Characterizing the ligand-binding affinity toward SARS-CoV-2 Mproviaphysics- and knowledge-based approaches

Son Tung Ngo, Trung Hai Nguyen, Nguyen Thanh Tung, Van V. Vu, Minh Quan Pham and Binh Khanh Mai

Phys. Chem. Chem. Phys., 2022, 24, 29266
DOI: 10.1039/D2CP04476E

Discovery of SARS-CoV-2 Mpro peptide inhibitors from modelling substrate and ligand binding

H. T. Henry Chan, Marc A. Moesser, Rebecca K. Walters, Tika R. Malla, Rebecca M. Twidale, Tobias John, Helen M. Deeks, Tristan Johnston-Wood, Victor Mikhailov, Richard B. Sessions, William Dawson, Eidarus Salah, Petra Lukacik, Claire Strain-Damerell, C. David Owen, Takahito Nakajima, Katarzyna Świderek, Alessio Lodola, Vicent Moliner, David R. Glowacki, James Spencer, Martin A. Walsh, Christopher J. Schofield, Luigi Genovese, Deborah K. Shoemark, Adrian J. Mulholland, Fernanda Duarte and Garrett M. Morris

Chem. Sci., 2021, 12, 13686
DOI: 10.1039/D1SC03628A

Estimating the binding energetics of reversible covalent inhibitors of the SARS-CoV-2 main protease: an in silico study

Ernest Awoonor-Williams

Phys. Chem. Chem. Phys., 2022, 24, 23391
DOI: 10.1039/D2CP03080B

Influence of charge configuration on substrate binding to SARS-CoV-2 main protease

Natalia Díaz and Dimas Suárez

Chem. Commun., 2021, 57, 5314
DOI: 10.1039/D1CC01449H

Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design

Dénes Berta, Magd Badaoui, Sam Alexander Martino, Pedro J. Buigues, Andrei V. Pisliakov, Nadia Elghobashi-Meinhardt, Geoff Wells, Sarah A. Harris, Elisa Frezza and Edina Rosta

Chem. Sci., 2021, 12, 13492
DOI: 10.1039/D1SC02775A

Covalent and non-covalent binding free energy calculations for peptidomimetic inhibitors of SARS-CoV-2 main protease

Ernest Awoonor-Williams and Abd Al-Aziz A. Abu-Saleh

Phys. Chem. Chem. Phys., 2021, 23, 6746
DOI: 10.1039/D1CP00266J

Quinazolines and thiazolidine-2,4-dions as SARS-CoV-2 inhibitors: repurposing, in silico molecular docking and dynamics simulation

Sanadelaslam S. A. El-Hddad, Mohamed H. Sobhy, Ahmed El-morsy, Nabil A. Shoman and Khaled El-Adl

RSC Adv., 2024, 14, 13237
DOI: 10.1039/D4RA02029D

Computationally driven discovery of SARS-CoV-2 Mproinhibitors: from design to experimental validation

Léa El Khoury, Zhifeng Jing, Alberto Cuzzolin, Alessandro Deplano, Daniele Loco, Boris Sattarov, Florent Hédin, Sebastian Wendeborn, Chris Ho, Dina El Ahdab, Theo Jaffrelot Inizan, Mattia Sturlese, Alice Sosic, Martina Volpiana, Angela Lugato, Marco Barone, Barbara Gatto, Maria Ludovica Macchia, Massimo Bellanda, Roberto Battistutta, Cristiano Salata, Ivan Kondratov, Rustam Iminov, Andrii Khairulin, Yaroslav Mykhalonok, Anton Pochepko, Volodymyr Chashka-Ratushnyi, Iaroslava Kos, Stefano Moro, Matthieu Montes, Pengyu Ren, Jay W. Ponder, Louis Lagardère, Jean-Philip Piquemal and Davide Sabbadin

Chem. Sci., 2022, 13, 3674
DOI: 10.1039/D1SC05892D

Microscopic interactions between ivermectin and key human and viral proteins involved in SARS-CoV-2 infection

Antonio Francés-Monerris, Cristina García-Iriepa, Isabel Iriepa, Cécilia Hognon, Tom Miclot, Giampaolo Barone, Antonio Monari and Marco Marazzi

Phys. Chem. Chem. Phys., 2021, 23, 22957
DOI: 10.1039/D1CP02967C

Artificial intelligence-aiding lab-on-a-chip workforce designed oral [3.1.0] bi and [4.2.0] tricyclic catalytic interceptors inhibiting multiple SARS-CoV-2 protomers assisted by double-shell deep learning

Surachate Kalasin and Werasak Surareungchai

RSC Adv., 2024, 14, 26897
DOI: 10.1039/D4RA03965C

Antiviral activities of natural compounds and ionic liquids to inhibit the Mpro of SARS-CoV-2: a computational approach

Kandhan Palanisamy, S. M. Esther Rubavathy, Muthuramalingam Prakash, Ramasamy Thilagavathi, Maryam S. Hosseini-Zare and Chelliah Selvam

