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 (
    5522, 5492, 5497, 5494, 5510, 5495, 5499, 
    5520, 5488, 5487, 5490, 5507, 5496, 
    5493, 5508, 5500, 5491, 5498, 5504, 
    5506, 5489, 5505, 5509, 5502
  ) 
  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 0.00061

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": 24,
      "filtered": 93.46080017,
      "index_condition": "cscart_product_prices.product_id in (5522,5492,5497,5494,5510,5495,5499,5520,5488,5487,5490,5507,5496,5493,5508,5500,5491,5498,5504,5506,5489,5505,5509,5502)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}