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Article ; Online: Quantifying the adhesive strength between the SARS-CoV-2 S-proteins and human receptor and its effect in therapeutics.

Ponga, Mauricio

2020 Volume 10, Issue 1, Page(s) 17538

Abstract: The binding affinity and adhesive strength between the spike (S) glycoproteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the human angiotensin-converting enzyme 2 (ACE2) receptor is computed using molecular dynamics (MD) ... ...

Abstract	The binding affinity and adhesive strength between the spike (S) glycoproteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the human angiotensin-converting enzyme 2 (ACE2) receptor is computed using molecular dynamics (MD) simulations. The calculations indicate that the binding affinity is [Formula: see text] [Formula: see text] with a maximum adhesive force of [Formula: see text] pN. Our analysis suggests that only 27 (13 in S-protein, 14 in ACE2) residues are active during the initial fusion process between the S-protein and ACE2 receptor. With these insights, we investigated the effect of possible therapeutics in the size and wrapping time of virus particles by reducing the binding energy. Our analysis indicates that this energy has to be reduced significantly, around 50% or more, to block SARS-CoV-2 particles with radius in the order of [Formula: see text] nm. Our study provides concise target residues and target binding energy reduction between S-proteins and receptors for the development of new therapeutics treatments for COVID-19 guided by computational design.
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; Betacoronavirus/isolation & purification ; Binding Sites ; COVID-19 ; Coronavirus Infections/pathology ; Coronavirus Infections/virology ; Endocytosis ; Humans ; Molecular Dynamics Simulation ; Pandemics ; Peptidyl-Dipeptidase A/metabolism ; Pneumonia, Viral/pathology ; Pneumonia, Viral/virology ; Protein Binding ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/metabolism ; Static Electricity ; Thermodynamics
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Keywords	covid19
Language	English
Publishing date	2020-10-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-74189-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Quantifying the adhesive strength between the SARS-CoV-2 S-proteins and human receptor and its effect in therapeutics

Mauricio Ponga

Scientific Reports, Vol 10, Iss 1, Pp 1-

2020 Volume 7

Abstract: Abstract The binding affinity and adhesive strength between the spike (S) glycoproteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the human angiotensin-converting enzyme 2 (ACE2) receptor is computed using molecular ... ...

Abstract	Abstract The binding affinity and adhesive strength between the spike (S) glycoproteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the human angiotensin-converting enzyme 2 (ACE2) receptor is computed using molecular dynamics (MD) simulations. The calculations indicate that the binding affinity is $$e_{RS}= 12.6 \pm 1$$ e RS = 12.6 ± 1 $$\hbox {kCal}{\cdot }\hbox {mol}^{-1}$$ kCal · mol - 1 with a maximum adhesive force of $$\sim 102$$ ∼ 102 pN. Our analysis suggests that only 27 (13 in S-protein, 14 in ACE2) residues are active during the initial fusion process between the S-protein and ACE2 receptor. With these insights, we investigated the effect of possible therapeutics in the size and wrapping time of virus particles by reducing the binding energy. Our analysis indicates that this energy has to be reduced significantly, around 50% or more, to block SARS-CoV-2 particles with radius in the order of $$R\le 60$$ R ≤ 60 nm. Our study provides concise target residues and target binding energy reduction between S-proteins and receptors for the development of new therapeutics treatments for COVID-19 guided by computational design.
Keywords	Medicine ; R ; Science ; Q ; covid19
Subject code	612
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Quantifying the adhesive strength between the SARS-CoV-2 S-proteins and human receptor and its effect in therapeutics

Ponga, Mauricio

Sci Rep

Abstract	The binding affinity and adhesive strength between the spike (S) glycoproteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the human angiotensin-converting enzyme 2 (ACE2) receptor is computed using molecular dynamics (MD) simulations. The calculations indicate that the binding affinity is [Formula: see text] [Formula: see text] with a maximum adhesive force of [Formula: see text] pN. Our analysis suggests that only 27 (13 in S-protein, 14 in ACE2) residues are active during the initial fusion process between the S-protein and ACE2 receptor. With these insights, we investigated the effect of possible therapeutics in the size and wrapping time of virus particles by reducing the binding energy. Our analysis indicates that this energy has to be reduced significantly, around 50% or more, to block SARS-CoV-2 particles with radius in the order of [Formula: see text] nm. Our study provides concise target residues and target binding energy reduction between S-proteins and receptors for the development of new therapeutics treatments for COVID-19 guided by computational design.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #872728
Database	COVID19

