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 (
    3488, 3497, 3495, 3489, 3492, 3496, 3490, 
    3494, 6951, 3502, 3503, 3493, 3498, 
    3428, 12916, 12921, 12876, 12896, 12900, 
    12909
  ) 
  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 0.00082

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "27.51"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "product_id",
        "used_key_parts": [
          "product_id"
        ],
        "key_length": "3",
        "rows_examined_per_scan": 50,
        "rows_produced_per_join": 9,
        "filtered": "19.99",
        "index_condition": "(`test2_gaseus`.`cscart_product_prices`.`product_id` in (3488,3497,3495,3489,3492,3496,3490,3494,6951,3502,3503,3493,3498,3428,12916,12921,12876,12896,12900,12909))",
        "cost_info": {
          "read_cost": "26.51",
          "eval_cost": "1.00",
          "prefix_cost": "27.51",
          "data_read_per_join": "239"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`test2_gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`test2_gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}