<?xml version="1.0" encoding="us-ascii"?>
<!-- DFIN ActiveDisclosure(SM) XBRL Schema Document - http://www.dfinsolutions.com/ -->
<!-- Creation Date      : 2020-05-07T19:39:23.5072540+00:00 -->
<!-- Version            : 5.0.1.385 -->
<!-- Package ID         : c79a8c47e3614595b33287fef244074d -->
<!-- Copyright (c) 2020 Donnelley Financial Solutions, Inc. All Rights Reserved. -->
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  <xsd:element id="sndx_AdjustmentsToAdditionalPaidInCapitalDeemedDividendFromRepricingWarrants" name="AdjustmentsToAdditionalPaidInCapitalDeemedDividendFromRepricingWarrants" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="sndx_AdjustmentsToAdditionalPaidInCapitalRepricingWarrants" name="AdjustmentsToAdditionalPaidInCapitalRepricingWarrants" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="sndx_StockIssuedDuringPeriodValueAtTheMarketOfferingNet" name="StockIssuedDuringPeriodValueAtTheMarketOfferingNet" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="sndx_StockIssuedDuringPeriodValueCommonStockWarrantWithDirectOffering" name="StockIssuedDuringPeriodValueCommonStockWarrantWithDirectOffering" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="sndx_SeriesOneAndTwoMember" name="SeriesOneAndTwoMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sndx_StockIssuedDuringPeriodSharesAtTheMarketOfferingNet" name="StockIssuedDuringPeriodSharesAtTheMarketOfferingNet" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_StockIssuedDuringPeriodValueAtTheMarketOfferingExpenses" name="StockIssuedDuringPeriodValueAtTheMarketOfferingExpenses" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sndx_StockIssuedDuringPeriodValueDirectOfferingCommonStockWarrant" name="StockIssuedDuringPeriodValueDirectOfferingCommonStockWarrant" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="sndx_StockIssuedDuringPeriodValueOfferingExpenses" name="StockIssuedDuringPeriodValueOfferingExpenses" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sndx_StockIssuedDuringPeriodValuePreFundedCommonStockWarrant" name="StockIssuedDuringPeriodValuePreFundedCommonStockWarrant" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="sndx_StockIssuedDuringPeriodValuePreFundedCommonStockWarrantOfferingExpenses" name="StockIssuedDuringPeriodValuePreFundedCommonStockWarrantOfferingExpenses" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sndx_PaymentSpecifiedPercentageOfGrossProceedsFromSaleOfShares" name="PaymentSpecifiedPercentageOfGrossProceedsFromSaleOfShares" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_CowenAndCompanyLLCMember" name="CowenAndCompanyLLCMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sndx_AtTheMarketEquityOfferingSalesAgreementMember" name="AtTheMarketEquityOfferingSalesAgreementMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sndx_SeriesWarrantsMember" name="SeriesWarrantsMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sndx_SeriesOneWarrantsMember" name="SeriesOneWarrantsMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sndx_SeriesTwoWarrantsMember" name="SeriesTwoWarrantsMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sndx_NumberOfSeriesOfWarrants" name="NumberOfSeriesOfWarrants" type="xbrli:integerItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_ClassOfWarrantOrRightTerm" name="ClassOfWarrantOrRightTerm" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_OfferingPricePerShare" name="OfferingPricePerShare" type="num:perShareItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_GrossProceedsFromOffering" name="GrossProceedsFromOffering" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sndx_OfferingCost" name="OfferingCost" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sndx_WeightedAverageExercisePriceOfWarrants" name="WeightedAverageExercisePriceOfWarrants" type="num:perShareItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_AdjustedWeightedAverageExercisePriceOfWarrants" name="AdjustedWeightedAverageExercisePriceOfWarrants" type="num:perShareItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_MaximumPeriodAllowedToIncreaseBeneficialOwnershipLimitationAfterNotice" name="MaximumPeriodAllowedToIncreaseBeneficialOwnershipLimitationAfterNotice" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_ExerciseOfWarrantsLowerLimitAfterExerciseAsPercentageOfCommonStock" name="ExerciseOfWarrantsLowerLimitAfterExerciseAsPercentageOfCommonStock" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_MaximumBeneficialOwnershipLimitationPercentage" name="MaximumBeneficialOwnershipLimitationPercentage" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_FairValueOfWarrants" name="FairValueOfWarrants" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="sndx_Series1And2WarrantsMember" name="Series1And2WarrantsMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sndx_UnderwrittenPublicOfferingMember" name="UnderwrittenPublicOfferingMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sndx_UnderwritersMember" name="UnderwritersMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
</xsd:schema>
