A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats

Lorenzo  Casalino; Carlos A Ramos Guzman; Rommie E Amaro; Carlos Simmerling; Alessio Lodola; Adrian J Mulholland; Katarzyna Świderek; Vicent Moliner

doi:10.1021/acs.jpclett.4c03654#

A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats

Lorenzo Casalino, Carlos A Ramos Guzman, Rommie E Amaro^*, Carlos Simmerling^*, Alessio Lodola^*, Adrian J Mulholland^*, Katarzyna Świderek^*, Vicent Moliner^*

^*Corresponding author for this work

Research output: Contribution to journal › Review article (Academic Journal) › peer-review

Abstract

Molecular simulations play important roles in understanding the lifecycle of the SARS-CoV-2 virus and contribute to the design and development of antiviral agents and diagnostic tests for COVID. Here, we discuss the insights that such simulations have provided and the challenges involved, focusing on the SARS-CoV-2 main protease (Mpro) and the spike glycoprotein. Mpro is the leading target for antivirals, while the spike glycoprotein is the target for vaccine design. Finally, we reflect on lessons from this pandemic for the simulation community. Data sharing initiatives and collaborations across the international research community contributed to advancing knowledge and should be built on to help in future pandemics and other global challenges such as antimicrobial resistance.

Original language	English
Pages (from-to)	3249-3263
Number of pages	15
Journal	The Journal of Physical Chemistry Letters
Volume	16
Issue number	13
Early online date	21 Mar 2025
DOIs	https://doi.org/10.1021/acs.jpclett.4c03654#
Publication status	Published - 3 Apr 2025

Bibliographical note

Publisher Copyright:
© 2025 The Authors.

Keywords

SARS-CoV-2
Mpro
Spike
QM/MM
Molecular Simulations
Exascale Simulations

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1021/acs.jpclett.4c03654#Licence: CC BY-NC-ND

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Cite this

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title = "A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats",

abstract = "Molecular simulations play important roles in understanding the lifecycle of the SARS-CoV-2 virus and contribute to the design and development of antiviral agents and diagnostic tests for COVID. Here, we discuss the insights that such simulations have provided and the challenges involved, focusing on the SARS-CoV-2 main protease (Mpro) and the spike glycoprotein. Mpro is the leading target for antivirals, while the spike glycoprotein is the target for vaccine design. Finally, we reflect on lessons from this pandemic for the simulation community. Data sharing initiatives and collaborations across the international research community contributed to advancing knowledge and should be built on to help in future pandemics and other global challenges such as antimicrobial resistance.",

keywords = "SARS-CoV-2, Mpro, Spike, QM/MM, Molecular Simulations, Exascale Simulations",

author = "Lorenzo Casalino and {Ramos Guzman}, {Carlos A} and Amaro, {Rommie E} and Carlos Simmerling and Alessio Lodola and Mulholland, {Adrian J} and Katarzyna {\'S}widerek and Vicent Moliner",

note = "Publisher Copyright: {\textcopyright} 2025 The Authors.",

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doi = "10.1021/acs.jpclett.4c03654#",

language = "English",

volume = "16",

pages = "3249--3263",

journal = "The Journal of Physical Chemistry Letters",

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T1 - A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats

AU - Casalino, Lorenzo

AU - Ramos Guzman, Carlos A

AU - Amaro, Rommie E

AU - Simmerling, Carlos

AU - Lodola, Alessio

AU - Mulholland, Adrian J

AU - Świderek, Katarzyna

AU - Moliner, Vicent

PY - 2025/4/3

Y1 - 2025/4/3

N2 - Molecular simulations play important roles in understanding the lifecycle of the SARS-CoV-2 virus and contribute to the design and development of antiviral agents and diagnostic tests for COVID. Here, we discuss the insights that such simulations have provided and the challenges involved, focusing on the SARS-CoV-2 main protease (Mpro) and the spike glycoprotein. Mpro is the leading target for antivirals, while the spike glycoprotein is the target for vaccine design. Finally, we reflect on lessons from this pandemic for the simulation community. Data sharing initiatives and collaborations across the international research community contributed to advancing knowledge and should be built on to help in future pandemics and other global challenges such as antimicrobial resistance.

AB - Molecular simulations play important roles in understanding the lifecycle of the SARS-CoV-2 virus and contribute to the design and development of antiviral agents and diagnostic tests for COVID. Here, we discuss the insights that such simulations have provided and the challenges involved, focusing on the SARS-CoV-2 main protease (Mpro) and the spike glycoprotein. Mpro is the leading target for antivirals, while the spike glycoprotein is the target for vaccine design. Finally, we reflect on lessons from this pandemic for the simulation community. Data sharing initiatives and collaborations across the international research community contributed to advancing knowledge and should be built on to help in future pandemics and other global challenges such as antimicrobial resistance.

KW - SARS-CoV-2

KW - Mpro

KW - Spike

KW - QM/MM

KW - Molecular Simulations

KW - Exascale Simulations

U2 - 10.1021/acs.jpclett.4c03654#

DO - 10.1021/acs.jpclett.4c03654#

M3 - Review article (Academic Journal)

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JO - The Journal of Physical Chemistry Letters

JF - The Journal of Physical Chemistry Letters

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ER -

A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats

Abstract

Bibliographical note

Keywords

UN SDGs

Access to Document

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Equipment

HPC (High Performance Computing) and HTC (High Throughput Computing) Facilities

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