SELECT 
  cscart_product_prices.product_id, 
  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 
  cscart_product_prices.product_id IN (
    116529, 22384, 116423, 116425, 312436, 
    312019, 116427, 116525, 116539, 116517, 
    312888, 390924
  ) 
  AND cscart_product_prices.lower_limit = 1 
  AND cscart_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  cscart_product_prices.product_id

Query time 0.00063

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost": 0.050158501,
    "nested_loop": [
      {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "range",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "usergroup",
          "key_length": "9",
          "used_key_parts": ["product_id", "usergroup_id", "lower_limit"],
          "loops": 1,
          "rows": 24,
          "cost": 0.04252208,
          "filtered": 49.99988174,
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (116529,22384,116423,116425,312436,312019,116427,116525,116539,116517,312888,390924) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}