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 (
    5558, 4470, 1906, 780, 2230, 1149, 1186, 
    1124, 1178, 1169, 1158, 1159, 1164, 
    1129, 1116, 1150
  ) 
  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 0.00441

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "38.41"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "membership",
          "product_id",
          "lower_limit",
          "membership_id"
        ],
        "key": "product_id",
        "used_key_parts": [
          "product_id"
        ],
        "key_length": "3",
        "rows_examined_per_scan": 16,
        "rows_produced_per_join": 3,
        "filtered": "19.99",
        "index_condition": "(`ea201_francemaqu`.`cscart_product_prices`.`product_id` in (5558,4470,1906,780,2230,1149,1186,1124,1178,1169,1158,1159,1164,1129,1116,1150))",
        "cost_info": {
          "read_cost": "37.77",
          "eval_cost": "0.64",
          "prefix_cost": "38.41",
          "data_read_per_join": "76"
        },
        "used_columns": [
          "product_id",
          "price",
          "lower_limit",
          "usergroup_id",
          "percentage_discount"
        ],
        "attached_condition": "((`ea201_francemaqu`.`cscart_product_prices`.`lower_limit` = 1) and (`ea201_francemaqu`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}