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 (
    309587, 359772, 309590, 359805, 309585, 
    359808, 309561, 359744, 309550, 359752, 
    359758, 366904, 389637, 359478, 391690, 
    309567, 359747, 359740, 415550, 387078
  ) 
  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 0.00228

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "56.07"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "usergroup",
        "used_key_parts": [
          "product_id",
          "usergroup_id",
          "lower_limit"
        ],
        "key_length": "9",
        "rows_examined_per_scan": 40,
        "rows_produced_per_join": 40,
        "filtered": "100.00",
        "cost_info": {
          "read_cost": "48.07",
          "eval_cost": "8.00",
          "prefix_cost": "56.07",
          "data_read_per_join": "2K"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`webmarco`.`cscart_product_prices`.`lower_limit` = 1) and (`webmarco`.`cscart_product_prices`.`product_id` in (309587,359772,309590,359805,309585,359808,309561,359744,309550,359752,359758,366904,389637,359478,391690,309567,359747,359740,415550,387078)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}