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 (
    1562, 1509, 1952, 1700, 1589, 1492, 1316, 
    1690, 1729, 1637, 1731, 1636, 1638, 
    1639, 1629, 1631, 1630, 1622, 1615, 
    1621, 1907, 1955, 1663, 1674
  ) 
  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 0.00111

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": 28,
      "filtered": 4.897957802,
      "index_condition": "cscart_product_prices.product_id in (1562,1509,1952,1700,1589,1492,1316,1690,1729,1637,1731,1636,1638,1639,1629,1631,1630,1622,1615,1621,1907,1955,1663,1674)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}