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 (
    460948, 190, 461277, 391037, 391032, 
    391031, 391030, 460955, 242, 243, 116541, 
    116547, 172, 168, 167, 169, 156, 175, 
    12702, 312043, 391029, 246, 312051, 
    461038, 173, 312048, 12712, 391035, 
    21914, 391033, 391036, 391034, 154, 
    161, 165, 166, 163, 155, 184, 183, 145, 
    12710, 12698, 157, 461039, 461275, 
    391040, 461037
  ) 
  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 0.00140

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost": 0.198543966,
    "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": 96,
          "cost": 0.16771496,
          "filtered": 49.99988556,
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (460948,190,461277,391037,391032,391031,391030,460955,242,243,116541,116547,172,168,167,169,156,175,12702,312043,391029,246,312051,461038,173,312048,12712,391035,21914,391033,391036,391034,154,161,165,166,163,155,184,183,145,12710,12698,157,461039,461275,391040,461037) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}