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 (
    1781, 3620, 35254, 20932, 47598, 6558, 
    6559, 6554, 6555, 6367, 3975, 1784, 
    18748, 35187, 40760, 992, 5998, 2805, 
    5765, 1517, 18749, 18747, 2163, 41017, 
    6543, 38129, 5759, 40309, 47652, 5770, 
    41418, 5635
  ) 
  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 0.00294

JSON explain

{
  "query_block": {
    "select_id": 1,
    "nested_loop": [
      {
        "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": 32,
          "filtered": 99.9960556,
          "index_condition": "cscart_product_prices.product_id in (1781,3620,35254,20932,47598,6558,6559,6554,6555,6367,3975,1784,18748,35187,40760,992,5998,2805,5765,1517,18749,18747,2163,41017,6543,38129,5759,40309,47652,5770,41418,5635)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}