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 (
    16346, 16334, 16348, 15749, 14660, 14650, 
    16347, 14651, 14656, 14654, 14661, 
    15751, 16338, 15753, 16340, 15747, 
    16351, 15750, 14652, 14658, 15746, 
    16337, 16336, 15745
  ) 
  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 0.00044

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost": 0.061901185,
    "nested_loop": [
      {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "range",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "usergroup",
          "key_length": "9",
          "used_key_parts": ["product_id", "usergroup_id", "lower_limit"],
          "loops": 1,
          "rows": 48,
          "cost": 0.04656984,
          "filtered": 49.95539856,
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (16346,16334,16348,15749,14660,14650,16347,14651,14656,14654,14661,15751,16338,15753,16340,15747,16351,15750,14652,14658,15746,16337,16336,15745) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}