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 (
    312881, 312873, 312841, 312842, 312847, 
    312848, 312840, 312846, 312838, 312839, 
    312854, 312876, 312843, 312845, 312837, 
    312855, 312834, 312864, 312852, 312853, 
    312851, 312866, 312844, 312867, 312862, 
    312833, 312835, 312856, 312857, 312859, 
    312860, 312861, 312872, 312869, 312858, 
    312863, 312879, 312875, 312878, 312836, 
    312880, 312865, 312874, 312868, 312849, 
    312850, 312877
  ) 
  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 0.00096

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost": 0.194420019,
    "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": 94,
          "cost": 0.16423738,
          "filtered": 49.99988174,
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (312881,312873,312841,312842,312847,312848,312840,312846,312838,312839,312854,312876,312843,312845,312837,312855,312834,312864,312852,312853,312851,312866,312844,312867,312862,312833,312835,312856,312857,312859,312860,312861,312872,312869,312858,312863,312879,312875,312878,312836,312880,312865,312874,312868,312849,312850,312877) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}