelling against NSP9, including some other viral and host targets and evaluation of polypharmacological indications.Main methods: A manually curated library of 521 phytochemicals (from 19 medicinal plants) was virtually screened using Mcule server and binding interactions were studied using DS Visualiser. Docking thresholds were set based on the scores of standard controls and rigorous ADMET properties were used to finally get the potential inhibitors. Free binding energies of the docked complexes were calculated employing MM-GBSA method. MM-GBSA informed our choice for MD simulation studies performed against NSP9 to study the stability of the drug-receptor interaction. NSP9 structure comparison was also performed. Key findings: Extensive screening of the molecules identified 5 leads for NSP9, 23 for Furin, 18 for ORF3a, and 19 for interleukin-6. Ochnaflavone and Licoflavone B, obtained from Lonicera japonica (Japanese Honeysuckle) and Glycyrrhiza glabra (Licorice), respectively, were identified to have the highest potential multi-target inhibition properties for NSP9, furin, ORF3a, and IL-6. Additionally, molecular dynamics simulation supports the robust stability of Ochnaflavone and Licoflavone B against NSP9 at the active sites via hydrophobic interactions, H-bonding, and H-bonding facilitated by water.Significance: These compounds with the highest drug-like ranking against multiple viral and host targets have the potential to be drug candidates for the treatment of SARS-CoV-2 infection that may possibly act on multiple pathways simultaneously to inhibit viral entry and replication as well as disease progression.

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