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 (
    5540, 5541, 5542, 5543, 5544, 5545, 5546, 
    5547, 5548, 5549, 5550, 5551, 5552, 
    5553, 5554, 5555, 5556, 5557, 5558, 
    5559, 1457, 5166, 1447, 5156, 5169, 
    3162, 1450, 5159, 1440, 5149, 1451, 
    5160, 1441, 5150, 1453, 5162, 1443, 
    5152, 1770, 1771, 1772, 1773, 1774, 
    1775, 1776, 1777, 1778, 1779
  ) 
  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 0.00094

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "33.61"
    },
    "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": 48,
        "rows_produced_per_join": 9,
        "filtered": "20.00",
        "index_condition": "(`gaseus`.`cscart_product_prices`.`product_id` in (5540,5541,5542,5543,5544,5545,5546,5547,5548,5549,5550,5551,5552,5553,5554,5555,5556,5557,5558,5559,1457,5166,1447,5156,5169,3162,1450,5159,1440,5149,1451,5160,1441,5150,1453,5162,1443,5152,1770,1771,1772,1773,1774,1775,1776,1777,1778,1779))",
        "cost_info": {
          "read_cost": "32.65",
          "eval_cost": "0.96",
          "prefix_cost": "33.61",
          "data_read_per_join": "230"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}