RSC Adv., 2022, 12, 3687
DOI: 10.1039/D1RA08604A

A microscopic description of SARS-CoV-2 main protease inhibition with Michael acceptors. Strategies for improving inhibitor design

Carlos A. Ramos-Guzmán, J. Javier Ruiz-Pernía and Iñaki Tuñón

Chem. Sci., 2021, 12, 3489
DOI: 10.1039/D0SC04978F

Searching and designing potential inhibitors for SARS-CoV-2 Mpro from natural sources using atomistic and deep-learning calculations

Nguyen Minh Tam, Duc-Hung Pham, Dinh Minh Hiep, Phuong-Thao Tran, Duong Tuan Quang and Son Tung Ngo

RSC Adv., 2021, 11, 38495
DOI: 10.1039/D1RA06534C

Dynamic Cooperativity of Ligand–Residue Interactions Evaluated with the Fragment Molecular Orbital Method

Shigenori Tanaka, Shusuke Tokutomi, Ryo Hatada, Koji Okuwaki, Kazuki Akisawa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama and Yuji Mochizuki

J. Phys. Chem. B, 2021, 125, 6501
DOI: 10.1021/acs.jpcb.1c03043

Selective Targeting of SARS-CoV-2 Mpro with Novel Ebsulfur-Based Compounds: A Computational Drug Discovery Approach Combining Molecular Dynamics and DFT Simulations

Seifollah Jalili, S. M. Hossein Rahmati and Atena Pakzadiyan

J. Comput. Biophys. Chem., 2026, 25, 511
DOI: 10.1142/S2737416525500280

Son Tung Ngo, Nguyen Minh Tam, Minh Quan Pham and Trung Hai Nguyen

J. Chem. Inf. Model., 2021, 61, 2302
DOI: 10.1021/acs.jcim.1c00159

The Inhibitory Potential of Ferulic Acid Derivatives against the SARS-CoV-2 Main Protease: Molecular Docking, Molecular Dynamics, and ADMET Evaluation

Io Antonopoulou, Eleftheria Sapountzaki, Ulrika Rova and Paul Christakopoulos

Biomedicines, 2022, 10, 1787
DOI: 10.3390/biomedicines10081787

The Potential of Ebselen Against Bipolar Disorder: A Perspective on the Interaction with Inositol Monophosphatase (IMPase)

Giovanni Ribaudo, Andrea Madabeni, Pablo Andrei Nogara, Chiara Pavan, Marco Bortoli, Joao Batista Teixeira Rocha and Laura Orian

COC, 2022, 26, 1503
DOI: 10.2174/1385272827666221130122416

Theobroma cacao L. compounds: Theoretical study and molecular modeling as inhibitors of main SARS-CoV-2 protease

Osvaldo Yañez, Manuel Isaías Osorio, Carlos Areche, Alejandro Vasquez-Espinal, Jessica Bravo, Angélica Sandoval-Aldana, José M. Pérez-Donoso, Fernando González-Nilo, Maria João Matos, Edison Osorio, Olimpo García-Beltrán and William Tiznado

Biomedicine & Pharmacotherapy, 2021, 140, 111764
DOI: 10.1016/j.biopha.2021.111764

Benchmarking the Ability of Common Docking Programs to Correctly Reproduce and Score Binding Modes in SARS-CoV-2 Protease Mpro

Shani Zev, Keren Raz, Renana Schwartz, Reem Tarabeh, Prashant Kumar Gupta and Dan T. Major

J. Chem. Inf. Model., 2021, 61, 2957
DOI: 10.1021/acs.jcim.1c00263

Unrevealing the Proteolytic Activity of RgpB Gingipain from Computational Simulations

Santiago Movilla, Sergio Martí, Maite Roca and Vicent Moliner

J. Chem. Inf. Model., 2021, 61, 4582
DOI: 10.1021/acs.jcim.1c00666

Applications of density functional theory in COVID-19 drug modeling

Naike Ye, Zekai Yang and Yuchen Liu

Drug Discovery Today, 2022, 27, 1411
DOI: 10.1016/j.drudis.2021.12.017

On the Origin of the Different Reversible Characters of Salinosporamide A and Homosalinosporamide A in the Covalent Inhibition of the Human 20S Proteasome

Natalia Serrano-Aparicio, Vicent Moliner and Katarzyna Świderek

ACS Catal., 2021, 11, 11806
DOI: 10.1021/acscatal.1c02614

Structural insights into the substrate‐binding site of main protease for the structure‐based COVID‐19 drug discovery

Rohoullah Firouzi, Mitra Ashouri and Mohammad Hossein Karimi‐Jafari

Proteins, 2022, 90, 1090
DOI: 10.1002/prot.26318

Michael Acceptors as Anti-Cancer Compounds: Coincidence or Causality?

