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 (
    40437, 40451, 2320, 2319, 48846, 40445, 
    40442, 47024, 41293, 40446, 47020, 
    47023, 47022, 40443, 40449, 40448, 
    40447, 49811, 40444, 41292, 40436, 
    47012, 40450, 41291, 41294, 40435, 
    47014, 40438, 47015, 40441
  ) 
  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 0.00860

JSON explain

{
  "query_block": {
    "select_id": 1,
    "nested_loop": [
      {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "range",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "product_id",
          "key_length": "3",
          "used_key_parts": ["product_id"],
          "rows": 30,
          "filtered": 99.9960556,
          "index_condition": "cscart_product_prices.product_id in (40437,40451,2320,2319,48846,40445,40442,47024,41293,40446,47020,47023,47022,40443,40449,40448,40447,49811,40444,41292,40436,47012,40450,41291,41294,40435,47014,40438,47015,40441)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}