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 (
    351129, 355878, 357053, 358162, 358206, 
    350435, 350635, 351079, 353921, 353943, 
    354921, 357257, 358677, 349908, 349924, 
    351514, 351548, 352292, 352334, 352983, 
    353212, 354550, 354562, 355648, 356623, 
    357450, 352115, 354086, 354909, 355214, 
    355331, 356759, 357099, 357149, 351171, 
    351655, 352957, 353084, 353716, 354016, 
    354670, 358291, 351056, 351219, 352947, 
    353838, 355070, 356141, 356169, 357847, 
    350313, 350442, 350900, 351041, 352184, 
    354737, 355817, 356099, 356934, 357299, 
    357933, 359097, 349751, 351006, 351330, 
    351616, 351669, 351702, 352389, 354654, 
    354910, 355213, 356047, 356259, 356447, 
    357041, 358900, 359413, 350381, 350809, 
    350823, 350887, 352113, 353083, 353155, 
    353981, 354768, 354825, 356351, 356587, 
    357594, 357614, 357717, 357750, 351712, 
    354183, 357596, 350755, 351167, 351482
  ) 
  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 0.00125

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 (351129,355878,357053,358162,358206,350435,350635,351079,353921,353943,354921,357257,358677,349908,349924,351514,351548,352292,352334,352983,353212,354550,354562,355648,356623,357450,352115,354086,354909,355214,355331,356759,357099,357149,351171,351655,352957,353084,353716,354016,354670,358291,351056,351219,352947,353838,355070,356141,356169,357847,350313,350442,350900,351041,352184,354737,355817,356099,356934,357299,357933,359097,349751,351006,351330,351616,351669,351702,352389,354654,354910,355213,356047,356259,356447,357041,358900,359413,350381,350809,350823,350887,352113,353083,353155,353981,354768,354825,356351,356587,357594,357614,357717,357750,351712,354183,357596,350755,351167,351482)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}