Celia María Curieses Andrés, José Manuel Pérez de la Lastra, Elena Bustamante Munguira, Celia Andrés Juan and Eduardo Pérez-Lebeña

IJMS, 2024, 25, 6099
DOI: 10.3390/ijms25116099

Mechanistic aspects of thiol additions to Michael acceptors: Insights from computations

Ras Baizureen Roseli, Angus B. Keto and Elizabeth H. Krenske

WIREs Comput Mol Sci, 2023, 13
DOI: 10.1002/wcms.1636

Multiscale Simulations of SARS-CoV-2 3CL Protease Inhibition with Aldehyde Derivatives. Role of Protein and Inhibitor Conformational Changes in the Reaction Mechanism

Carlos A. Ramos-Guzmán, J. Javier Ruiz-Pernía and Iñaki Tuñón

ACS Catal., 2021, 11, 4157
DOI: 10.1021/acscatal.0c05522

Inhibition Mechanism of SARS‐CoV‐2 Main Protease with Ketone‐Based Inhibitors Unveiled by Multiscale Simulations: Insights for Improved Designs**

Carlos A. Ramos‐Guzmán, J. Javier Ruiz‐Pernía and Iñaki Tuñón

Angew Chem Int Ed, 2021, 60, 25933
DOI: 10.1002/anie.202110027

CHARMM-GUI EnzyDocker for Protein–Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes

Donghyuk Suh, Renana Schwartz, Prashant Kumar Gupta, Shani Zev, Dan T. Major and Wonpil Im

J. Chem. Theory Comput., 2025, 21, 2118
DOI: 10.1021/acs.jctc.4c01691

Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 Mpro Explored by QM/MM Simulations

Sergio Martí, Kemel Arafet, Alessio Lodola, Adrian J. Mulholland, Katarzyna Świderek and Vicent Moliner

ACS Catal., 2022, 12, 698
DOI: 10.1021/acscatal.1c04661

Inhibition Mechanism of SARS‐CoV‐2 Main Protease with Ketone‐Based Inhibitors Unveiled by Multiscale Simulations: Insights for Improved Designs**

Carlos A. Ramos‐Guzmán, J. Javier Ruiz‐Pernía and Iñaki Tuñón

Angewandte Chemie, 2021, 133, 26137
DOI: 10.1002/ange.202110027

Multiscale Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms

Bella L. Grigorenko, Igor V. Polyakov, Maria G. Khrenova, Goran Giudetti, Shirin Faraji, Anna I. Krylov and Alexander V. Nemukhin

J. Am. Chem. Soc., 2023, 145, 13204
DOI: 10.1021/jacs.3c02229

Mechanism-Based and Computational-Driven Covalent Drug Design

Yun Lyna Luo

J. Chem. Inf. Model., 2021, 61, 5307
DOI: 10.1021/acs.jcim.1c01278

Combinatorial chemistry-driven In silico design and computational evaluation of covalent peptidomimetic SARS-CoV-2 main protease inhibitors via structure-based virtual screening and multivariate analysis

Alessia Bono, Gabriele La Monica, Federica Alamia, Francesco Mingoia, Annamaria Martorana and Antonino Lauria

Journal of Molecular Graphics and Modelling, 2025, 140, 109100
DOI: 10.1016/j.jmgm.2025.109100

Covalent small-molecule inhibitors of SARS-CoV-2 Mpro: Insights into their design, classification, biological activity, and binding interactions

Ahmed M. Shawky, Faisal A. Almalki, Hayat Ali Alzahrani, Ashraf N. Abdalla, Bahaa G.M. Youssif, Nashwa A. Ibrahim, Mohammed Gamal, Hany A.M. El-Sherief, Maha M. Abdel-Fattah, Ahmed A. Hefny, Ahmed H. Abdelazeem and Ahmed M. Gouda

European Journal of Medicinal Chemistry, 2024, 277, 116704
DOI: 10.1016/j.ejmech.2024.116704

New insights into the catalytic mechanism of the SARS-CoV-2 main protease: an ONIOM QM/MM approach

Henrique S. Fernandes, Sérgio F. Sousa and Nuno M. F. S. A. Cerqueira

Mol Divers, 2022, 26, 1373
DOI: 10.1007/s11030-021-10259-7

The Se–S Bond Formation in the Covalent Inhibition Mechanism of SARS-CoV-2 Main Protease by Ebselen-like Inhibitors: A Computational Study

Angela Parise, Isabella Romeo, Nino Russo and Tiziana Marino

IJMS, 2021, 22, 9792
DOI: 10.3390/ijms22189792

The Potential of Stilbene Compounds to Inhibit Mpro Protease as a Natural Treatment Strategy for Coronavirus Disease-2019

Ayesha Naseem, Fatima Rasool, Abrar Ahmed and Wayne G. Carter

CIMB, 2022, 45, 12
DOI: 10.3390/cimb45010002

Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design

Laura Zanetti-Polzi, Micholas Dean Smith, Chris Chipot, James C. Gumbart, Diane L. Lynch, Anna Pavlova, Jeremy C. Smith and Isabella Daidone