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Book ; Online: Engineering ultra-strong Mg-Li-Al-based light-weight alloys from first principles

Orhan, Okan K. / Ponga, Mauricio

2022

Abstract: Light-weight alloys are essential pillars of transportation technologies. They also play a crucial role to achieve a more green and cost-effective aerospace technologies. Magnesium-lithium-aluminum (Mg-Li-Al) alloys are auspicious candidates due to their ...

Abstract	Light-weight alloys are essential pillars of transportation technologies. They also play a crucial role to achieve a more green and cost-effective aerospace technologies. Magnesium-lithium-aluminum (Mg-Li-Al) alloys are auspicious candidates due to their promising mechanical strengths at low densities. We herein present a systematic first-principles investigation of the Mg-Li-Al-based alloys to provide insights for designing ultra-strong light-weight alloys. Initial analysis indicates that the Mg-Li-Al mixtures are not thermally stabilized into random-solid solutions. Following this hint, the base-centered cubic (BCC)-based intermetallics of Mg, Li and Al are investigated for their thermal and elastic stabilities.Three simple figures of merits are used to further assess their mechanical strengths. The most-frequently observed intermetallics are used to predict the yield strength of the hetero-structures from the recent experimental works. The rule of mixing works reasonable well to predict the mechanical properties of complex structures starting from isolated intermetallics.
Keywords	Condensed Matter - Materials Science
Subject code	669
Publishing date	2022-11-25
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations.

Hendy, Mohamed / Kaufman, Samuel / Ponga, Mauricio

Scientific reports

2021 Volume 11, Issue 1, Page(s) 21735

Abstract: The COVID19 pandemic, caused by SARS-CoV-2, has infected more than 200 million people worldwide. Due to the rapid spreading of SARS-CoV-2 and its impact, it is paramount to find effective treatments against it. Human neutralizing antibodies are an ... ...

Abstract	The COVID19 pandemic, caused by SARS-CoV-2, has infected more than 200 million people worldwide. Due to the rapid spreading of SARS-CoV-2 and its impact, it is paramount to find effective treatments against it. Human neutralizing antibodies are an effective method to fight viral infection. However, the recent discovery of new strains that substantially change the S-protein sequence has raised concern about vaccines and antibodies' effectiveness. Here, using molecular simulations, we investigated the binding mechanisms between the S-protein and several antibodies. Multiple mutations were included to understand the strategies for antibody escape in new variants. We found that the combination of mutations K417N, E484K, L452R, and T478K produced higher binding energy to ACE2 than the wild type, suggesting higher efficiency to enter host cells. The mutations' effect depends on the antibody class. While Class I enhances the binding avidity in the presence of N501Y mutation, class II antibodies showed a sharp decline in the binding affinity. Our simulations suggest that Class I antibodies will remain effective against the new strains. In contrast, Class II antibodies will have less affinity to the S-protein, potentially affecting these antibodies' efficiency.
MeSH term(s)	Angiotensin-Converting Enzyme 2/chemistry ; Antibodies, Neutralizing/chemistry ; Antibodies, Viral/chemistry ; Antibodies, Viral/immunology ; COVID-19/immunology ; COVID-19/virology ; Cluster Analysis ; Computational Biology ; Computer Simulation ; Humans ; Hydrogen Bonding ; Molecular Conformation ; Molecular Dynamics Simulation ; Mutation ; Protein Binding ; SARS-CoV-2/genetics ; Signal Transduction ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2021-11-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-01081-0
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online: Surface-plasmon properties of noble metals with exotic phases

Orhan, Okan K. / Ponga, Mauricio

2021

Abstract: Noble-metal nanoparticles have been the industry standard for plasmonic applications due to their highly populated plasmon generations. Despite their remarkable plasmonic performance, their widespread use in plasmonic applications is commonly hindered ... ...

