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 (
    3788, 3789, 3790, 3791, 3792, 3793, 3794, 
    3795, 3796, 3797, 3798, 3799, 3800, 
    3801, 3802, 3803, 3804, 3805, 3806, 
    3807, 3808, 3809, 3810, 3811, 3812, 
    3813, 3814, 3815, 3816, 3817, 3818, 
    3819, 3820, 3821, 3822, 3823, 3824, 
    3825, 3826, 3827, 3828, 3829, 3830, 
    3831, 3832, 3778, 2103, 2104
  ) 
  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 0.00104

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "33.61"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "product_id",
        "used_key_parts": [
          "product_id"
        ],
        "key_length": "3",
        "rows_examined_per_scan": 48,
        "rows_produced_per_join": 9,
        "filtered": "20.00",
        "index_condition": "(`gaseus`.`cscart_product_prices`.`product_id` in (3788,3789,3790,3791,3792,3793,3794,3795,3796,3797,3798,3799,3800,3801,3802,3803,3804,3805,3806,3807,3808,3809,3810,3811,3812,3813,3814,3815,3816,3817,3818,3819,3820,3821,3822,3823,3824,3825,3826,3827,3828,3829,3830,3831,3832,3778,2103,2104))",
        "cost_info": {
          "read_cost": "32.65",
          "eval_cost": "0.96",
          "prefix_cost": "33.61",
          "data_read_per_join": "230"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}