J. Phys. Chem. Lett., 2021, 12, 4195
DOI: 10.1021/acs.jpclett.1c00425

Polarizable MD and QM/MM investigation of acrylamide-based leads to target the main protease of SARS-CoV-2

Jorge Nochebuena and G. Andrés Cisneros

The Journal of Chemical Physics, 2022, 157
DOI: 10.1063/5.0123698

Elucidating the Dual Mode of Action of Dipeptidyl Enoates in the Inhibition of Rhodesain Cysteine Proteases

Kemel Arafet, Florenci V. González and Vicent Moliner

Chemistry A European J, 2021, 27, 10142
DOI: 10.1002/chem.202100892

Synthesis, characterization, proteolytic activity inhibition, ADMET prediction, and molecular docking studies of novel indole derivatives as potential SARS-CoV-2 protease inhibitors

Abdelali Chihab, Nabil El Brahmi, Abdelmoula El Abbouchi, Abdelaziz El Alaoui, Mostapha Bousmina, Elmostafa El Fahime and Saïd El Kazzouli

Journal of Molecular Structure, 2025, 1323, 140707
DOI: 10.1016/j.molstruc.2024.140707

Novel ciprofloxacin and norfloxacin-tetrazole hybrids as potential antibacterial and antiviral agents: Targeting S. aureus topoisomerase and SARS-CoV-2-MPro

Jaime Cardoso-Ortiz, Socorro Leyva-Ramos, Kim M. Baines, Cesar Fernando Azael Gómez-Durán, Hiram Hernández-López, Francisco José Palacios-Can, José Antonio Valcarcel-Gamiño, Mario Alberto Leyva-Peralta and Rodrigo Said Razo-Hernández

Journal of Molecular Structure, 2023, 1274, 134507
DOI: 10.1016/j.molstruc.2022.134507

Mechanistic investigation of SARS-CoV-2 main protease to accelerate design of covalent inhibitors

Hoshin Kim, Darin Hauner, Joseph A. Laureanti, Kruel Agustin, Simone Raugei and Neeraj Kumar

Sci Rep, 2022, 12
DOI: 10.1038/s41598-022-23570-6

Structure-Based Discovery of Novel Nonpeptide Inhibitors Targeting SARS-CoV-2 Mpro

Jingyi Yang, Xiaoyuan Lin, Na Xing, Zhao Zhang, Haiwei Zhang, Haibo Wu and Weiwei Xue

J. Chem. Inf. Model., 2021, 61, 3917
DOI: 10.1021/acs.jcim.1c00355

Protease-Responsive Peptide-Conjugated Mitochondrial-Targeting AIEgens for Selective Imaging and Inhibition of SARS-CoV-2-Infected Cells

Yong Cheng, Alex E. Clark, Jiajing Zhou, Tengyu He, Yi Li, Raina M. Borum, Matthew N. Creyer, Ming Xu, Zhicheng Jin, Jingcheng Zhou, Wonjun Yim, Zhuohong Wu, Pavla Fajtová, Anthony J. O’Donoghue, Aaron F. Carlin and Jesse V. Jokerst

ACS Nano, 2022, 16, 12305
DOI: 10.1021/acsnano.2c03219

A potential allosteric inhibitor of SARS-CoV-2 main protease (Mpro) identified through metastable state analysis

Asma Fatima, Anupriya M. Geethakumari, Wesam S. Ahmed and Kabir H. Biswas

Front. Mol. Biosci., 2024, 11
DOI: 10.3389/fmolb.2024.1451280

The role of quantum chemistry in covalent inhibitor design

Levente M. Mihalovits, György G. Ferenczy and György M. Keserű

Int J of Quantum Chemistry, 2022, 122
DOI: 10.1002/qua.26768

SARS‐CoV‐2 main protease inhibitors: What is moving in the field of peptides and peptidomimetics?

Sergio Algar‐Lizana, María Ángeles Bonache and Rosario González‐Muñiz

Journal of Peptide Science, 2023, 29
DOI: 10.1002/psc.3467

A Molecular Mechanics Energy Partitioning Software for Biomolecular Systems

Henrique S. Fernandes, Nuno M. F. S. A. Cerqueira, Sérgio F. Sousa and André Melo

Molecules, 2022, 27, 5524
DOI: 10.3390/molecules27175524

In Silico Drug Repositioning to Target the SARS-CoV-2 Main Protease as Covalent Inhibitors Employing a Combined Structure-Based Virtual Screening Strategy of Pharmacophore Models and Covalent Docking

Luis Heriberto Vázquez-Mendoza, Humberto L. Mendoza-Figueroa, Juan Benjamín García-Vázquez, José Correa-Basurto and Jazmín García-Machorro

IJMS, 2022, 23, 3987
DOI: 10.3390/ijms23073987

Protein–ligand interactions from a quantum fragmentation perspective: The case of the SARS-CoV-2 main protease interacting with α-ketoamide inhibitors

