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 (
    4078, 4779, 5006, 5108, 4103, 4104, 3983, 
    4106, 4105, 3984, 4107, 3981, 3985, 
    3982, 4034, 4491, 5616, 5246, 6825, 
    6826, 4996, 6827, 6136, 6814
  ) 
  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 0.00064

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": 50,
      "filtered": 96,
      "index_condition": "cscart_product_prices.product_id in (4078,4779,5006,5108,4103,4104,3983,4106,4105,3984,4107,3981,3985,3982,4034,4491,5616,5246,6825,6826,4996,6827,6136,6814)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}