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 (
    18201, 40824, 41441, 6099, 49306, 1897, 
    401, 27360, 6058, 41442, 6061, 40761, 
    2471, 6063, 5890, 6062, 41170, 1429, 
    5834, 6057, 47085, 3471, 4280, 27362, 
    31642, 6556, 36399, 5894, 47660, 6056, 
    6561, 4894
  ) 
  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 0.00298

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 (18201,40824,41441,6099,49306,1897,401,27360,6058,41442,6061,40761,2471,6063,5890,6062,41170,1429,5834,6057,47085,3471,4280,27362,31642,6556,36399,5894,47660,6056,6561,4894)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}