Luigi Genovese, William Dawson, Takahito Nakajima, Viviana Cristiglio, Valérie Vallet and Michel Masella

The Journal of Chemical Physics, 2023, 158
DOI: 10.1063/5.0148064

Computational Screening of Phenylamino-Phenoxy-Quinoline Derivatives against the Main Protease of SARS-CoV-2 Using Molecular Docking and the ONIOM Method

Suwicha Patnin, Arthit Makarasen, Pongsit Vijitphan, Apisara Baicharoen, Apinya Chaivisuthangkura, Mayuso Kuno and Supanna Techasakul

Molecules, 2022, 27, 1793
DOI: 10.3390/molecules27061793

Haste makes waste: A critical review of docking‐based virtual screening in drug repurposing for SARS‐CoV‐2 main protease (M‐pro) inhibition

Guillem Macip, Pol Garcia‐Segura, Júlia Mestres‐Truyol, Bryan Saldivar‐Espinoza, María José Ojeda‐Montes, Aleix Gimeno, Adrià Cereto‐Massagué, Santiago Garcia‐Vallvé and Gerard Pujadas

Medicinal Research Reviews, 2022, 42, 744
DOI: 10.1002/med.21862

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

Lorenzo Casalino, Carlos A. Ramos-Guzmán, Rommie E. Amaro, Carlos Simmerling, Alessio Lodola, Adrian J. Mulholland, Katarzyna Świderek and Vicent Moliner

J. Phys. Chem. Lett., 2025, 16, 3249
DOI: 10.1021/acs.jpclett.4c03654

New Strategies for Responding to SARS-CoV-2: The Present and Future of Dual-Target Drugs

Wenyi Zhang, Lecheng Xiao, Dianyang Li, Yuxuan Hu and Wenying Yu

J. Med. Chem., 2024, 67, 11522
DOI: 10.1021/acs.jmedchem.4c00384

Template-Based Docking Using Automated Maximum Common Substructure Identification with EnzyDock: Mechanistic and Inhibitor Docking

Renana Schwartz, Amit Hadar-Volk, Kwangho Nam and Dan T. Major

J. Chem. Inf. Model., 2025, 65, 5596
DOI: 10.1021/acs.jcim.5c00201

How Reproducible Are QM/MM Simulations? Lessons from Computational Studies of the Covalent Inhibition of the SARS-CoV-2 Main Protease by Carmofur

Goran Giudetti, Igor Polyakov, Bella L. Grigorenko, Shirin Faraji, Alexander V. Nemukhin and Anna I. Krylov

J. Chem. Theory Comput., 2022, 18, 5056
DOI: 10.1021/acs.jctc.2c00286

HCovDock: an efficient docking method for modeling covalent protein–ligand interactions

Qilong Wu and Sheng-You Huang

Briefings in Bioinformatics, 2023, 24
DOI: 10.1093/bib/bbac559

Density Functional Theory, Molecular Dynamics, and AlteQ Studies of Baimantuoluoamide A and Baimantuoluoamide B to Identify Potential Inhibitors of Mpro Proteins: a Novel Target for the Treatment of SARS COVID-19

K. Gurushankar, S. Ch. Jeyaseelan, M. Grishina, I. Sisvanto, R. Tiwari and N. N.T Puspaningsih

Pisʹma v žurnal êksperimentalʹnoj i teoretičeskoj fiziki, 2023, 117, 783
DOI: 10.31857/S1234567823100117

Co-crystallization and structure determination: An effective direction for anti-SARS-CoV-2 drug discovery

Zhonglei Wang, Liyan Yang and Xian-En Zhao

Computational and Structural Biotechnology Journal, 2021, 19, 4684
DOI: 10.1016/j.csbj.2021.08.029

Impact of the Recognition Part of Dipeptidyl Nitroalkene Compounds on the Inhibition Mechanism of Cysteine Proteases Cruzain and Cathepsin L

Kemel Arafet, Santiago Royo, Tanja Schirmeister, Fabian Barthels, Florenci V. González and Vicent Moliner

ACS Catal., 2023, 13, 6289
DOI: 10.1021/acscatal.3c01035

Computing Metal‐Binding Proteins for Therapeutic Benefit

Angelo Spinello, Jure Borišek, Matic Pavlin, Pavel Janoš and Alessandra Magistrato

ChemMedChem, 2021, 16, 2034
DOI: 10.1002/cmdc.202100109

How exascale computing can shape drug design: A perspective from multiscale QM/MM molecular dynamics simulations and machine learning-aided enhanced sampling algorithms

Giulia Rossetti and Davide Mandelli

Current Opinion in Structural Biology, 2024, 86, 102814
DOI: 10.1016/j.sbi.2024.102814

Targeting SARS-CoV-2 Main Protease for Treatment of COVID-19: Covalent Inhibitors Structure–Activity Relationship Insights and Evolution Perspectives

