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

Studies on the selectivity of the SARS-CoV-2 papain-like protease reveal the importance of the P2′ proline of the viral polyprotein

H. T. Henry Chan, Lennart Brewitz, Petra Lukacik, Claire Strain-Damerell, Martin A. Walsh, Christopher J. Schofield and Fernanda Duarte

RSC Chem. Biol., 2024, 5, 117
DOI: 10.1039/D3CB00128H

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

Structural insights into Nirmatrelvir (PF-07321332)-3C-like SARS-CoV-2 protease complexation: a ligand Gaussian accelerated molecular dynamics study

Yeng-Tseng Wang, Jun-Min Liao, Wen-Wei Lin, Chia-Ching Li, Bo-Cheng Huang, Tian-Lu Cheng and Tun-Chieh Chen

Phys. Chem. Chem. Phys., 2022, 24, 22898
DOI: 10.1039/D2CP02882D

Dihydropyrimidine-2-thione derivatives as SARS-CoV-2 main protease inhibitors: synthesis, SAR and in vitro profiling

Anees Saeed, Ayesha Tahir, Muhammad Shah, Fahad Hussain, Abdul Sadiq and Umer Rashid

RSC Adv., 2025, 15, 6424
DOI: 10.1039/D4RA08449G

Optimization of potential non-covalent inhibitors for the SARS-CoV-2 main protease inspected by a descriptor of the subpocket occupancy

Yujia Sun, Bodi Zhao, Yuqi Wang, Zitong Chen, Huaiyu Zhang, Lingbo Qu, Yuan Zhao and Jinshuai Song

Phys. Chem. Chem. Phys., 2022, 24, 29940
DOI: 10.1039/D2CP03681A

The impact of SARS-CoV-2 3CL protease mutations on nirmatrelvir inhibitory efficiency. Computational insights into potential resistance mechanisms

Carlos A. Ramos-Guzmán, Milorad Andjelkovic, Kirill Zinovjev, J. Javier Ruiz-Pernía and Iñaki Tuñón

Chem. Sci., 2023, 14, 2686
DOI: 10.1039/D2SC06584C

Insights into the binding and covalent inhibition mechanism of PF-07321332 to SARS-CoV-2 Mpro

Son Tung Ngo, Trung Hai Nguyen, Nguyen Thanh Tung and Binh Khanh Mai

RSC Adv., 2022, 12, 3729
DOI: 10.1039/D1RA08752E

Identification and validation of novel microtubule suppressors with an imidazopyridine scaffold through structure-based virtual screening and docking

Samia A. Elseginy, A. Sofia F. Oliveira, Deborah K. Shoemark and Richard B. Sessions

RSC Med. Chem., 2022, 13, 929
DOI: 10.1039/D1MD00392E

Innovative strategies for modeling peptide–protein interactions and rational peptide drug design

Lara Scharbert and Birgit Strodel

Current Opinion in Structural Biology, 2025, 93, 103083
DOI: 10.1016/j.sbi.2025.103083

Roadmap on electronic structure codes in the exascale era

Vikram Gavini, Stefano Baroni, Volker Blum, David R Bowler, Alexander Buccheri, James R Chelikowsky, Sambit Das, William Dawson, Pietro Delugas, Mehmet Dogan, Claudia Draxl, Giulia Galli, Luigi Genovese, Paolo Giannozzi, Matteo Giantomassi, Xavier Gonze, Marco Govoni, François Gygi, Andris Gulans, John M Herbert, Sebastian Kokott, Thomas D Kühne, Kai-Hsin Liou, Tsuyoshi Miyazaki, Phani Motamarri, Ayako Nakata, John E Pask, Christian Plessl, Laura E Ratcliff, Ryan M Richard, Mariana Rossi, Robert Schade, Matthias Scheffler, Ole Schütt, Phanish Suryanarayana, Marc Torrent, Lionel Truflandier, Theresa L Windus, Qimen Xu, Victor W-Z Yu and D Perez

Modelling Simul. Mater. Sci. Eng., 2023, 31, 063301
DOI: 10.1088/1361-651X/acdf06

Computational and Experimental Study of the Conformational Variation of the Catalytic Residue His41 of the SARS-CoV-2 Main Protease

Jiao Zhou, Xiang Liu, Yan Xu, Juan Wang, Tingli Qian, Xiaohong Sang, Md Nazmul Hasan, Arieh Warshel, Jing An, Arjun Saha and Ziwei Huang

