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 (
    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, 1780, 1781, 1782, 1783, 
    1784, 1785, 1786, 1787, 1788, 1789, 
    1790, 1791, 1792, 1793, 1794, 1795, 
    1796, 1797, 1798, 1799, 1800, 1801, 
    1802, 1803, 1804, 1805, 1806, 1807, 
    1808, 1809, 1810, 1811, 1812, 1813, 
    1814, 1815, 1816, 1817, 1818, 1819, 
    3744, 3745, 3746, 3747, 5461, 5462, 
    5463, 5464, 5465, 5466, 5467, 5468, 
    5469, 5470, 5471, 5472, 5473
  ) 
  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 0.00165

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "67.21"
    },
    "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": 96,
        "rows_produced_per_join": 19,
        "filtered": "20.00",
        "index_condition": "(`gaseus`.`cscart_product_prices`.`product_id` in (5549,5550,5551,5552,5553,5554,5555,5556,5557,5558,5559,1457,5166,1447,5156,5169,3162,1450,5159,1440,5149,1451,5160,1441,5150,1453,5162,1443,5152,1770,1771,1772,1773,1774,1775,1776,1777,1778,1779,1780,1781,1782,1783,1784,1785,1786,1787,1788,1789,1790,1791,1792,1793,1794,1795,1796,1797,1798,1799,1800,1801,1802,1803,1804,1805,1806,1807,1808,1809,1810,1811,1812,1813,1814,1815,1816,1817,1818,1819,3744,3745,3746,3747,5461,5462,5463,5464,5465,5466,5467,5468,5469,5470,5471,5472,5473))",
        "cost_info": {
          "read_cost": "65.29",
          "eval_cost": "1.92",
          "prefix_cost": "67.21",
          "data_read_per_join": "460"
        },
        "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)))"
      }
    }
  }
}