DNA/RNA-Small Molecule Interaction Modeling Service
Understanding the interactions between DNA or RNA molecules and small molecules is crucial in various fields such as drug discovery, medicinal chemistry, and molecular biology. CD ComputaBio provides DNA/RNA-small molecule interaction modeling services using state-of-the-art algorithms. Our scientists use cutting-edge computational techniques to predict how small molecules interact with nucleic acids, assess binding affinities, and explore the dynamic behavior of these complexes under different conditions.
Introduction to DNA/RNA-Small Molecule Interaction Modeling
The interaction between nucleic acid molecules and small molecules is the basis of many biological processes and is of great significance in fields such as drug discovery, medicinal chemistry and molecular biology. A typical example is the breakthrough in the field of drug discovery with structured RNA. Researchers have identified certain RNAs as druggable targets for small molecules for the treatment of a variety of human diseases. Computer-aided modeling, as an emerging field, complements experimental methods by providing detailed atomic-level insights, enabling researchers to predict the binding mode of nucleic acid-small molecule, evaluate binding affinity and explore the dynamics of these complexes under various conditions. This analysis provides detailed insights into the mechanism of action of small molecules, which helps to rationally design new treatments and understand basic biological processes.
Fig. 1 Computational methods and interaction modeling analysis for RNA-small molecule drug discovery. (Manigrasso J, et al.; 2021)
Our Services
CD ComputaBio provides a one-stop DNA/RNA-small molecule interaction modeling services, from structure preparation, molecular docking to molecular dynamics simulation and free energy calculation. Our advanced computational technologies enable us to handle any difficulties and challenges encountered in nucleic acid-small molecule interaction modeling.
DNA-Small Molecule Interaction Modeling Service
DNA-Small Molecule Intercalator Interaction Modeling
- Simulating and analyzing how small molecule intercalators are inserted into base pairs between DNA double helices, affecting DNA replication and transcription.
- Assisting clients develop anticancer drugs, such as anthracycline antibiotics, and understanding the effects of drugs on DNA structure.
DNA-Alkylating Agent Interaction Modeling
- Analyzing the covalent binding process of alkylating agents to DNA and simulating DNA damage and repair mechanisms.
- Evaluating the effectiveness and toxicity of alkylating agents to support the development of anticancer drugs.
DNA-Cross linking Agent Interaction Modeling
- Simulating how small molecule drugs bind to the minor groove region of DNA and affect the regulation of gene expression.
- Supporting the design of antibacterial and antiviral drugs, and gene regulation mechanisms study.
DNA-Minor Groove Binder Interaction Modeling
- Analyzing the double-strand cross-linking process of small molecule cross-linkers and DNA to simulate DNA damage, cell apoptosis, and repair mechanisms.
- Supporting the development and optimization of anti-cancer drugs, such as cisplatin, and the evaluation of the effectiveness and safety of cross-linkers.
G-Quadruplex DNA-Small Molecule Interaction Modeling
- Simulating the interaction of small molecules with G-quadruplex DNA structures to explain how small molecules stabilize G-quadruplex DNA and regulate its biological functions.
- Supporting clients in developing novel therapeutics targeting telomeres and oncogene regulatory regions to improve cancer treatment.
Triplex DNA-Small Molecule Interaction Modeling
- Studying the binding mode of small molecule ligands to triple-stranded DNA structures, and analyze how they stabilize triple-stranded DNA and adjust the gene expression regulation of triple-stranded DNA.
- Assisting clients in developing gene regulation tools and therapeutic drugs.
RNA-Small Molecule Interaction Modeling Service
miRNA-Small Molecule Interaction Modeling
- Analyzing how small molecules affect the function and expression of miRNAs and simulate their interactions.
- Supporting therapeutic research in areas such as cancer and cardiovascular disease and developing miRNA regulators.
siRNA-Small Molecule Interaction Modeling
- Simulating the interaction between small molecules and siRNA, and analyze the effect of small molecules on siRNA stability and function.
- Supporting the development of nucleic acid drugs to improve the efficiency of RNA interference technology.
lncRNA-Small Molecule Interaction Modeling
- Studying how small molecules bind to long noncoding RNA (lncRNA) and modeling their effects on gene regulation and cell function.
- Supporting therapeutic research for diseases such as cancer and helping clients develop regulators targeting lncRNA.
RNA Aptamer-Small Molecule Interaction Modeling
- Studying the highly specific binding between RNA aptamers and small molecules and simulating their three-dimensional structure and interaction mode.
- Supporting the development of diagnostics, therapeutics and biosensors.
Ribosomal RNA-Small Molecule Interaction Modeling
- Simulating the interaction of small molecules such as antibiotics with ribosomal RNA to study their effects on protein synthesis.
- Assisting clients in designing and optimizing antibiotics to overcome drug resistance.
Riboswitch-Small Molecule Interaction Modeling
- Simulating the binding of small molecules to the riboswitch region in mRNA to study the regulatory mechanism of gene expression.
- Supporting the development of new antimicrobial drugs to regulate the expression of specific genes.
Workflow for DNA/RNA-Small Molecule Interaction Modeling
Preparation of Nucleic Acid and Small Molecule Structure
Download known DNA/RNA structures, if available, and small molecule structures from the database and perform preprocessing. If the experimental structure of DNA/RNA is unknown, we will use 3D-DART, nucleic acid builder to generate standard B-DNA or A-DNA structures based on sequences. Or, tools such as RNAfold, mfold are used to predict RNA secondary structures, and then generate three-dimensional structures through Rosetta or SimRNA.
Various general tools such as AutoDock Vina, GOLD, Schrödinger Glide and nucleic acid-specific tools such as NLDock for nucleic acid-ligand docking and DOCK6 for support nucleic acid docking are used to predict the binding mode and binding site between small molecules and nucleic acid.
Molecular Dynamics Simulations
The docked DNA/RNA-small molecule complex is performed nanosecond simulations using GROMACS, AMBER or NAMD to observe the stability of the complex binding mode and the interaction details, including hydrogen bonds, hydrophobic contacts, intercalation, and electrostatic interactions.
Binding Free Energy Calculation
A series of representative conformations from the MD simulation trajectory are extracted to quantitatively evaluate the binding affinity between small molecules and nucleic acid and compare the binding ability of different small molecules.
A detailed analysis and professional report is provided, including methods, results, charts and conclusions, as well as optimization suggestions.
CD ComputaBio is dedicated to advancing scientific research through high-quality computational modeling services. Our mission is to provide researchers and institutions with insights that drive innovation and discovery in biotechnology, pharmaceuticals, and molecular biology. Please don't hesitate to contact us, if you are interested in our nucleic acid-small molecule interaction modeling.
References:
- Manigrasso J, et al. Computer-aided design of RNA-targeted small molecules: A growing need in drug discovery. Cellpress. 2021;11(7):2965-2988.
- Krishnan SR, et al. Reliable method for predicting the binding affinity of RNA-small molecule interactions using machine learning. Brief Bioinform. 2024;25(2):bbae002.
- Zhu W, et al. Identifying RNA-small Molecule Binding Sites Using Geometric Deep Learning with Language Models. J Mol Biol. Published online February 15, 2025.
* For Research Use Only.
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