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 (
    5578, 5472, 5457, 5588, 5462, 5579, 5590, 
    5478, 5580, 31887, 31891, 5960, 5957, 
    5961, 31894, 16802, 35733, 5448, 31893, 
    4363, 5956, 31895, 4361, 5451, 5479, 
    4366, 4360, 5591, 5485, 5587, 31889, 
    5963
  ) 
  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 0.00156

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 (5578,5472,5457,5588,5462,5579,5590,5478,5580,31887,31891,5960,5957,5961,31894,16802,35733,5448,31893,4363,5956,31895,4361,5451,5479,4366,4360,5591,5485,5587,31889,5963)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}