J. Phys. Chem. B, 2025, 129, 5198
DOI: 10.1021/acs.jpcb.5c01718

COVID-19 Treatment—Current Status, Advances, and Gap

Chian Ho and Ping-Chin Lee

Pathogens, 2022, 11, 1201
DOI: 10.3390/pathogens11101201

Mass spectrometric assays monitoring the deubiquitinase activity of the SARS-CoV-2 papain-like protease inform on the basis of substrate selectivity and have utility for substrate identification

Lennart Brewitz, H.T. Henry Chan, Petra Lukacik, Claire Strain-Damerell, Martin A. Walsh, Fernanda Duarte and Christopher J. Schofield

Bioorganic & Medicinal Chemistry, 2023, 95, 117498
DOI: 10.1016/j.bmc.2023.117498

Identification of novel and potent inhibitors of SARS-CoV-2 main protease from DNA-encoded chemical libraries

Dario Akaberi, Monireh Pourghasemi Lati, Janina Krambrich, Julia Berger, Grace Neilsen, Emilia Strandback, S. Pauliina Turunen, Johan Wannberg, Hjalmar Gullberg, Martin Moche, Praveen Kumar Chinthakindi, Tomas Nyman, Stefan G. Sarafianos, Anja Sandström, Josef D. Järhult, Kristian Sandberg, Åke Lundkvist, Oscar Verho, Johan Lennerstrand and Miguel Angel Martinez

Antimicrob Agents Chemother, 2024, 68
DOI: 10.1128/aac.00909-24

Multiplexed detection of viral proteases through dual response peptide-assisted nanopore sensing

Xin Zhou, Baixue Chu, Ruping Tang, Yao Jiang, Dongmei Xi and Shusheng Zhang

Sensors and Actuators B: Chemical, 2024, 409, 135634
DOI: 10.1016/j.snb.2024.135634

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

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

Upgrading nirmatrelvir to inhibit SARS-CoV-2 Mpro via DeepFrag and free energy calculations

Nguyen Minh Tam, Trung Hai Nguyen, Minh Quan Pham, Nam Dao Hong, Nguyen Thanh Tung, Van V. Vu, Duong Tuan Quang and Son Tung Ngo

Journal of Molecular Graphics and Modelling, 2023, 124, 108535
DOI: 10.1016/j.jmgm.2023.108535

Molecular Modelling, Synthesis, and In-Vitro Assay to Identify Potential Antiviral Peptides Targeting the 3-Chymotrypsin-Like Protease of SARS-CoV-2

Ryan Faddis, Sydney Du, James Stewart, Mohammad Mehedi Hasan, Noam Lewit, Md Ackas Ali, Cladie B. White, Patience Okoto, Sures Thallapuranam and Mohammad A. Halim

Int J Pept Res Ther, 2023, 29
DOI: 10.1007/s10989-023-10563-w

3-Chymotrypsin-like Protease (3CLpro) of SARS-CoV-2: Validation as a Molecular Target, Proposal of a Novel Catalytic Mechanism, and Inhibitors in Preclinical and Clinical Trials

Vitor Martins de Freitas Amorim, Eduardo Pereira Soares, Anielle Salviano de Almeida Ferrari, Davi Gabriel Salustiano Merighi, Robson Francisco de Souza, Cristiane Rodrigues Guzzo and Anacleto Silva de Souza

Viruses, 2024, 16, 844
DOI: 10.3390/v16060844

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

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

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

Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket

Chia-Ying Huang, Alexander Metz, Roland Lange, Nadia Artico, Céline Potot, Julien Hazemann, Manon Müller, Marina Dos Santos, Alain Chambovey, Daniel Ritz, Deniz Eris, Solange Meyer, Geoffroy Bourquin, May Sharpe and Aengus Mac Sweeney

Acta Crystallogr D Struct Biol, 2024, 80, 123
DOI: 10.1107/S2059798324000329

Probing the mutational landscape of the SARS-CoV-2 spike protein via quantum mechanical modeling of crystallographic structures

Marco Zaccaria, Luigi Genovese, William Dawson, Viviana Cristiglio, Takahito Nakajima, Welkin Johnson, Michael Farzan, Babak Momeni and Karen E Nelson