Gabriele La Monica, Alessia Bono, Antonino Lauria and Annamaria Martorana

J. Med. Chem., 2022, 65, 12500
DOI: 10.1021/acs.jmedchem.2c01005

Mechanism-Based Redesign of GAP to Activate Oncogenic Ras

Dénes Berta, Sascha Gehrke, Kinga Nyíri, Beáta G. Vértessy and Edina Rosta

J. Am. Chem. Soc., 2023, 145, 20302
DOI: 10.1021/jacs.3c04330

Advanced technologies for screening and identifying covalent inhibitors

Yaolin Guo, Wen shuai, Aiping Tong and Yuxi Wang

TrAC Trends in Analytical Chemistry, 2024, 178, 117833
DOI: 10.1016/j.trac.2024.117833

Investigating novel thiazolyl-indazole derivatives as scaffolds for SARS-CoV-2 MPro inhibitors

Justin Airas, Catherine A. Bayas, Abdellah N'Ait Ousidi, Moulay Youssef Ait Itto, Aziz Auhmani, Mohamed Loubidi, M'hamed Esseffar, Julie A. Pollock and Carol A. Parish

European Journal of Medicinal Chemistry Reports, 2022, 4, 100034
DOI: 10.1016/j.ejmcr.2022.100034

Chemical Reactivity Prediction: Current Methods and Different Application Areas

Peter Ertl, Grégori Gerebtzoff, Richard Lewis, Hagen Muenkler, Nadine Schneider, Finton Sirockin, Nikolaus Stiefl and Paolo Tosco

Molecular Informatics, 2022, 41
DOI: 10.1002/minf.202100277

Density Functional Theory, Molecular Dynamics, and AlteQ Studies of Baimantuoluoamide A and Baimantuoluoamide B to Identify Potential Inhibitors of Mpro Proteins: a Novel Target for the Treatment of SARS COVID-19

K. Gurushankar, S. Ch. Jeyaseelan, M. Grishina, I. Siswanto, R. Tiwari and N. N. T. Puspaningsih

Jetp Lett., 2023, 117, 781
DOI: 10.1134/S0021364023600039

Deconstructing PET: Advances in enzyme engineering for sustainable plastic degradation

Jiaxin Yao, Yao Liu, Zhenghua Gu, Liang Zhang and Zhongpeng Guo

Chemical Engineering Journal, 2024, 497, 154183
DOI: 10.1016/j.cej.2024.154183

Reactivity of Covalent Fragments and Their Role in Fragment Based Drug Discovery

Kirsten McAulay, Alan Bilsland and Marta Bon

Pharmaceuticals, 2022, 15, 1366
DOI: 10.3390/ph15111366

Exploring the Role of Chemical Reactions in the Selectivity of Tyrosine Kinase Inhibitors

Mojgan Asadi, Wen Jun Xie and Arieh Warshel

J. Am. Chem. Soc., 2022, 144, 16638
DOI: 10.1021/jacs.2c07307

Design of aggregation-induced emission materials for biosensing of molecules and cells

Yuying Zhang, Yi Wang, Yue Zhao, Rong Hu and Huanxiang Yuan

Biosensors and Bioelectronics, 2025, 267, 116805
DOI: 10.1016/j.bios.2024.116805

Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies

Brigitta Elsässer and Peter Goettig

IJMS, 2021, 22, 3232
DOI: 10.3390/ijms22063232

Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2

Kaifu Gao, Rui Wang, Jiahui Chen, Limei Cheng, Jaclyn Frishcosy, Yuta Huzumi, Yuchi Qiu, Tom Schluckbier, Xiaoqi Wei and Guo-Wei Wei

Chem. Rev., 2022, 122, 11287
DOI: 10.1021/acs.chemrev.1c00965

In silico molecular docking, dynamics simulation and repurposing of some VEGFR-2 inhibitors based on the SARS-CoV-2-main-protease inhibitor N3

Sanadelaslam El-Hddad, Mohamed Sobhy, Ahmed Ayoub and Khaled El-Adl

Journal of Biomolecular Structure and Dynamics, 2023, 41, 9267
DOI: 10.1080/07391102.2022.2148000

Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites

Eunice Cho, Margarida Rosa, Ruhi Anjum, Saman Mehmood, Mariya Soban, Moniza Mujtaba, Khair Bux, Syed T. Moin, Mohammad Tanweer, Sarath Dantu, Alessandro Pandini, Junqi Yin, Heng Ma, Arvind Ramanathan, Barira Islam, Antonia S. J. S. Mey, Debsindhu Bhowmik and Shozeb Haider

J. Chem. Inf. Model., 2021, 61, 3058
DOI: 10.1021/acs.jcim.1c00449

Peptidyl nitroalkene inhibitors of main protease rationalized by computational and crystallographic investigations as antivirals against SARS-CoV-2

