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 (
    12554, 12555, 12556, 12557, 12558, 12559, 
    12560, 12561, 12562, 12563, 12564, 
    12565, 12566, 12567, 12568, 12569, 
    12570, 12571, 12572, 12573, 12574, 
    12575, 12576, 12577, 12578, 12579, 
    12580, 12581, 12582, 12583, 12584, 
    12585, 12586, 12587, 12588, 12589, 
    12590, 12591, 12592, 12593
  ) 
  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 0.00133

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "28.01"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "product_id",
        "used_key_parts": [
          "product_id"
        ],
        "key_length": "3",
        "rows_examined_per_scan": 40,
        "rows_produced_per_join": 7,
        "filtered": "19.99",
        "index_condition": "(`test2_gaseus`.`cscart_product_prices`.`product_id` in (12554,12555,12556,12557,12558,12559,12560,12561,12562,12563,12564,12565,12566,12567,12568,12569,12570,12571,12572,12573,12574,12575,12576,12577,12578,12579,12580,12581,12582,12583,12584,12585,12586,12587,12588,12589,12590,12591,12592,12593))",
        "cost_info": {
          "read_cost": "27.21",
          "eval_cost": "0.80",
          "prefix_cost": "28.01",
          "data_read_per_join": "191"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`test2_gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`test2_gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}