Abstract	Noble-metal nanoparticles have been the industry standard for plasmonic applications due to their highly populated plasmon generations. Despite their remarkable plasmonic performance, their widespread use in plasmonic applications is commonly hindered due to limitations on the available laser sources and relatively low operating temperatures needed to retain mechanical strength in these materials. Motivated by recent experimental works, in which exotic hexagonal-closed-packed (HCP) phases have been identified in gold (Au), silver (Ag) and copper (Cu), we present the plasmonic performance of two HCP polytypes in these materials using high-accuracy first-principles simulations. The isolated HCP phases commonly reach thermal and mechanical stability at high temperatures due to monotonically decreasing Gibbs free energy differences compared to the face-centered cubic (FCC) phases. We find that several of these polytypes are harder and produce bulk plasmons at lower energies with comparable lifetimes than their conventional FCC counterparts. It also leads to the localized surface-plasmon resonance (LSPR) in perfectly spherical HCP-phased nanoparticles, embedded onto dielectric matrices, at substantially lower energies with comparable lifetimes to their FCC counterparts. LSPR peak locations and lifetimes can be tuned by controlling the operational temperature, the dielectric permittivity of hosting matrix and the grain size. Our work suggests that noble-metal nanoparticles can be tailored to develop exotic HCP phases to obtain novel plasmonic properties. Comment: 21 pages and 10 figures in the main text. 16 pages and 6 figures in the Supporting Information
Keywords	Condensed Matter - Materials Science ; Physics - Computational Physics ; Physics - Optics
Subject code	669
Publishing date	2021-04-13
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Surface-Plasmon Properties of Noble Metals with Exotic Phases

Orhan, Okan K. / Ponga, Mauricio

Journal of physical chemistry. 2021 Sept. 23, v. 125, no. 39

2021

Abstract	Noble-metal nanoparticles have been the industry standard for plasmonic applications due to their highly populated plasmon generations. Despite their remarkable plasmonic performance, their widespread use in plasmonic applications is commonly hindered due to limitations on the available laser sources and relatively low operating temperatures needed to retain mechanical strength in these materials. Motivated by recent experimental works, in which exotic hexagonal-closed-packed (HCP) phases have been identified in gold (Au), silver (Ag), and copper (Cu), we present the plasmonic performance of two HCP polytypes in these materials using high-accuracy first-principles simulations. The isolated HCP phases commonly reach thermal and mechanical stability at high temperatures due to monotonically decreasing Gibbs free-energy differences compared to face-centered cubic (FCC) phases. We find that several of these polytypes are harder and produce bulk plasmons at lower energies with comparable lifetimes than their conventional FCC counterparts. It also leads to the localized surface-plasmon resonance (LSPR) in perfectly spherical HCP-phased nanoparticles, embedded onto dielectric matrices, at substantially lower energies with comparable lifetimes to their FCC counterparts. LSPR peak locations and lifetimes can be tuned by controlling the operational temperature, the dielectric permittivity of the hosting matrix, and the grain size. Our work suggests that noble-metal nanoparticles can be tailored to develop exotic HCP phases to obtain novel plasmonic properties.
Keywords	copper ; dielectric permittivity ; gold ; industry ; physical chemistry ; silver ; strength (mechanics) ; temperature
Language	English
Dates of publication	2021-0923
Size	p. 21521-21532.
Publishing place	American Chemical Society
Document type	Article
ISSN	1932-7455
DOI	10.1021/acs.jpcc.1c06110
Database	NAL-Catalogue (AGRICOLA)

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Book ; Online: Electronic effects on the radiation damage in high-entropy alloys

Orhan, Okan K. / Hendy, Mohamed / Ponga, Mauricio

2022

Abstract: High-entropy alloys (HEAs) are exceptional candidates for radiation-resistant materials due to their complex local chemical environment and slow defect migration. Despite commonly overlooked, electronic effects on defects evolution in radiation ... ...