Francisco J. Medrano, Sergio de la Hoz-Rodríguez, Sergio Martí, Kemel Arafet, Tanja Schirmeister, Stefan J. Hammerschmidt, Christin Müller, Águeda González-Martínez, Elena Santillana, John Ziebuhr, Antonio Romero, Collin Zimmer, Annabelle Weldert, Robert Zimmermann, Alessio Lodola, Katarzyna Świderek, Vicent Moliner and Florenci V. González

Commun Chem, 2024, 7
DOI: 10.1038/s42004-024-01104-7

Inhibitors of SARS-CoV-2 Main Protease (Mpro) as Anti-Coronavirus Agents

Agnieszka Zagórska, Anna Czopek, Monika Fryc and Jakub Jończyk

Biomolecules, 2024, 14, 797
DOI: 10.3390/biom14070797

Fullerenes against COVID-19: Repurposing C60 and C70 to Clog the Active Site of SARS-CoV-2 Protease

Tainah Dorina Marforio, Edoardo Jun Mattioli, Francesco Zerbetto and Matteo Calvaresi

Molecules, 2022, 27, 1916
DOI: 10.3390/molecules27061916

Synthesis of Amino-Acid-Based Nitroalkenes

Velisaria-Eleni Gerogianni, Giorgos S. Koutoulogenis, Dimitrios Triantafyllos Gerokonstantis and George Kokotos

Organics, 2022, 3, 137
DOI: 10.3390/org3020011

Structural Insight into the Binding of Cyanovirin-N with the Spike Glycoprotein, Mpro and PLpro of SARS-CoV-2: Protein–Protein Interactions, Dynamics Simulations and Free Energy Calculations

Devashan Naidoo, Pallab Kar, Ayan Roy, Taurai Mutanda, Joseph Bwapwa, Arnab Sen and Akash Anandraj

Molecules, 2021, 26, 5114
DOI: 10.3390/molecules26175114

Electrophilic warheads in covalent drug discovery: an overview

Nikolett Péczka, Zoltán Orgován, Péter Ábrányi-Balogh and György Miklós Keserű

Expert Opinion on Drug Discovery, 2022, 17, 413
DOI: 10.1080/17460441.2022.2034783

Synthesis, SARS-CoV-2 main protease inhibition, molecular docking and in silico ADME studies of furanochromene-quinoline hydrazone derivatives

Blake M. Shellenberger, Olivia N. Basile, Joel Cassel, Morgan R. Olsen, Joseph M. Salvino, Luis J. Montaner, Ian Tietjen and Geneive E. Henry

Bioorganic & Medicinal Chemistry Letters, 2024, 102, 129679
DOI: 10.1016/j.bmcl.2024.129679

Withanolides of Athenaea velutina with potential inhibitory properties against SARS coronavirus main protease (m pro ): molecular modeling studies

Pabllo Abreu Alves, Késya Amanda Dantas Rocha, Lucas Lima Bezerra, Alejandro Pedro Ayala, Norberto de Kássio Vieira Monteiro and Otília Deusdênia Loiola Pessoa

Journal of Biomolecular Structure and Dynamics, 2023, 41, 12267
DOI: 10.1080/07391102.2023.2167863

Identification of a dual acting SARS-CoV-2 proteases inhibitor through in silico design and step-by-step biological characterization

Veronica Di Sarno, Gianluigi Lauro, Simona Musella, Tania Ciaglia, Vincenzo Vestuto, Marina Sala, Maria Carmina Scala, Gerardina Smaldone, Francesca Di Matteo, Sara Novi, Mario Felice Tecce, Ornella Moltedo, Giuseppe Bifulco, Pietro Campiglia, Isabel M. Gomez-Monterrey, Robert Snoeck, Graciela Andrei, Carmine Ostacolo and Alessia Bertamino

European Journal of Medicinal Chemistry, 2021, 226, 113863
DOI: 10.1016/j.ejmech.2021.113863

Isolation, structural elucidation and molecular docking studies against SARS-CoV-2 main protease of new stigmastane-type steroidal glucosides isolated from the whole plants of Vernonia gratiosa

Pham Van Cong, Hoang Le Tuan Anh, Nguyen Quang Trung, Bui Quang Minh, Ngo Viet Duc, Nguyen Van Dan, Nguyen Minh Trang, Nguyen Viet Phong, Le Ba Vinh, Le Tuan Anh and Ki Yong Lee

Natural Product Research, 2023, 37, 2342
DOI: 10.1080/14786419.2022.2042534

Elucidating Atomistic Insight into the Dynamical Responses of the SARS-CoV-2 Main Protease for the Binding of Remdesivir Analogues: Leveraging Molecular Mechanics To Decode the Inhibition Mechanism

Pabitra Narayan Samanta, Devashis Majumdar and Jerzy Leszczynski

J. Chem. Inf. Model., 2023, 63, 3404
DOI: 10.1021/acs.jcim.3c00105

Identifying Inhibitor-SARS-CoV2-3CLpro Binding Mechanism Through Molecular Docking, GaMD Simulations, Correlation Network Analysis and MM-GBSA Calculations

