{"doi":"10.1101/2020.09.07.286344","title":"Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease","abstract":"Abstract The main protease (M pro ) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many high-resolution apo and inhibitor-bound structures of M pro , a cysteine protease, have been determined, facilitating structure-based drug design. M pro plays a central role in the viral life cycle by catalyzing the cleavage of SARS-CoV-2 polyproteins. In addition to the catalytic dyad His41-Cys145, M pro contains multiple histidines including His163, His164, and His172. The protonation states of these histidines and the catalytic nu-cleophile Cys145 have been debated in previous studies of SARS-CoV M pro , but have yet to be investigated for SARS-CoV-2. In this work we have used molecular dynamics simulations to determine the structural stability of SARS-CoV-2 M pro as a function of the protonation assignments for these residues. We simulated both the apo and inhibitor-bound enzyme and found that the conformational stability of the binding site, bound inhibitors, and the hydrogen bond networks of M pro are highly sensitive to these assignments. Additionally, the two inhibitors studied, the peptidomimetic N3 and an α -ketoamide, display distinct His41/His164 protonation-state-dependent stabilities. While the apo and the N3-bound systems favored N δ (HD) and N ϵ (HE) protonation of His41 and His164, respectively, the α -ketoamide was not stably bound in this state. Our results illustrate the importance of using appropriate histidine protonation states to accurately model the structure and dynamics of SARS-CoV-2 M pro in both the apo and inhibitor-bound states, a necessary prerequisite for drug-design efforts.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":127331,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.961,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":322882,"name":"Diane L. Lynch","orcid":"0009-0005-8763-1503","position":1,"is_corresponding":false},{"id":322883,"name":"Isabella Daidone","orcid":"0000-0001-8970-8408","position":2,"is_corresponding":false},{"id":576633,"name":"Laura Zanetti-Polzi","orcid":null,"position":3,"is_corresponding":false},{"id":322885,"name":"Micholas Dean Smith","orcid":"0000-0002-0777-7539","position":4,"is_corresponding":false},{"id":324607,"name":"Chris Chipot","orcid":null,"position":5,"is_corresponding":false},{"id":226918,"name":"Daniel W. Kneller","orcid":"0000-0002-5416-5789","position":6,"is_corresponding":false},{"id":226924,"name":"Andrey Kovalevsky","orcid":"0000-0003-4459-9142","position":7,"is_corresponding":false},{"id":226923,"name":"Leighton Coates","orcid":"0000-0003-2342-049X","position":8,"is_corresponding":false},{"id":324608,"name":"Andrei A. Golosov","orcid":null,"position":9,"is_corresponding":false},{"id":322886,"name":"Callum J. Dickson","orcid":"0000-0003-4013-6394","position":10,"is_corresponding":false},{"id":576634,"name":"Camilo Velez-Vega","orcid":null,"position":11,"is_corresponding":false},{"id":322888,"name":"José S. Duca","orcid":"0000-0002-0880-5618","position":12,"is_corresponding":false},{"id":322889,"name":"Josh V. Vermaas","orcid":"0000-0003-3139-6469","position":13,"is_corresponding":false},{"id":322890,"name":"Yui Tik Pang","orcid":"0000-0003-4843-4468","position":14,"is_corresponding":false},{"id":322891,"name":"Atanu Acharya","orcid":"0000-0002-6960-7789","position":15,"is_corresponding":false},{"id":303820,"name":"Jerry M. Parks","orcid":"0000-0002-3103-9333","position":16,"is_corresponding":false},{"id":56176,"name":"Jeremy C. Smith","orcid":"0000-0002-2978-3227","position":17,"is_corresponding":false},{"id":98033,"name":"James C. Gumbart","orcid":"0000-0002-1510-7842","position":18,"is_corresponding":false},{"id":400326,"name":"Anna Pavlova","orcid":"0000-0002-3974-5662","position":0,"is_corresponding":true}],"reference_count":66,"raw_metadata":null,"created_at":"2026-07-18T23:15:30.930746Z","pmid":"32935106","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}