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 (
    1788, 1697, 1657, 1687, 1921, 1238, 1197, 
    1307, 1306, 1940, 1941, 1660, 1751, 
    1677, 1305, 1588, 1662, 1635, 1747, 
    1587, 1771, 1709, 1957, 1707, 1768, 
    1710, 1954, 1953, 1730, 1686, 1593, 
    1594, 1616, 1773, 1701, 1584, 1585, 
    1868, 1579, 1956, 1495, 1739, 1740, 
    1912, 1913, 1650, 56, 1836, 1336, 1837, 
    1820, 1304, 1738, 1893, 1895, 1894, 
    1641, 1500, 1317, 1670, 1658, 1558, 
    1644, 1262, 1552, 1398, 1595, 1576, 
    1870, 1691, 1776, 1785, 1633, 1563, 
    1564, 1667, 1786, 1945, 1910, 1787, 
    1308, 1642, 1772, 1736, 1277, 1672, 
    1325, 1665, 1778, 1775, 1671, 1649, 
    1909, 1948, 1612, 1267
  ) 
  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 0.00349

JSON explain

{
  "query_block": {
    "select_id": 1,
    "table": {
      "table_name": "cscart_product_prices",
      "access_type": "range",
      "possible_keys": ["usergroup", "product_id", "lower_limit", "usergroup_id"],
      "key": "product_id",
      "key_length": "3",
      "used_key_parts": ["product_id"],
      "rows": 112,
      "filtered": 23.46938133,
      "index_condition": "cscart_product_prices.product_id in (1788,1697,1657,1687,1921,1238,1197,1307,1306,1940,1941,1660,1751,1677,1305,1588,1662,1635,1747,1587,1771,1709,1957,1707,1768,1710,1954,1953,1730,1686,1593,1594,1616,1773,1701,1584,1585,1868,1579,1956,1495,1739,1740,1912,1913,1650,56,1836,1336,1837,1820,1304,1738,1893,1895,1894,1641,1500,1317,1670,1658,1558,1644,1262,1552,1398,1595,1576,1870,1691,1776,1785,1633,1563,1564,1667,1786,1945,1910,1787,1308,1642,1772,1736,1277,1672,1325,1665,1778,1775,1671,1649,1909,1948,1612,1267)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
56 32000.00000000
1197 58000.00000000
1238 40000.00000000
1262 54000.00000000
1267 48000.00000000
1277 315000.00000000
1304 62000.00000000
1305 82000.00000000
1306 0.00000000
1307 0.00000000
1308 70000.00000000
1317 42000.00000000
1325 130000.00000000
1336 60000.00000000
1398 75000.00000000
1495 60000.00000000
1500 62000.00000000
1552 25000.00000000
1558 178000.00000000
1563 26000.00000000
1564 26000.00000000
1576 25000.00000000
1579 54000.00000000
1584 56000.00000000
1585 56000.00000000
1587 0.00000000
1588 70000.00000000
1593 82000.00000000
1594 89000.00000000
1595 25000.00000000
1612 50000.00000000
1616 61000.00000000
1633 26000.00000000
1635 30000.00000000
1641 200000.00000000
1642 44000.00000000
1644 58000.00000000
1649 18000.00000000
1650 50000.00000000
1657 82000.00000000
1658 85000.00000000
1660 82000.00000000
1662 48000.00000000
1665 70000.00000000
1667 72000.00000000
1670 0.00000000
1671 55000.00000000
1672 55000.00000000
1677 76000.00000000
1686 78000.00000000
1687 82000.00000000
1691 26000.00000000
1697 28000.00000000
1701 52000.00000000
1707 32000.00000000
1709 70000.00000000
1710 32000.00000000
1730 78000.00000000
1736 215000.00000000
1738 50000.00000000
1739 0.00000000
1740 0.00000000
1747 183000.00000000
1751 78000.00000000
1768 72000.00000000
1771 32000.00000000
1772 32000.00000000
1773 32000.00000000
1775 60000.00000000
1776 60000.00000000
1778 32000.00000000
1785 40000.00000000
1786 72000.00000000
1787 28000.00000000
1788 38000.00000000
1820 60000.00000000
1836 62000.00000000
1837 62000.00000000
1868 20000.00000000
1870 70000.00000000
1893 158000.00000000
1894 158000.00000000
1895 158000.00000000
1909 60000.00000000
1910 32000.00000000
1912 60000.00000000
1913 60000.00000000
1921 60000.00000000
1940 62000.00000000
1941 62000.00000000
1945 70000.00000000
1948 50000.00000000
1953 17000.00000000
1954 17000.00000000
1956 40000.00000000
1957 70000.00000000