Jianzhong Chen, Jian Wang, Wanchun Yang, Lu Zhao and Xiaoyan Xu

Molecules, 2025, 30, 805
DOI: 10.3390/molecules30040805

Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development

Kwangho Nam, Yihan Shao, Dan T. Major and Magnus Wolf-Watz

ACS Omega, 2024
DOI: 10.1021/acsomega.3c09084

Computational Study of the Inhibition of RgpB Gingipain, a Promising Target for the Treatment of Alzheimer’s Disease

Santiago Movilla, Sergio Martí, Maite Roca and Vicent Moliner

J. Chem. Inf. Model., 2023, 63, 950
DOI: 10.1021/acs.jcim.2c01198

SARS-CoV-2 proteins structural studies using synchrotron radiation

Maksim Kosenko, Galina Onkhonova, Ivan Susloparov and Alexander Ryzhikov

Biophys Rev, 2023, 15, 1185
DOI: 10.1007/s12551-023-01153-7

Decoding Drug Discovery: Exploring A-to-Z In Silico Methods for Beginners

Hezha O. Rasul, Dlzar D. Ghafour, Bakhtyar K. Aziz, Bryar A. Hassan, Tarik A. Rashid and Arif Kivrak

Appl Biochem Biotechnol, 2025, 197, 1453
DOI: 10.1007/s12010-024-05110-2

Dynamical Nonequilibrium Molecular Dynamics Simulations Identify Allosteric Sites and Positions Associated with Drug Resistance in the SARS-CoV-2 Main Protease

H. T. Henry Chan, A. Sofia F. Oliveira, Christopher J. Schofield, Adrian J. Mulholland and Fernanda Duarte

JACS Au, 2023, 3, 1767
DOI: 10.1021/jacsau.3c00185

Molecular docking and network pharmacology highlight salvianolic acids as potential inhibitors and therapeutic agents for COVID-19 treatment

Anathi Msobo, Manamele Dannies Mashabela, Gerrit Koorsen, Teboho Nicolus Tsotetsi, Lizelle Ann Piater, Ntakadzeni Edwin Madala, Tendamudzimu Tshiwawa and Msizi Innocent Mhlongo

Phytochemistry Letters, 2025, 68, 102991
DOI: 10.1016/j.phytol.2025.102991

CarsiDock-Cov: A deep learning-guided approach for automated covalent docking and screening

Chao Shen, Hongyan Du, Xujun Zhang, Shukai Gu, Heng Cai, Yu Kang, Peichen Pan, Qingwei Zhao and Tingjun Hou

Acta Pharmaceutica Sinica B, 2025
DOI: 10.1016/j.apsb.2025.07.043

(E)-2-Benzylidenecyclanones: Part XX—Reaction of Cyclic Chalcone Analogs with Cellular Thiols: Unexpected Increased Reactivity of 4-Chromanone- Compared to 1-Tetralone Analogs in Thia-Michael Reactions

Gábor Bognár, Fatemeh Kenari, Zoltán Pintér, Igor D. Borges, Ademir J. Camargo, Heibbe C. B. Oliveira, Flávio Olimpio Sanches-Neto, Valter H. Carvalho-Silva, Hamilton B. Napolitano and Pál Perjési

Molecules, 2024, 29, 5493
DOI: 10.3390/molecules29235493

Exploring the covalent inhibition mechanisms of inhibitors with two different warheads acting on SARS-CoV-2 Mpro by QM/MM simulations

Xiaoyue Yang, Mengguo Chen, Fanru Yuan, Jiangnan Zhang, Jinshuai Song and Longhua Yang

Computational and Theoretical Chemistry, 2024, 1242, 114979
DOI: 10.1016/j.comptc.2024.114979

Beyond the vaccines: a glance at the small molecule and peptide-based anti-COVID19 arsenal

Kunal Nepali, Ram Sharma, Sachin Sharma, Amandeep Thakur and Jing-Ping Liou

J Biomed Sci, 2022, 29
DOI: 10.1186/s12929-022-00847-6

Combined Theoretical and Experimental Study to Unravel the Differences in Promiscuous Amidase Activity of Two Nonhomologous Enzymes

Miquel À. Galmés, Alexander R. Nödling, Louis Luk, Katarzyna Świderek and Vicent Moliner

ACS Catal., 2021, 11, 8635
DOI: 10.1021/acscatal.1c02150

Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents

Kemel Arafet, Laura Scalvini, Francesca Galvani, Sergio Martí, Vicent Moliner, Marco Mor and Alessio Lodola

J. Chem. Inf. Model., 2023, 63, 1301
DOI: 10.1021/acs.jcim.2c01586

Repurposing of FDA‐approved drugs against active site and potential allosteric drug‐binding sites of COVID‐19 main protease

Merve Yuce, Erdem Cicek, Tugce Inan, Aslihan Basak Dag, Ozge Kurkcuoglu and Fethiye Aylin Sungur

Proteins, 2021, 89, 1425
DOI: 10.1002/prot.26164