PNAS Nexus, 2022, 1
DOI: 10.1093/pnasnexus/pgac180

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

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

Antiviral peptides inhibiting the main protease of SARS‐CoV‐2 investigated by computational screening and in vitro protease assay

James Stewart, Jakaria Shawon, Md Ackas Ali, Blaise Williams, A. D. A. Shahinuzzaman, Sharmin Akther Rupa, Taha Al‐Adhami, Ruoqing Jia, Cole Bourque, Ryan Faddis, Kaylee Stone, Md Abu Sufian, Rajib Islam, Andrew C. McShan, Khondaker Miraz Rahman and Mohammad A. Halim

Journal of Peptide Science, 2024, 30
DOI: 10.1002/psc.3553

Non-covalent cyclic peptides simultaneously targeting Mpro and NRP1 are highly effective against Omicron BA.2.75

Shengnan Yin, Shuang Mei, Zhiqin Li, Zhen Xu, Yuting Wu, Xiujuan Chen, Dongmei Liu, Miao-Miao Niu and Jindong Li

Front. Pharmacol., 2022, 13
DOI: 10.3389/fphar.2022.1037993

Crystal structures of main protease (Mpro) mutants of SARS-CoV-2 variants bound to PF-07304814

Haihai Jiang, Xiaofang Zou, Pei Zeng, Xiangyi Zeng, Xuelan Zhou, Jie Wang, Jin Zhang and Jian Li

Mol Biomed, 2023, 4
DOI: 10.1186/s43556-023-00134-2

NanoVer Server: A Python Package for Serving Real-Time Multi-User Interactive Molecular Dynamics in Virtual Reality

Harry J. Stroud, Mark D. Wonnacott, Jonathan Barnoud, Rhoslyn Roebuck Williams, Mohamed Dhouioui, Adam McSloy, Ludovica Aisa, Luis E. Toledo, Phil Bates, Adrian J. Mulholland and David R. Glowacki

JOSS, 2025, 10, 8118
DOI: 10.21105/joss.08118

Computation of Absolute Binding Free Energies for Noncovalent Inhibitors with SARS-CoV-2 Main Protease

Mohammad M. Ghahremanpour, Anastasia Saar, Julian Tirado-Rives and William L. Jorgensen

J. Chem. Inf. Model., 2023, 63, 5309
DOI: 10.1021/acs.jcim.3c00874

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

Silaproline-bearing nirmatrelvir derivatives are potent inhibitors of the SARS-CoV-2 main protease highlighting the value of silicon-derivatives in structure-activity-relationship studies

Dóra Laczi, Sofia Schönbauer Huamán, Taylah Andrews-Clark, Stephen M. Laidlaw, Eidarus Salah, Leo Dumjahn, Petra Lukacik, Hani Choudhry, Martin A. Walsh, Miles W. Carroll, Christopher J. Schofield and Lennart Brewitz

European Journal of Medicinal Chemistry, 2025, 291, 117603
DOI: 10.1016/j.ejmech.2025.117603

Hydroxamate and thiosemicarbazone: Two highly promising scaffolds for the development of SARS-CoV-2 antivirals

Yin-Sui Xu, Jia-Zhu Chigan, Jia-Qi Li, Huan-Huan Ding, Le-Yun Sun, Lu Liu, Zhenxin Hu and Ke-Wu Yang

Bioorganic Chemistry, 2022, 124, 105799
DOI: 10.1016/j.bioorg.2022.105799

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

Complexity reduction in density functional theory: Locality in space and energy

William Dawson, Eisuke Kawashima, Laura E. Ratcliff, Muneaki Kamiya, Luigi Genovese and Takahito Nakajima

The Journal of Chemical Physics, 2023, 158
DOI: 10.1063/5.0142652

Cyclic β2,3-amino acids improve the serum stability of macrocyclic peptide inhibitors targeting the SARS-CoV-2 main protease

Takashi Miura, Tika R Malla, Lennart Brewitz, Anthony Tumber, Eidarus Salah, Kang Ju Lee, Naohiro Terasaka, C David Owen, Claire Strain-Damerell, Petra Lukacik, Martin A Walsh, Akane Kawamura, Christopher J Schofield, Takayuki Katoh and Hiroaki Suga

Bulletin of the Chemical Society of Japan, 2024, 97
DOI: 10.1093/bulcsj/uoae018

Decoding SARS‐CoV‐2 Inhibition: Insights From Molecular Dynamics Simulation of Condensed Amino Thiourea Scaffold Small Molecules

