SecureMCP-Agentic

SecureMCP-Agentic is a research prototype for secure tool selection in LLM-based agents. It adds a security-aware verification layer between top-k tool retrieval and tool execution to reduce prompt injection and tool-poisoning attacks in MCP-enabled agent systems.

Current Status

The current implementation is a working heuristic baseline. It includes:

• Local MCP server with benign, high-risk, and simulated malicious tools

• ChromaDB-based top-k tool retrieval

• Prompt-injection phrase detection

• Intent-mismatch approximation

• Permission-risk scoring

• Execution-impact scoring

• MCP server/tool trust scoring

• Threshold-based risk classification

• Human approval for high-risk actions

• Docker-isolated tool execution

• JSONL experiment logging

The planned next stage is a multi-LLM verification framework with specialized security, intent, permission, execution, trust, and judge verifiers.

Related MCP server: permitd MCP Server

Proposed Workflow

User Prompt
    ↓
Intent Context
    ↓
MCP Tool Discovery
    ↓
Top-k Tool Retrieval
    ↓
Risk Verification
    ↓
Risk-Aware Tool Selection
    ↓
Execute / Final Verify / Human Approval / Reject
    ↓
Docker Sandbox
    ↓
Audit Log

Current Risk Algorithm

For each candidate tool, the prototype calculates:

R = 0.40S + 0.20A + 0.20P + 0.10E + 0.10T

Where:

• S = prompt-injection or suspicious-description score

• A = intent-mismatch score

• P = permission-risk score

• E = execution-impact score

• T = MCP server or tool-source trust risk

The security-adjusted selection score is:

Secure Utility = Relevance × (1 - Risk)

Critical-risk tools are excluded before final selection.

Risk Thresholds

These values are preliminary heuristic settings and will later be calibrated using validation data.

Project Structure

securemcp-sandbox/
│
├── .vscode/
│   ├── launch.json
│   └── tasks.json
│
├── data/
│   └── tools.json
│
├── executor/
│   ├── Dockerfile
│   └── executor.py
│
├── logs/
│
├── src/
│   ├── main.py
│   ├── mcp_server.py
│   ├── retriever.py
│   ├── risk_engine.py
│   └── runner.py
│
├── .gitignore
├── requirements.txt
└── README.md

Requirements

• Python 3.11 or 3.12

• Docker Desktop

• Node.js and npm

• Visual Studio Code

• Git

Setup

1. Clone the repository

git clone https://github.com/Nafeeul/SecureMCP-Agentic.git
cd SecureMCP-Agentic

2. Create a virtual environment

py -m venv .venv
.\.venv\Scripts\Activate.ps1

3. Install dependencies

python -m pip install --upgrade pip
python -m pip install -r requirements.txt

4. Build the Docker executor

Make sure Docker Desktop is running.

docker build -t securemcp-executor .\executor

5. Run the SecureMCP experiment

python .\src\main.py

Example prompt:

Find a New Year's gift under $80 with at least 4.5 stars.

Run the MCP Server

Start the MCP Inspector from the project root:

npx -y @modelcontextprotocol/inspector .venv/Scripts/python.exe src/mcp_server.py

Then open:

Tools → List Tools

The current MCP server exposes:

• product_search

• gift_suggestion

• simulated_email_sender

• priority_product_tool

The malicious tool is simulated only. It does not access real data or make network requests.

Docker Safety Controls

Approved tools run inside a restricted Docker container with:

• No network access

• Read-only root filesystem

• Non-root execution

• Dropped Linux capabilities

• No privilege escalation

• CPU and memory limits

• Process-count limits

• Execution timeout

• Explicit tool allow-list

Do not mount personal folders, credentials, Docker sockets, or production services into the sandbox.

Experiment Logs

Each run is saved to:

logs/experiments.jsonl

The log includes:

• User prompt

• Retrieved top-k tools

• Relevance scores

• Individual risk scores

• Final risk level

• Baseline-selected tool

• SecureMCP-selected tool

• Decision

• Sandbox execution result

• Latency

Benchmark Datasets

The planned evaluation will use:

ToolBench

Repository:

https://github.com/OpenBMB/ToolBench

Planned use:

• Large-scale API metadata

• Tool descriptions

• Retrieval experiments

• User instructions

• Top-k candidate testing

API-Bank

Repository:

https://github.com/AlibabaResearch/DAMO-ConvAI/tree/main/api-bank

Planned use:

• User prompts

• Tool-use dialogues

• Expected API calls

• Expected parameters

The benchmark data will be converted into a unified SecureMCP format before testing. Controlled poisoned variants will be generated from selected benign tool descriptions. Real external APIs will not be executed.