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 (
    220173, 339556, 254330, 339744, 339676, 
    339576, 339461, 391686, 339748, 392163, 
    387088, 339667, 339645, 151062, 339684, 
    151100, 254331, 339583, 387086, 339588, 
    339708, 387055, 339826, 339454, 339547, 
    339553, 339633, 387090, 339580, 339548, 
    339657, 339777, 339632, 339649, 339711, 
    339743, 339719, 339647, 339716, 339773, 
    339776, 387065, 339474, 339756, 339745, 
    339471, 387054, 265037, 339577, 339848, 
    339666, 339552, 339665, 339669, 339767, 
    339670, 387066, 339833, 339698, 339703, 
    220171, 339557, 339544, 339646, 339651, 
    339749, 339824, 339455, 339628, 339591, 
    387052, 339784, 339549, 339565, 339673, 
    339614, 339789, 339575, 339662, 265040, 
    339595, 339834, 339853, 339653, 339658, 
    339818, 339626, 339631, 339717, 339852, 
    339559, 339470, 339545, 339487, 339542, 
    339822, 339579, 339567, 271697, 339850
  ) 
  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 0.00173

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 (220173,339556,254330,339744,339676,339576,339461,391686,339748,392163,387088,339667,339645,151062,339684,151100,254331,339583,387086,339588,339708,387055,339826,339454,339547,339553,339633,387090,339580,339548,339657,339777,339632,339649,339711,339743,339719,339647,339716,339773,339776,387065,339474,339756,339745,339471,387054,265037,339577,339848,339666,339552,339665,339669,339767,339670,387066,339833,339698,339703,220171,339557,339544,339646,339651,339749,339824,339455,339628,339591,387052,339784,339549,339565,339673,339614,339789,339575,339662,265040,339595,339834,339853,339653,339658,339818,339626,339631,339717,339852,339559,339470,339545,339487,339542,339822,339579,339567,271697,339850)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}