ArticleChemical biology & drug design2021
Fragment-based in silico design of SARS-CoV-2 main protease inhibitors.
Article in Chemical biology & drug design, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
10 citing papers in PubMed.
- PROTACs in Antivirals: Current Advancements and Future Perspectives.Molecules (Basel, Switzerland) · 2025Review
- Fragment-based Drug Discovery Strategy and its Application to the Design of SARS-CoV-2 Main Protease Inhibitor.Current medicinal chemistry · 2024Review
- In Silico Design of New Dual Inhibitors of SARS-CoV-2 MInternational journal of molecular sciences · 2023Article
- Dock-able linear and homodetic di, tri, tetra and pentapeptide library from canonical amino acids: SARS-CoV-2 Mpro as a case study.Journal of pharmaceutical analysis · 2023Article
- Novel ciprofloxacin and norfloxacin-tetrazole hybrids as potential antibacterial and antiviral agents: TargetingJournal of molecular structure · 2023Article
- Discovery of Rift Valley fever virus natural pan-inhibitors by targeting its multiple key proteins through computational approaches.Scientific reports · 2022Article
- Structural Elucidation of Rift Valley Fever Virus L Protein towards the Discovery of Its Potential Inhibitors.Pharmaceuticals (Basel, Switzerland) · 2022Article
- Fragment-based design of SARS-CoV-2 Mpro inhibitors.Structural chemistry · 2022Article
- Fragment-based in silico design of SARS-CoV-2 main protease inhibitors.Chemical biology & drug design · 2021Article
- Antimicrobial and Hepatoprotective Properties of Pods ofDose-response : a publication of International Hormesis SocietyArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
3CLpro is essential for SARS-CoV-2 replication and infection; its inhibition using small molecules is a potential therapeutic strategy. In this study, a comprehensive crystallography-guided fragment-based drug discovery approach was employed to design new inhibitors for SARS-CoV-2 3CLpro. All small molecules co-crystallized with SARS-CoV-2 3CLpro with structures deposited in the Protein Data Bank were used as inputs. Fragments sitting in the binding pocket (87) were grouped into eight geographical types. They were interactively coupled using various synthetically reasonable linkers to generate larger molecules with divalent binding modes taking advantage of two different fragments' interactions. In total, 1,251 compounds were proposed, and 7,158 stereoisomers were screened using Glide (standard precision and extra precision), AutoDock Vina, and Prime MMGBSA. The top 22 hits having conformations approaching the linear combination of their constituent fragments were selected for MD simulation on Desmond. MD simulation suggested 15 of these did adopt conformations very close to their constituent pieces with far higher binding affinity than either constituent domain alone. These structures could provide a starting point for the further design of SARS-CoV-2 3CLpro inhibitors with improved binding, and structures are provided.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.