BioLLM Wiki β€Ί Targeted Small Molecules

Molecular Docking

These papers use molecular docking to screen or investigate compounds against targets including PI3Kalpha in gastric cancer, PDE5A/PDE6A, glioma-associated proteins, SARS-CoV-2 Mpro, and Mycobacterium tuberculosis DNA gyrase. Docking is combined across the studies with virtual screening, QSAR or machine-learning models, molecular dynamics, network pharmacology, MM-GBSA or MMPBSA analyses, and biochemical or cellular experiments.

Papers
8,079
Jan 2024 – Aug 2026
2024 share
6.29%
of the month's papers, on average
2025 share
7.78%
of the month's papers, on average
2026 share
6.41%
of the month's papers, on average
Change
β–² +1.9%
2024 β†’ 2026, relative

Share of papers by month

Peak 9.2% in Dec 2025. Month-by-month values and sub-terms are on Keyword Trends.

Jan 2024Aug 2026

Virtual screening pipelines

Molecular docking was used within multistep computational workflows. Examples include using machine-learning QSAR screening of 9,214 DrugBank compounds targeting PI3KΞ±, followed by drug-likeness filtering and docking; screening approximately 90,000 natural compounds against CDK8 after Lipinski, ADME/toxicity, and pan-assay interference filters; and hierarchical docking of 23,740 phytochemicals against MELK followed by binding-interaction analysis (PMID 38507171; PMID 39149808; PMID 39868843). Other workflows combined e-pharmacophore mapping, Glide docking, MM-GBSA, and molecular dynamics to identify compounds more selective for PDE5A than PDE6A, or used dynamic structure-based pharmacophore modeling, virtual screening, docking, molecular dynamics, and steered molecular dynamics to identify potential inhibitors of the MKK3–MYC interaction (PMID 37545162; PMID 40157686).

πŸ“„ Applied biochemistry and biotechnology β†—πŸ“„ Omics : a journal of integrative biology β†—πŸ“„ Chemistry & biodiversity β†—πŸ“„ Journal of biomolecular structure & dynamics β†—πŸ“„ International journal of biological macromolecules β†—

Natural products and formulas

Docking was combined with phytochemical characterization, enzyme assays, network pharmacology, or other experimental approaches in several studies. Quercetin and stigmasta-5,22-dien-3Ξ²-ol isolated from Euphorbia milii were evaluated in antioxidant assays and Ξ±-amylase and Ξ±-glucosidase inhibition assays, with molecular docking to Ξ±-d-glucose and PTP1B (PMID 38284643). Oxypeucedanin and osthol isolated from Prangos aricakensis were tested for antioxidant and AChE, BChE, tyrosinase, and urease inhibition, using enzyme kinetics, molecular docking, and DFT calculations (PMID 38214506). Radix Paeoniae Rubra was investigated in glioma using network pharmacology, molecular docking, and in vitro and in vivo experiments (PMID 38381309). Dachaihu decoction was studied in septic rats and LPS-stimulated Caco-2 cells using chemical profiling, transcriptomics, network pharmacology, molecular docking, and experimental validation (PMID 39419306). Ela tablet constituents were chemically and metabolically profiled, and blood-absorbable compounds were evaluated by molecular docking for interactions with PDE5 (PMID 40056491). Naokang II decoction was investigated for vascular dementia using chemical profiling, network pharmacology, single-nucleus RNA sequencing, molecular docking, and in vitro validation (PMID 42099108).

πŸ“„ Natural product research β†—πŸ“„ Journal of biomolecular structure & dynamics β†—πŸ“„ Applied biochemistry and biotechnology β†—πŸ“„ Journal of ethnopharmacology β†—πŸ“„ Journal of pharmaceutical and biomedical analysis β†—πŸ“„ Journal of natural products β†—

Structure-guided inhibitor design

Several studies used structural, structure–activity relationship, or mechanistic approaches to guide inhibitor design and investigate binding modes. Isoquinolinone isosteres were explored as DHODH inhibitor cores using co-crystal structures, and the positioning of nitrogen was found to affect potency. N-phenyl ureidobenzenesulfonates were developed as DHODH inhibitors; molecular docking suggested binding in the brequinar-binding site, which was supported by DHODH inhibition assays (PMID 39284456; PMID 39637752). Pyrimidine-2,4-dione derivatives were optimized against SARS-CoV-2 Mpro, and crystallography of an Mpro–compound 15 complex identified a T-shaped π–π interaction with His41, while fragment growth against carbonic anhydrase II produced inhibitors with an L-shaped configuration occupying the active site and subnanomolar inhibitory activity (PMID 41043330; PMID 42290333). A separate pyrrolo[2,3-d]pyrimidin-4-one series was investigated through mechanistic studies that supported an allosteric-covalent mode in PDI involving the bβ€² domain and cysteine C312 (PMID 41574754).

πŸ“„ Bioorganic & medicinal chemistry letters β†—πŸ“„ Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie β†—πŸ“„ Bioorganic chemistry β†—πŸ“„ Journal of medicinal chemistry β†—πŸ“„ Journal of medicinal chemistry β†—

Anti-infective target discovery

Computational studies have investigated bacterial enzymes and SARS-CoV-2 Mpro as targets for inhibitor discovery. For Klebsiella pneumoniae aspartate Ξ²-semialdehyde dehydrogenase, active-site binding interactions with two established lead compounds informed inhibitor design, followed by virtual screening and computational evaluation of candidate compounds (PMID 40617981). Phytochemicals from an Indian medicinal plant database were screened against wild-type and mutant Mycobacterium tuberculosis DNA gyrase using virtual screening, ADMET-based refinement, and molecular dynamics; MMPBSA analysis supported IM7 as a promising inhibitor (PMID 41308238). In the NDM-1 study, amifostine inhibited NDM-1 hydrolytic activity and restored meropenem antibacterial activity against NDM-1-positive E. coli in vitro; the combination also improved survival and reduced bacterial burden in infected mice (PMID 41223586). For MRSA, cyclic heptapeptides were designed computationally, synthesized, and experimentally tested; Ala6 showed the strongest activity among the evaluated peptides (PMID 41359057). Viral studies assessed amphibian peptides against SARS-CoV-2 Mpro, with docking and molecular dynamics used to investigate Hp-1081 binding after inhibition assays (PMID 39854653). Synthetic spiro-N-(4-sulfamoylphenyl)-2-carboxamide derivatives were evaluated by molecular docking against SARS-CoV-2 Mpro, and compounds 5 and 6 had the strongest reported binding scores (PMID 37946070).

πŸ“„ Molecular diversity β†—πŸ“„ Computers in biology and medicine β†—πŸ“„ Bioorganic chemistry β†—πŸ“„ Naunyn-Schmiedeberg's archives of pharmacology β†—πŸ“„ Chemistry & biodiversity β†—πŸ“„ Molecular diversity β†—

Written by gpt-5.6-luna from 96 of this keyword's papers, a few from every whole month through Aug 2026; every paragraph was checked against the abstracts it cites. A paper counts for the keyword when its title, abstract, keywords or MeSH headings match the keyword's terms. Not medical advice; see the Disclaimer.