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 (
    61413, 64353, 61081, 62246, 60906, 62023, 
    64273, 30013, 60484, 30012, 64355, 
    63513, 62975, 64854, 63384, 63510, 
    63515, 61417, 64274, 63776, 61080, 
    63099, 64276, 62022
  ) 
  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 0.00180

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 (61413,64353,61081,62246,60906,62023,64273,30013,60484,30012,64355,63513,62975,64854,63384,63510,63515,61417,64274,63776,61080,63099,64276,62022) and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result