SELECT 
  MIN(
    IF(
      cscart_product_prices.percentage_discount = 0, 
      cscart_product_prices.price, 
      cscart_product_prices.price - (
        cscart_product_prices.price * cscart_product_prices.percentage_discount
      )/ 100
    )
  ) as price 
FROM 
  cscart_product_prices 
WHERE 
  lower_limit <= 1 
  AND cscart_product_prices.product_id = 368409 
  AND cscart_product_prices.usergroup_id IN (0, 0, 1) 
ORDER BY 
  lower_limit DESC 
LIMIT 
  1

Query time 0.00069

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "2.40"
    },
    "table": {
      "table_name": "cscart_product_prices",
      "access_type": "range",
      "possible_keys": [
        "usergroup",
        "product_id",
        "lower_limit",
        "usergroup_id"
      ],
      "key": "usergroup",
      "used_key_parts": [
        "product_id",
        "usergroup_id",
        "lower_limit"
      ],
      "key_length": "9",
      "rows_examined_per_scan": 2,
      "rows_produced_per_join": 0,
      "filtered": "100.00",
      "cost_info": {
        "read_cost": "2.00",
        "eval_cost": "0.06",
        "prefix_cost": "2.40",
        "data_read_per_join": "19"
      },
      "used_columns": [
        "product_id",
        "price",
        "percentage_discount",
        "lower_limit",
        "usergroup_id"
      ],
      "attached_condition": "((`webmarco`.`cscart_product_prices`.`product_id` = 368409) and (`webmarco`.`cscart_product_prices`.`lower_limit` <= 1) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,0,1)))"
    }
  }
}