Abstract	High-entropy alloys (HEAs) are exceptional candidates for radiation-resistant materials due to their complex local chemical environment and slow defect migration. Despite commonly overlooked, electronic effects on defects evolution in radiation environments also play a crucial role by dissipating excess energy through electron-phonon coupling and electronic heat conduction during cascade events. We present a systematic study on electronic properties in random-solid solutions (RSS) in four and five principal elements HEAs and their effect on defect formation, clustering, and recombination. Electronic properties, including electron-phonon coupling factor, the electronic specific heat, and the electronic thermal conductivity, are computed within first-principles calculations. Using the two-temperature molecular dynamics simulations, we show that the electron-phonon coupling factor and electronic specific heat play a critical role in Frenkel pairs formation. Specifically, the electron-phonon coupling factor quickly dissipates the kinetic energy during primary knock-on atom events via plasmon excitations and is subsequently dissipated via the free-electrons conduction. We show that these effects are more critical than the elastic distortion effects produced by the atomic mismatch. Of tremendous interest, we show that including lighter elements helps to increase the electron-phonon coupling factor, suggesting the possibility to improve radiation resistance in HEA through optimal composition.
Keywords	Condensed Matter - Materials Science
Subject code	541
Publishing date	2022-03-07
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations

Mohamed Hendy / Samuel Kaufman / Mauricio Ponga

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 11

Abstract: Abstract The COVID19 pandemic, caused by SARS-CoV-2, has infected more than 200 million people worldwide. Due to the rapid spreading of SARS-CoV-2 and its impact, it is paramount to find effective treatments against it. Human neutralizing antibodies are ... ...

Abstract	Abstract The COVID19 pandemic, caused by SARS-CoV-2, has infected more than 200 million people worldwide. Due to the rapid spreading of SARS-CoV-2 and its impact, it is paramount to find effective treatments against it. Human neutralizing antibodies are an effective method to fight viral infection. However, the recent discovery of new strains that substantially change the S-protein sequence has raised concern about vaccines and antibodies’ effectiveness. Here, using molecular simulations, we investigated the binding mechanisms between the S-protein and several antibodies. Multiple mutations were included to understand the strategies for antibody escape in new variants. We found that the combination of mutations K417N, E484K, L452R, and T478K produced higher binding energy to ACE2 than the wild type, suggesting higher efficiency to enter host cells. The mutations’ effect depends on the antibody class. While Class I enhances the binding avidity in the presence of N501Y mutation, class II antibodies showed a sharp decline in the binding affinity. Our simulations suggest that Class I antibodies will remain effective against the new strains. In contrast, Class II antibodies will have less affinity to the S-protein, potentially affecting these antibodies’ efficiency.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations

Hendy, Mohamed / Kaufman, Samuel / Ponga, Mauricio

bioRxiv

Abstract: The COVID19 pandemic, caused by SARS-CoV-2, has infected more than 100 million people worldwide. Due to the rapid spreading of SARS-CoV-2 and its impact, it is paramount to find effective treatments against it. Human neutralizing antibodies are an ... ...

Abstract	The COVID19 pandemic, caused by SARS-CoV-2, has infected more than 100 million people worldwide. Due to the rapid spreading of SARS-CoV-2 and its impact, it is paramount to find effective treatments against it. Human neutralizing antibodies are an effective method to fight viral infection. However, the recent discovery of new strains that substantially change the S-protein sequence has raised concern about vaccines and antibodies9 effectiveness. Here, we investigated the binding mechanisms between the S-protein and several antibodies. Multiple mutations were included to understand the strategies for antibody escape in new variants. We found that the combination of mutations K417N and E484K produced higher binding energy to ACE2 than the wild type, suggesting higher efficiency to enter host cells. The mutations9 effect depends on the antibody class. While Class I enhances the binding avidity in the presence of N501Y mutation, class II antibodies showed a sharp decline in the binding affinity. Our simulations suggest that Class I antibodies will remain effective against the new strains. In contrast, Class II antibodies will have less affinity to the S-protein, potentially affecting these antibodies9 efficiency.
Keywords	covid19
Language	English
Publishing date	2021-03-05
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2021.03.04.433970
Database	COVID19

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