Xiaoli Shen, Hao Zhang, Pengyin Zhang, Xuerui Zhao, Chang Liu, Jianan Ju, Aijun Liu and Song Wang

J of Cellular Biochemistry, 2025, 126
DOI: 10.1002/jcb.70005

Determination of SARS-CoV-2 Main Protease (Mpro) Activity Based on Electrooxidation of Tyrosine Residue of a Model Peptide

Tatiana A. Filippova, Rami A. Masamrekh, Tatiana E. Farafonova, Yulia Yu. Khudoklinova, Victoria V. Shumyantseva, Sergei A. Moshkovskii and Alexey V. Kuzikov

Biochemistry Moscow, 2025, 90, 120
DOI: 10.1134/S0006297924603836

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

In vitro selection of macrocyclic peptide inhibitors containing cyclic γ2,4-amino acids targeting the SARS-CoV-2 main protease

Takashi Miura, Tika R. Malla, C. David Owen, Anthony Tumber, Lennart Brewitz, Michael A. McDonough, Eidarus Salah, Naohiro Terasaka, Takayuki Katoh, Petra Lukacik, Claire Strain-Damerell, Halina Mikolajek, Martin A. Walsh, Akane Kawamura, Christopher J. Schofield and Hiroaki Suga

Nat. Chem., 2023, 15, 998
DOI: 10.1038/s41557-023-01205-1

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

The emerging potential of interactive virtual reality in drug discovery

Rebecca K. Walters, Ella M. Gale, Jonathan Barnoud, David R. Glowacki and Adrian J. Mulholland

Expert Opinion on Drug Discovery, 2022, 17, 685
DOI: 10.1080/17460441.2022.2079632

Identification, characterization and biological studies of kinesine spindle protein inhibitor, benzo[b][1,4]oxazine-6-carboxamide derivative, via 3D-pharmacophore virtual screening

Samia A. Elseginy

Journal of Molecular Structure, 2024, 1312, 138508
DOI: 10.1016/j.molstruc.2024.138508

De Novo Discovery of a Noncovalent Cell-Penetrating Bicyclic Peptide Inhibitor Targeting SARS-CoV-2 Main Protease

Yahong Tan, Jinyue Yang, Min Wang, Qi Peng, Yongqi Li, Lifeng Fu, Mengmeng Zhang, Jiang Wu, Guanya Yang, Christopher John Hipolito, Youming Zhang, Jianxun Qi, Yi Shi and Yizhen Yin

J. Med. Chem., 2024, 67, 20258
DOI: 10.1021/acs.jmedchem.4c01639

Concordance of X-ray and AlphaFold2 Models of SARS-CoV-2 Main Protease with Residual Dipolar Couplings Measured in Solution

Angus J. Robertson, Joseph M. Courtney, Yang Shen, Jinfa Ying and Ad Bax

J. Am. Chem. Soc., 2021, 143, 19306
DOI: 10.1021/jacs.1c10588

Discovery of a Highly Promising Disulfide Derivative Scaffold as Inhibitor of SARS‐CoV‐2 Main Protease

Yin‐Sui Xu, Yang Xiang, Le Zhai, Cheng Chen, Xiao‐Rong Wu, Wei‐Ya Chen, Lu Liu, Mu‐Han Zhao, Xiao‐Long Liu and Ke‐Wu Yang

Chemistry & Biodiversity, 2024, 21
DOI: 10.1002/cbdv.202401034

Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets

Filip Mihalič, Caroline Benz, Eszter Kassa, Richard Lindqvist, Leandro Simonetti, Raviteja Inturi, Hanna Aronsson, Eva Andersson, Celestine N. Chi, Norman E. Davey, Anna K. Överby, Per Jemth and Ylva Ivarsson

Nat Commun, 2023, 14
DOI: 10.1038/s41467-023-41312-8

Dual-targeting cyclic peptides of receptor-binding domain (RBD) and main protease (Mpro) as potential drug leads for the treatment of SARS-CoV-2 infection

Zhen Xu, Yunting Zou, Xi Gao, Miao-Miao Niu, Jindong Li, Lu Xue and Su Jiang

Front. Pharmacol., 2022, 13
DOI: 10.3389/fphar.2022.1041331

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

The S1′–S3′ Pocket of the SARS‐CoV‐2 Main Protease Is Critical for Substrate Selectivity and Can Be Targeted with Covalent Inhibitors

