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 (
    431615, 431616, 431617, 431618, 431619, 
    431620, 431621, 431622, 431623, 431624, 
    431625, 431626, 431627, 431628, 431629, 
    431630, 431631, 431632, 431633, 431634, 
    431635, 431636, 431637, 431638, 431639, 
    431640, 431641, 431642, 431643, 431644, 
    431645, 431646, 431647, 431648, 431649, 
    431650, 431651, 431652, 431653, 431654, 
    431655, 431656, 431657, 431658
  ) 
  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 0.00229

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "123.34"
    },
    "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": 88,
        "rows_produced_per_join": 88,
        "filtered": "100.00",
        "cost_info": {
          "read_cost": "105.74",
          "eval_cost": "17.60",
          "prefix_cost": "123.34",
          "data_read_per_join": "5K"
        },
        "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 (431615,431616,431617,431618,431619,431620,431621,431622,431623,431624,431625,431626,431627,431628,431629,431630,431631,431632,431633,431634,431635,431636,431637,431638,431639,431640,431641,431642,431643,431644,431645,431646,431647,431648,431649,431650,431651,431652,431653,431654,431655,431656,431657,431658)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}