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 (
    58884, 62123, 29986, 60914, 29983, 29992, 
    29989, 63034, 62012, 61430, 62240, 
    63755, 62259, 61340, 61337, 62252, 
    61336, 62253, 62254, 62260, 64941, 
    62258, 64942, 64943
  ) 
  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 0.00107

JSON explain

{
  "query_block": {
    "select_id": 1,
    "table": {
      "table_name": "cscart_product_prices",
      "access_type": "range",
      "possible_keys": ["usergroup", "product_id", "lower_limit", "usergroup_id"],
      "key": "product_id",
      "key_length": "9",
      "used_key_parts": ["product_id", "usergroup_id", "lower_limit"],
      "rowid_filter": {
        "range": {
          "key": "lower_limit",
          "used_key_parts": ["lower_limit", "product_id", "usergroup_id"]
        },
        "rows": 48,
        "selectivity_pct": 1.779095626
      },
      "rows": 48,
      "filtered": 100,
      "index_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (58884,62123,29986,60914,29983,29992,29989,63034,62012,61430,62240,63755,62259,61340,61337,62252,61336,62253,62254,62260,64941,62258,64942,64943) and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result