{"doi":"10.1101/2023.11.29.569293","title":"TSAR, “Thermal Shift Analysis in R”, identifies endogenous molecules that interact with HIV-1 capsid hexamers","abstract":"Abstract The thermal shift assay (TSA) is a versatile biophysical technique for studying protein-ligand interactions in vitro . Here, we report a free, open-source software tool, TSAR (“Thermal Shift Analysis in R”), to expedite the analysis of TSA data. The TSAR package incorporates multiple workflows that facilitate TSA analyses, returns publication-ready graphics, and includes an optional graphic user interface. The package is available at https://bioconductor.org/packages/TSAR/ . Applying TSAR, we screened two chemical libraries and found multiple molecules that potentially interact in vitro with the capsid protein (CA) of human immunodeficiency virus type 1 (HIV-1). First, a library of vitamins exemplifies the different graphic outputs of TSAR, and we report a change in the 50% melting temperature (ΔT m ) for folic acid-treated CA hexamers (CA HEX ). Since HIV-1 CA HEX interacts with host-derived acids like inositol hexaphosphate (IP6) or dNTPs, a second library was screened containing 96 organic, acidic metabolites; multiple anionic ligands caused a ΔT m for CA HEX . Subsequent investigation of these interactions includes biolayer interferometry, antiviral activity against pseudotyped HIV-1, and endogenous reverse transcriptase assays that were used to validate and investigate the biological impact of these native ligands that thermally-stabilize CA HEX . One compound hit, gallic acid, exhibited anti–HIV-1 activity as previously reported, and we show interacts with CA HEX as a potentially novel mechanism. Overall, the TSAR package facilitated quick analysis of TSA data from multiple libraries to help identify a biologically relevant hit, gallic acid, as a molecule that can inhibit HIV-1 replication and targets CA HEX . Importance The TSAR package is freely available (AGPL-3) and is designed for both experienced or new R users, having command-line code for handling large and challenging datasets while also including an optional GUI that enables easy use by non-programmers. This is the first TSA analysis program written in R, a free and open-source language; TSAR simplifies TSA analysis while maintaining diverse visualization options for small-to-large libraries and multidimensional analysis. Additionally, we report multiple endogenous metabolites that potentially interact with the HIV-1 capsid protein hexamers (CA HEX ) in vitro , including folic acid, gallic acid, and multiple others, primarily from the tricarboxylic acid (TCA) cycle. Various methods validate gallic acid interactions with CA HEX , leading to a novel suggested mechanism of action, and in-line with previous reports, this metabolite has potential for natural-based treatments of HIV-1. Further, we advance the understanding of the potential mechanism(s) for HIV-1 inhibition by gallic acid treatment.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":401748,"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":0.9487,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1178703,"name":"Xinlin Gao","orcid":"0009-0002-2518-235X","position":1,"is_corresponding":false},{"id":1178704,"name":"Zhijiang Ye","orcid":"0009-0005-5464-7306","position":2,"is_corresponding":false},{"id":182307,"name":"Xin Wen","orcid":null,"position":3,"is_corresponding":false},{"id":900031,"name":"Zachary C. Lorson","orcid":"0009-0002-1404-9086","position":4,"is_corresponding":false},{"id":1178705,"name":"Hua Zheng","orcid":"0000-0002-5511-6137","position":5,"is_corresponding":false},{"id":1179128,"name":"Jessica Fahim","orcid":null,"position":6,"is_corresponding":false},{"id":1179129,"name":"Andres E. Castaner","orcid":null,"position":7,"is_corresponding":false},{"id":494263,"name":"Karen A. Kirby","orcid":"0000-0003-2468-4796","position":8,"is_corresponding":false},{"id":253448,"name":"Stefan G. Sarafianos","orcid":"0000-0002-5840-154X","position":9,"is_corresponding":false},{"id":651516,"name":"William M. McFadden","orcid":"0000-0001-6911-2172","position":0,"is_corresponding":true}],"reference_count":39,"raw_metadata":null,"created_at":"2026-07-19T01:20:12.316631Z","pmid":null,"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":[]}