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 (
    388667, 388724, 390315, 388825, 390230, 
    389353, 389570, 415522, 388707, 389545, 
    388757, 389180, 389076, 415471, 389864, 
    415713, 389469, 388829, 388841, 388805, 
    389133, 389090, 389565, 389438, 389016, 
    389478, 388733, 389032, 388804, 388918, 
    388855, 435229, 389517, 390280, 388849, 
    389592, 388928, 388417, 389176, 388883, 
    389526, 391774, 388960, 389343, 435233, 
    388751, 389185, 389129, 389293, 389070, 
    388793, 388910, 389106, 388721, 415658, 
    389092, 389233, 389568, 388719, 388750, 
    389197, 390155, 390248, 388709, 389299, 
    388764, 388771, 389595, 390130, 415391, 
    415607, 389344, 415612, 388741, 390165, 
    388908, 388528, 389332, 415510, 388493, 
    389135, 388848, 388917, 388860, 389037, 
    390317, 388549, 389140, 389210, 389012, 
    389134, 415627, 390138, 389007, 388587, 
    388951, 388534, 388808, 415502, 388902
  ) 
  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 0.00234

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "280.31"
    },
    "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": 200,
        "rows_produced_per_join": 200,
        "filtered": "100.00",
        "cost_info": {
          "read_cost": "240.31",
          "eval_cost": "40.00",
          "prefix_cost": "280.31",
          "data_read_per_join": "12K"
        },
        "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 (388667,388724,390315,388825,390230,389353,389570,415522,388707,389545,388757,389180,389076,415471,389864,415713,389469,388829,388841,388805,389133,389090,389565,389438,389016,389478,388733,389032,388804,388918,388855,435229,389517,390280,388849,389592,388928,388417,389176,388883,389526,391774,388960,389343,435233,388751,389185,389129,389293,389070,388793,388910,389106,388721,415658,389092,389233,389568,388719,388750,389197,390155,390248,388709,389299,388764,388771,389595,390130,415391,415607,389344,415612,388741,390165,388908,388528,389332,415510,388493,389135,388848,388917,388860,389037,390317,388549,389140,389210,389012,389134,415627,390138,389007,388587,388951,388534,388808,415502,388902)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}