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 (
    339766, 339763, 339613, 339560, 339830, 
    339472, 339682, 339823, 339543, 339558, 
    339785, 339480, 339561, 339854, 339815, 
    339639, 339566, 339819, 339563, 339772, 
    339585, 339837, 339680, 339661, 339640, 
    339788, 381694, 381692, 339840, 339555, 
    339634, 339672, 339629, 339598, 339578, 
    339832, 339641, 339790, 339688, 220162, 
    339627, 339842, 381689, 381685, 339475, 
    339568, 339546, 339844, 339827, 339642, 
    339612, 265036, 339605, 381682, 220170, 
    339687, 339564, 339562, 430574, 271695, 
    339663, 339624, 339462, 271696, 339800, 
    431190, 339690, 392159, 381688, 381691, 
    339792, 381693, 339554, 339764, 431106, 
    339793, 435505, 220169, 431092, 339592, 
    381690, 339459, 339590, 220166, 431147, 
    220178, 339473, 339795, 339799, 339803, 
    339679, 339791, 339813, 339660, 339801, 
    339786, 430849, 339678, 339659, 339465
  ) 
  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 0.00159

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 (339766,339763,339613,339560,339830,339472,339682,339823,339543,339558,339785,339480,339561,339854,339815,339639,339566,339819,339563,339772,339585,339837,339680,339661,339640,339788,381694,381692,339840,339555,339634,339672,339629,339598,339578,339832,339641,339790,339688,220162,339627,339842,381689,381685,339475,339568,339546,339844,339827,339642,339612,265036,339605,381682,220170,339687,339564,339562,430574,271695,339663,339624,339462,271696,339800,431190,339690,392159,381688,381691,339792,381693,339554,339764,431106,339793,435505,220169,431092,339592,381690,339459,339590,220166,431147,220178,339473,339795,339799,339803,339679,339791,339813,339660,339801,339786,430849,339678,339659,339465)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}