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, 60749, 
    29992, 29989, 60748, 63034, 62012, 
    60739, 60745, 61430, 62240, 63755, 
    60753, 64625, 62259, 64624, 61340, 
    61337, 64616, 60746, 64617, 60736, 
    64615, 62252, 61336, 62253, 64614, 
    60731, 60726, 60750, 60734, 61388, 
    64622, 60741, 64623, 64626, 60747, 
    62254, 60730, 62260, 60740, 61387, 
    60742, 61171
  ) 
  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 0.00156

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": 96,
        "selectivity_pct": 3.558191253
      },
      "rows": 96,
      "filtered": 100,
      "index_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (58884,62123,29986,60914,29983,60749,29992,29989,60748,63034,62012,60739,60745,61430,62240,63755,60753,64625,62259,64624,61340,61337,64616,60746,64617,60736,64615,62252,61336,62253,64614,60731,60726,60750,60734,61388,64622,60741,64623,64626,60747,62254,60730,62260,60740,61387,60742,61171) and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result