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 (
    245, 238, 239, 331, 335, 339, 341, 355, 
    356, 357, 358, 359, 360, 361, 362, 363, 
    364, 365, 366, 367, 368, 369, 370, 379, 
    380, 381, 382, 383, 384, 385, 386, 387
  ) 
  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 0.00092

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "84.20"
    },
    "grouping_operation": {
      "using_temporary_table": true,
      "using_filesort": true,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "ref",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "lower_limit",
        "used_key_parts": [
          "lower_limit"
        ],
        "key_length": "3",
        "ref": [
          "const"
        ],
        "rows_examined_per_scan": 376,
        "rows_produced_per_join": 7,
        "filtered": "2.04",
        "index_condition": "(`pankajecarter_systemfour`.`cscart_product_prices`.`lower_limit` <=> 1)",
        "cost_info": {
          "read_cost": "9.00",
          "eval_cost": "1.53",
          "prefix_cost": "84.20",
          "data_read_per_join": "183"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`pankajecarter_systemfour`.`cscart_product_prices`.`product_id` in (245,238,239,331,335,339,341,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,379,380,381,382,383,384,385,386,387)) and (`pankajecarter_systemfour`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}