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 (
    45574, 45816, 45817, 45818, 45819, 45820, 
    45821, 45822, 45823, 45824, 45825, 
    45826, 45827, 45828, 45829, 45830, 
    45831, 45832, 45833, 45834, 45835, 
    45836, 45837, 45838, 45839, 45840, 
    45841, 45842, 45843, 45844, 45845, 
    45846, 45847, 45848, 45849, 45850, 
    45851, 45852, 45853, 45854
  ) 
  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 0.04367

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "cscart_product_prices.product_id",
      "temporary_table": {
        "nested_loop": [
          {
            "table": {
              "table_name": "cscart_product_prices",
              "access_type": "ref",
              "possible_keys": [
                "usergroup",
                "product_id",
                "lower_limit",
                "usergroup_id"
              ],
              "key": "lower_limit",
              "key_length": "3",
              "used_key_parts": ["lower_limit"],
              "ref": ["const"],
              "rows": 25327,
              "filtered": 12.6262579,
              "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (45574,45816,45817,45818,45819,45820,45821,45822,45823,45824,45825,45826,45827,45828,45829,45830,45831,45832,45833,45834,45835,45836,45837,45838,45839,45840,45841,45842,45843,45844,45845,45846,45847,45848,45849,45850,45851,45852,45853,45854) and cscart_product_prices.usergroup_id in (0,1)"
            }
          }
        ]
      }
    }
  }
}