Computational design of oligosaccharide producing levansucrase from Bacillus licheniformis RN-01 to improve its thermostability for production of levan-type fructooligosaccharides from sucrose

2020

J. Phys. Chem. B

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SARS-CoV-2 is the novel coronavirus causing the COVID-19 pandemic. To enter human cells, the receptor-binding domain (RBD) of the S1 subunit of SARS-CoV-2 (SARS-CoV-2-RBD) initially binds to the peptidase domain of angiotensin-converting enzyme 2 receptor (ACE2-PD). Using peptides to inhibit SARS-CoV-2-RBD binding to ACE2 is a potential therapeutic solution for COVID-19. A previous study identified a 23-mer peptide (SBP1) that bound to SARS-CoV-2-RBD with comparable K D to ACE2. We employed computational protein design and molecular dynamics (MD) to design SARS-CoV-2-RBD 25-mer peptide binders (SPB25) with better predicted binding affinity than SBP1. Using residues 21−45 of the α1 helix of ACE2-PD as the template, our strategy is employing Rosetta to enhance SPB25 binding affinity to SARS-CoV-2-RBD and avoid disrupting existing favorable interactions by using residues that have not been reported to form favorable interactions with SARS-CoV-2-RBD as designed positions. Designed peptides with better predicted binding affinities, by Rosetta, than SPB25 were subjected to MD validation. The MD results show that five designed peptides (SPB25 F8N , SPB25 F8R , SPB25 L25R , SPB25 F8N/L25R , and SPB25 F8R/L25R ) have better predicted binding affinities, by the MM-GBSA method, than SPB25 and SBP1. This study developed an approach to design SARS-CoV-2-RBD peptide binders, and these peptides may be promising candidates as potential SARS-CoV-2 inhibitors.

Section: Methodsmentioning

confidence: 99%

Computational Design of 25-mer Peptide Binders of SARS-CoV-2

2020

J. Phys. Chem. B

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“…In this study, a hydrogen bond was considered to occur if the following criteria were met: (1) a proton donor–acceptor distance ≤ 3.5 Å and (2) a donor-H-acceptor bond angle ≥ 120° 42 , 54 , 55 , 64 . Hydrogen bond occupations were defined into four levels: (1) strong hydrogen bonds (hydrogen bond occupations > 75%), (2) medium hydrogen bonds (75% ≥ hydrogen bond occupations > 50%), (3) weak hydrogen bond interactions (50% ≥ hydrogen bond occupations > 25%) and (4) very weak hydrogen bond interactions (25% ≥ hydrogen bond occupations > 5%) 42 , 55 , 56 . To compute peptide helicities, Define Secondary Structure of Protein (DSSP) was employed.…”

Section: Methodsmentioning

confidence: 99%

“…Using protein.ff14SB 52 and GLYCAM06j-1 force field parameters 53 in AMBER18 46 , the structures of designed peptides/SARS-CoV-2-RBD complexes were constructed in isomeric truncated octahedral boxes of TIP3P water molecules with the buffer distance of 13 Å. Each system was minimized using the five-step procedure 42,[54][55][56][57][58][59] . All minimization steps include 2500 steps of steepest descent and www.nature.com/scientificreports/ 2500 steps of conjugate gradient with different restraints on the proteins to remove unfavorable interactions.…”

Section: Computational Protein Designmentioning

confidence: 99%

Computational design of SARS-CoV-2 peptide binders with better predicted binding affinities than human ACE2 receptor

2021

Sci Rep

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SARS-CoV-2 is coronavirus causing COVID-19 pandemic. To enter human cells, receptor binding domain of S1 subunit of SARS-CoV-2 (SARS-CoV-2-RBD) binds to peptidase domain (PD) of angiotensin-converting enzyme 2 (ACE2) receptor. Employing peptides to inhibit binding between SARS-CoV-2-RBD and ACE2-PD is a therapeutic solution for COVID-19. Previous experimental study found that 23-mer peptide (SBP1) bound to SARS-CoV-2-RBD with lower affinity than ACE2. To increase SBP1 affinity, our previous study used residues 21–45 of α1 helix of ACE2-PD (SPB25) to design peptides with predicted affinity better than SBP1 and SPB25 by increasing interactions of residues that do not form favorable interactions with SARS-CoV-2-RBD. To design SPB25 with better affinity than ACE2, we employed computational protein design to increase interactions of residues reported to form favorable interactions with SARS-CoV-2-RBD and combine newly designed mutations with the best single mutations from our previous study. Molecular dynamics show that predicted binding affinities of three peptides (SPB25Q22R, SPB25F8R/K11W/L25R and SPB25F8R/K11F/Q22R/L25R) are better than ACE2. Moreover, their predicted stabilities may be slightly higher than SBP1 as suggested by their helicities. This study developed an approach to design SARS-CoV-2 peptide binders with predicted binding affinities better than ACE2. These designed peptides are promising candidates as SARS-CoV-2 inhibitors.

“…LEaP module was employed to construct the structure of alternansucrase with glc-D635 intermediate. It was minimized with the five-step procedure [47][48][49][50][51][52][53]. Then, the system was heated, equilibrated and subsequently simulated for the production run at the experimental temperature of 310 K for 70 ns.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Unravelling Regioselectivity of Leuconostoc citreum ABK-1 Alternansucrase by Acceptor Site Engineering

Wangpaiboon

et al. 2021

IJMS

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Alternansucrase (ALT, EC 2.4.1.140) is a glucansucrase that can generate α-(1,3/1,6)-linked glucan from sucrose. Previously, the crystal structure of the first alternansucrase from Leuconostoc citreum NRRL B-1355 was successfully elucidated; it showed that alternansucrase might have two acceptor subsites (W675 and W543) responsible for the formation of alternating linked glucan. This work aimed to investigate the primary acceptor subsite (W675) by saturated mutagenesis using Leuconostoc citreum ABK-1 alternansucrase (LcALT). The substitution of other residues led to loss of overall activity, and formation of an alternan polymer with a nanoglucan was maintained when W675 was replaced with other aromatic residues. Conversely, substitution by nonaromatic residues led to the synthesis of oligosaccharides. Mutations at W675 could potentially cause LcALT to lose control of the acceptor molecule binding via maltose–acceptor reaction—as demonstrated by results from molecular dynamics simulations of the W675A variant. The formation of α-(1,2), α-(1,3), α-(1,4), and α-(1,6) linkages were detected from products of the W675A mutant. In contrast, the wild-type enzyme strictly synthesized α-(1,6) linkage on the maltose acceptor. This study examined the importance of W675 for transglycosylation, processivity, and regioselectivity of glucansucrases. Engineering glucansucrase active sites is one of the essential approaches to green tools for carbohydrate modification.