Ming Liu, Jihui Li, Wenqi Liu, Ying Yang, Manman Zhang, Yuxin Ye, Wenning Zhu, Cuiyan Zhou, Hongbin Zhai, Zhengshuang Xu, Guoliang Zhang and Hao Huang

Angewandte Chemie, 2023, 135
DOI: 10.1002/ange.202309657

An efficient computational protocol for template‐based design of peptides that inhibit interactions involving SARS‐CoV‐2 proteins

Akshay Chenna, Wajihul Hasan Khan, Rozaleen Dash, Saurabh Saraswat, Archana Chugh, Anurag S. Rathore and Gaurav Goel

Proteins, 2023, 91, 1222
DOI: 10.1002/prot.26511

Predicting potential SARS-CoV-2 mutations of concern via full quantum mechanical modelling

Marco Zaccaria, Luigi Genovese, Brigitte E. Lawhorn, William Dawson, Andrew S. Joyal, Jingqing Hu, Patrick Autissier, Takahito Nakajima, Welkin E. Johnson, Ismael Fofana, Michael Farzan and Babak Momeni

J. R. Soc. Interface., 2024, 21
DOI: 10.1098/rsif.2023.0614

Computational design of stapled peptide inhibitor against SARS‐CoV‐2 receptor binding domain

Asha Rani Choudhury, Atanu Maity, Sayantani Chakraborty and Rajarshi Chakrabarti

Peptide Science, 2022, 114
DOI: 10.1002/pep2.24267

Label‐free Sensing of Main Protease Activity of SARS‐CoV‐2 with an Aerolysin Nanopore

Xin Zhou, Ruping Tang, Yusen Li, Shusheng Zhang and Dongmei Xi

Chemistry An Asian Journal, 2022, 17
DOI: 10.1002/asia.202200747

Identification of a Dual Inhibitor of Secreted Phospholipase A2 (GIIA sPLA2) and SARS-CoV-2 Main Protease

Maria A. Theodoropoulou, Giorgos S. Koutoulogenis, Linlin Zhang, Ifigeneia Akrani, Emmanuel Mikros, Rolf Hilgenfeld and George Kokotos

Pharmaceuticals, 2022, 15, 961
DOI: 10.3390/ph15080961

Virtual reality in drug design: Benefits, applications and industrial perspectives

Marc Baaden and David R. Glowacki

Current Opinion in Structural Biology, 2025, 92, 103044
DOI: 10.1016/j.sbi.2025.103044

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

The S1′–S3′ Pocket of the SARS‐CoV‐2 Main Protease Is Critical for Substrate Selectivity and Can Be Targeted with Covalent Inhibitors

Ming Liu, Jihui Li, Wenqi Liu, Ying Yang, Manman Zhang, Yuxin Ye, Wenning Zhu, Cuiyan Zhou, Hongbin Zhai, Zhengshuang Xu, Guoliang Zhang and Hao Huang

Angew Chem Int Ed, 2023, 62
DOI: 10.1002/anie.202309657

Primer for Designing Main Protease (Mpro) Inhibitors of SARS-CoV-2

Abhishek Thakur, Gaurav Sharma, Vishnu Nayak Badavath, Venkatesan Jayaprakash, Kenneth M. Merz, Galia Blum and Orlando Acevedo

J. Phys. Chem. Lett., 2022, 13, 5776
DOI: 10.1021/acs.jpclett.2c01193

A New Advanced Approach: Design and Screening of Affinity Peptide Ligands Using Computer Simulation Techniques

Zheng Wei, Meilun Chen, Xiaoling Lu, Yijie Liu, Guangnan Peng, Jie Yang, Chunhua Tang and Peng Yu

CTMC, 2024, 24, 667
DOI: 10.2174/0115680266281358240206112605

Peptide-Based Strategies Against SARS-CoV-2 Attack: An Updated In Silico Perspective

G. Moroy and P. Tuffery

Front. Drug. Discov., 2022, 2
DOI: 10.3389/fddsv.2022.899477

Ultrafast one-minute electronic detection of SARS-CoV-2 infection by 3CLpro enzymatic activity in untreated saliva samples

Ella Borberg, Eran Granot and Fernando Patolsky

Nat Commun, 2022, 13
DOI: 10.1038/s41467-022-34074-2