SELECT 
  cscart_ult_product_prices.product_id, 
  MIN(
    IF(
      cscart_ult_product_prices.percentage_discount = 0, 
      cscart_ult_product_prices.price, 
      cscart_ult_product_prices.price - (
        cscart_ult_product_prices.price * cscart_ult_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_ult_product_prices 
WHERE 
  cscart_ult_product_prices.product_id IN (
    317, 189, 501, 293, 78, 35, 234, 331, 484, 
    287, 292, 79
  ) 
  AND cscart_ult_product_prices.lower_limit = 1 
  AND cscart_ult_product_prices.company_id = 1 
  AND cscart_ult_product_prices.usergroup_id IN (0, 0, 1) 
GROUP BY 
  cscart_ult_product_prices.product_id

Query time 0.00092

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "cscart_ult_product_prices.product_id",
      "temporary_table": {
        "table": {
          "table_name": "cscart_ult_product_prices",
          "access_type": "ref",
          "possible_keys": [
            "usergroup",
            "product_id",
            "company_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "company_id",
          "key_length": "4",
          "used_key_parts": ["company_id"],
          "ref": ["const"],
          "rows": 22,
          "filtered": 100,
          "attached_condition": "cscart_ult_product_prices.company_id <=> 1 and cscart_ult_product_prices.lower_limit = 1 and cscart_ult_product_prices.product_id in (317,189,501,293,78,35,234,331,484,287,292,79) and cscart_ult_product_prices.usergroup_id in (0,0,1)"
        }
      }
    }
  }
}