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 (
    3978, 3977, 49256, 36307, 4381, 1050, 
    3974, 2252, 33709, 3988, 36717, 43650, 
    36297, 2249, 40535, 33824, 353, 36295, 
    33721, 34678, 2260, 36300, 40532, 40527, 
    41230, 25159, 33713, 49309, 3979, 36293, 
    18710, 33835
  ) 
  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 0.00335

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 (3978,3977,49256,36307,4381,1050,3974,2252,33709,3988,36717,43650,36297,2249,40535,33824,353,36295,33721,34678,2260,36300,40532,40527,41230,25159,33713,49309,3979,36293,18710,33835)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}