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 (
    41428, 1775, 37665, 2248, 41445, 5467, 
    3996, 35733, 5448, 951, 4363, 31732, 
    2256, 4268, 4267, 3994, 2247, 5775, 
    41616, 36496, 2251, 36271, 37545, 45282, 
    41007, 5771, 4001, 41410, 41010, 41411, 
    41226, 5447
  ) 
  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 0.00554

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 (41428,1775,37665,2248,41445,5467,3996,35733,5448,951,4363,31732,2256,4268,4267,3994,2247,5775,41616,36496,2251,36271,37545,45282,41007,5771,4001,41410,41010,41411,41226,5447)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}