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 (
    1291, 1287, 1283, 1279, 1277, 1275, 1271, 
    1267, 1264, 1262, 1258, 1256, 1254, 
    1250, 1248, 1246, 1245, 1131, 1130, 
    1129, 1128, 1127, 1126, 1125, 1124, 
    1123, 1111, 1110, 1109, 1108, 1107, 
    1101, 1099, 1094, 1088, 1054, 1053, 
    1051, 1050, 1049, 1048, 967, 964, 963, 
    962, 960, 959, 958
  ) 
  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 0.00271

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "33.61"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "product_id",
        "used_key_parts": [
          "product_id"
        ],
        "key_length": "3",
        "rows_examined_per_scan": 48,
        "rows_produced_per_join": 9,
        "filtered": "19.94",
        "index_condition": "(`wearethehelpful_scalesta_net`.`cscart_product_prices`.`product_id` in (1291,1287,1283,1279,1277,1275,1271,1267,1264,1262,1258,1256,1254,1250,1248,1246,1245,1131,1130,1129,1128,1127,1126,1125,1124,1123,1111,1110,1109,1108,1107,1101,1099,1094,1088,1054,1053,1051,1050,1049,1048,967,964,963,962,960,959,958))",
        "cost_info": {
          "read_cost": "32.65",
          "eval_cost": "0.96",
          "prefix_cost": "33.61",
          "data_read_per_join": "229"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`wearethehelpful_scalesta_net`.`cscart_product_prices`.`lower_limit` = 1) and (`wearethehelpful_scalesta_net`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}